title: Stage E6.5 embryo 2 section 7 region EP

description:
E6.5_2.txt
E6.5_2_7EP


title: Condition 12-4wk replicate 2

status: Public on Aug 15 2023

type: SRA

city: Helsinki

first: Biswajyoti

last: Sahu

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
The sample quality of the RNA-seq datasets were evaluated by the tool FastQC. Sequence reads were aligned to the human reference genome (UCSC GRCh38/hg38) using STAR aligner (v2.7.5c) with default parameters. Samtools (v1.9) was used to sort the bam files.
Gene counts were quantified using HTSeq-count (v0.11.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Human foreskin fibroblasts

growth_protocol: HFFs (ATCC, #CRL-2429) were cultured in fibroblast medium (DMEM supplemented with 10% FBS, 2 mM L-Glutamine, 1 mM Sodium pyruvate and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen, #74134) following manufacturer’s instruction.
Libraries were prepared from 500ng of total RNA for each sample using KAPA mRNA HyperPrep Kit for Illumina (Roche, #KR1352) following manufacturer’s instruction.

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods). The reprogramming cells were collected at different time points for gene expression analysis. Mock HFFs were used as control.

tag: cell type

value: Human foreskin fibroblasts

tag: treatment

value: Transduced with 4-TF cocktail

tag: time point


title: Stable MGUS patient_165

type: RNA

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

country: USA

institute: University of Arkansas for Medical Sciences

description:
S165
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

hyb_protocol: Double-stranded complementary DNA (cDNA) and biotinylated complementary RNA (cRNA) were hybridized to GeneChip microarrays (Affymetrix, Santa Clara, CA), which were washed and scanned according to procedures developed by the manufacturer.

scan_protocol: The arrays were scanned using Hewlett Packard confocal laser scanner and visualized using Affymetrix 3.3 software (Affymetrix).

data_processing: The data were processed using Microarray Suite version 5.0 (MAS 5.0) with Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was standardized to a value of 100 as a reference point.

label: Biotin

source_name: Bone marrow Stable MGUS patient

label_protocol: Double-stranded cDNA is synthesized from 6 ug total RNA. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. The protocol according to the manufacturer's instructions Expression Analysis Technical Manual, 2001, Affymetrix.

growth_protocol: Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions from bone marrow aspirates in a central laboratory. All samples analyzed by microarray contained more than 85% plasma cells as determined by 2-color flow cytometry (CD38+ and CD45–/dim) performed after selection.

extract_protocol:
Fresh plasma cells were used directly for RNA extraction.
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: Bone marrow plasma cells

tag: disease state

value: Stable MGUS


title: Stage E6.5 embryo 2 section 6 region EA

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

description:
E6.5_2.txt
E6.5_2_6EA

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

treatment_protocol: Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.

tag: developmental stage

tag: strain

tag: tissue

value: embryo


title: Stage E6.5 embryo 2 section 6 region EP

description:
E6.5_2.txt
E6.5_2_6EP


title: Condition 12-4wk replicate 1


title: Stage E7.5 with L/R sections embryo 1 section 3 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_3EA


title: Stage E7.5 with L/R sections embryo 1 section 3 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_3A


title: Condition 12-6wk replicate 3


title: Condition 12-2wk replicate 3


title: Condition 12-2wk replicate 2


title: Stage E6.5 embryo 2 section 6 region A

description:
E6.5_2.txt
E6.5_2_6A


title: Stable MGUS patient_164

description:
S164
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 2 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_2MPR


title: Stage E7.5 with L/R sections embryo 1 section 2 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_2P


title: Stage E6.5 embryo 2 section 5 region EP

description:
E6.5_2.txt
E6.5_2_5EP


title: Condition 12-2wk replicate 1


title: Stage E7.5 with L/R sections embryo 1 section 3 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_3EP


title: Stage E6.5 embryo 2 section 5 region P

description:
E6.5_2.txt
E6.5_2_5P


title: Stage E7.5 with L/R sections embryo 1 section 2 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_2MPL


title: Stage E6.5 embryo 2 section 5 region EA

description:
E6.5_2.txt
E6.5_2_5EA


title: Stable MGUS patient_166

description:
S166
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Condition 10-6wk replicate 3

value: Transduced with 5-TF cocktail


title: Stage E7.5 with L/R sections embryo 1 section 2 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_2MAR


title: Condition 10-6wk replicate 2


title: Stage E6.5 embryo 2 section 5 region A

description:
E6.5_2.txt
E6.5_2_5A


title: Stage E6.5 embryo 2 section 4 region P

description:
E6.5_2.txt
E6.5_2_4P


title: Stage E7.5 with L/R sections embryo 1 section 2 region L

description:
E7.5_LR_1.txt
E7.5_LR_1_2L


title: Condition 10-6wk replicate 1


title: Stable MGUS patient_163

description:
S163
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_159

description:
S159
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_161

description:
S161
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_162

description:
S162
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_160

description:
S160
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 2 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_2EP


title: Stable MGUS patient_158

description:
S158
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Condition 10-4wk replicate 3


title: Condition 10-4wk replicate 2


title: Stage E7.5 with L/R sections embryo 1 section 2 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_2EA


title: Condition 10-4wk replicate 1


title: Stage E7.5 with L/R sections embryo 1 section 2 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_2A


title: Stage E6.5 embryo 2 section 4 region A

description:
E6.5_2.txt
E6.5_2_4A


title: Stage E6.5 embryo 2 section 3 region P

description:
E6.5_2.txt
E6.5_2_3P


title: Stage E6.5 embryo 2 section 4 region EA

description:
E6.5_2.txt
E6.5_2_4EA


title: Stage E7.5 with L/R sections embryo 1 section 1 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_1P


title: Stage E6.5 embryo 2 section 3 region EP

description:
E6.5_2.txt
E6.5_2_3EP


title: Stage E7.5 with L/R sections embryo 1 section 1 region EAP

description:
E7.5_LR_1.txt
E7.5_LR_1_1EAP


title: Stable MGUS patient_157

description:
S157
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Condition 10-2wk replicate 3


title: Stage E6.5 embryo 2 section 4 region EP

description:
E6.5_2.txt
E6.5_2_4EP


title: Stable MGUS patient_155

description:
S155
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 2 section 3 region EA

description:
E6.5_2.txt
E6.5_2_3EA


title: Stage E7.25 embryo 2 section 9 region R1

description:
E7.25_2.txt
E7.25_2_9R1


title: Stage E6.5 embryo 2 section 3 region A

description:
E6.5_2.txt
E6.5_2_3A


title: Stage E7.5 with L/R sections embryo 1 section 1 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_1A


title: Stable MGUS patient_156

description:
S156
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_152

description:
S152
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: THP-1 cells, EM DNA-IFNγ 24h

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
The variant libraries were trimmed and quality filtered with Agilent Genomics NextGen Toolkit (AGeNT) software
The methylation libraries were porcessed with nf-core/methylseq version 1.5 pipeline using Trim Galore version 0.6.4, Bismark version 0.22.3 (49), BWA-meth version 0.2.2 (arxiv.org/abs/1401.1129) and Picard MarkDuplicates version 1.5
DNA variant and methylation libraries were processed and mapped to GRCh38
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data from the variant libraries are text files containing genomic location (chr and position) and coverage.
Supplementary files format and content: Processed daat from the DNA methylation libraries are text files containg genomic location (chr, start, stop), methylation level (%), number of Ts, number of Cs and total coverage.
Library strategy: EM-Seq

molecule: genomic DNA

growth_protocol: THP-1 acute monocytic leukemic cell line (ATCC: The Global Bioresource Center) was expanded in complete RPMI medium composed of 10% Fetal Bovine Serum, supplemented with 1% Penicillin-Streptomycin (all from Merck KGaA) with the addition of L-glutamine, sodium pyruvate and 2-mercaptoethanol (1.7 mM, 0.87 mM and 0.02 mM, respectively)

extract_protocol:
Genomic DNA was extracted using the DNA/RNA Mini Kit (Qiagen) according to manufacturer’s instructions. A total amount of 3.3 μg was used for the construction of the libraries
The libraries were prepared using the SureSelectXT Methyl-Seq kit (Agilent, part# G9651B)

treatment_protocol: 20 ng/ml of interferon-gamma (IFNγ) and/or 5 ng/ml lipopolysaccharide (LPS) for 24 hours.

tag: cell line

value: IFNg


title: Stage E7.25 embryo 2 section 9 region P

description:
E7.25_2.txt
E7.25_2_9P


title: Stable MGUS patient_151

description:
S151
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_153

description:
S153
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: THP-1 cells, EM DNA-IFNγ/LPS 24h

value: IFNg/LPS


title: Condition 10-2wk replicate 2


title: Stage E6.5 embryo 2 section 2 region P

description:
E6.5_2.txt
E6.5_2_2P


title: THP-1 cells, BS DNA-IFNγ 24h

data_processing:
The variant libraries were trimmed and quality filtered with Agilent Genomics NextGen Toolkit (AGeNT) software
The methylation libraries were porcessed with nf-core/methylseq version 1.5 pipeline using Trim Galore version 0.6.4, Bismark version 0.22.3 (49), BWA-meth version 0.2.2 (arxiv.org/abs/1401.1129) and Picard MarkDuplicates version 1.5
DNA variant and methylation libraries were processed and mapped to GRCh38
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data from the variant libraries are text files containing genomic location (chr and position) and coverage.
Supplementary files format and content: Processed daat from the DNA methylation libraries are text files containg genomic location (chr, start, stop), methylation level (%), number of Ts, number of Cs and total coverage.


title: Stage E6.5 embryo 2 section 2 region EA

description:
E6.5_2.txt
E6.5_2_2EA


title: Stage E7.25 embryo 2 section 9 region MA

description:
E7.25_2.txt
E7.25_2_9MA


title: Condition 10-2wk replicate 1


title: THP-1 cells, BS DNA-IFNγ/LPS 24h


title: Stable MGUS patient_154

description:
S154
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 9 region L1

description:
E7.25_2.txt
E7.25_2_9L1


title: Stable MGUS patient_150

description:
S150
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_146

description:
S146
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: THP-1 cells, DNA-IFNγ 24h

data_processing:
The variant libraries were trimmed and quality filtered with Agilent Genomics NextGen Toolkit (AGeNT) software
The methylation libraries were porcessed with nf-core/methylseq version 1.5 pipeline using Trim Galore version 0.6.4, Bismark version 0.22.3 (49), BWA-meth version 0.2.2 (arxiv.org/abs/1401.1129) and Picard MarkDuplicates version 1.5
DNA variant and methylation libraries were processed and mapped to GRCh38
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data from the variant libraries are text files containing genomic location (chr and position) and coverage.
Supplementary files format and content: Processed daat from the DNA methylation libraries are text files containg genomic location (chr, start, stop), methylation level (%), number of Ts, number of Cs and total coverage.
Library strategy: DNA-Seq


title: Stable MGUS patient_149

description:
S149
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_145

description:
S145
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 9 region EP

description:
E7.25_2.txt
E7.25_2_9EP


title: Stable MGUS patient_147

description:
S147
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 2 section 1 region EAP

description:
E6.5_2.txt
E6.5_2_1EAP


title: THP-1 cells, DNA-IFNγ/LPS 24h


title: Stage E6.5 embryo 2 section 2 region EP

description:
E6.5_2.txt
E6.5_2_2EP


title: Stage E7.25 embryo 2 section 9 region MP

description:
E7.25_2.txt
E7.25_2_9MP


title: Stage E7.25 embryo 2 section 9 region EA

description:
E7.25_2.txt
E7.25_2_9EA


title: Stage E6.5 embryo 2 section 1 region AP

description:
E6.5_2.txt
E6.5_2_1AP


title: Stable MGUS patient_143

description:
S143
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Control_12 [MGD1546F RNA-seq]

city: Los Angeles

first: Valerie

last: Arboleda

state: CA

address: 615 Charles E. Young Drive South

department: Department of Pathology and Laboratory Medicine

institute: UCLA

data_processing:
Raw read quality, adaptor content, and duplication rates were assessed with FastQC
Raw reads were then aligned against the Gencode human genome version hg38 (GRCh38) version 31 using STAR 2.7.0e with default parameter
Gene counts from raw reads were generated using featureCounts 1.6.5 from the Subread package
Differential expression was quantified using DESeq2 v1.34.0
Assembly: hg38
Supplementary files format and content: csv file of normalized gene expression in TPM units with columns for differential expression between case and control groups

source_name: fibroblast cells,Control

growth_protocol: Fibroblast cell lines were cells were grown in DMEM (Gibco™), 10% FBS, 1% Non-essential Amino Acid (100X, Gibco™, 11140-050) and 1% PenStrep at 37℃ in 5% CO2 incubators. Cell lines were tested for mycoplasma on a monthly basis.

extract_protocol:
RNA was extracted from cells grown to 80-90% confluence using the PureLink RNA mini kit (Invitrogen #12183018A). Samples were processed for stranded total RNAseq libraries. The rRNA was depleted using the Qiagen QIAseq Fastselect-rRNA/Globin Kit (cat#335377) followed by illumina TruSeq® Stranded Total RNA Library Prep Gold (cat#20020599).
Illumina TruSeq® Stranded Total RNA Library Prep Gold (cat#20020599) was used for library construction

value: fibroblast

tag: Sex

value: M

tag: age

value: Control


title: Control_11 [GM00323 RNA-seq]


title: Stage E6.5 embryo 1 section 8 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_8P


title: Stage E7.25 embryo 2 section 8 region R1

description:
E7.25_2.txt
E7.25_2_8R1


title: Control_10 [MGD1558F RNA-seq]

value: F


title: Stage E6.5 embryo 1 section 8 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_8EP


title: Stage E6.5 embryo 2 section 2 region A

description:
E6.5_2.txt
E6.5_2_2A


title: Stage E6.5 embryo 1 section 8 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_8EA


title: Stage E7.25 embryo 2 section 8 region R2

description:
E7.25_2.txt
E7.25_2_8R2


title: Stable MGUS patient_148

description:
S148
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 8 region P

description:
E7.25_2.txt
E7.25_2_8P


title: Control_8 [MGD1548F RNA-seq]


title: Control_9 [GM01651G RNA-seq]


title: Stable MGUS patient_141

description:
S141
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 8 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_8A


title: Stable MGUS patient_144

description:
S144
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 8 region MP

description:
E7.25_2.txt
E7.25_2_8MP


title: Stage E7.25 embryo 2 section 9 region A

description:
E7.25_2.txt
E7.25_2_9A


title: Stage E6.5 embryo 1 section 7 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_7P


title: Stable MGUS patient_140

description:
S140
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Control_6 [MGD1551 RNA-seq]


title: Stage E6.5 embryo 1 section 7 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_7EP


title: Stage E7.25 embryo 2 section 8 region MA

description:
E7.25_2.txt
E7.25_2_8MA


title: Control_5 [ZKW1511 RNA-seq]


title: Stage E7.25 embryo 2 section 8 region L2

description:
E7.25_2.txt
E7.25_2_8L2


title: Stage E6.5 embryo 1 section 7 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_7EA


title: Control_1 [ZKW1743 RNA-seq]


title: Stable MGUS patient_139

description:
S139
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_138

description:
S138
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: KAT6A_MGD1360 [RNA-seq]

source_name: fibroblast cells,KAT6A


title: Stable MGUS patient_137

description:
S137
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_142

description:
S142
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 7 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_7A


title: Stable MGUS patient_136

description:
S136
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_135

description:
S135
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 6 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_6P


title: Stage E7.25 embryo 2 section 8 region A

description:
E7.25_2.txt
E7.25_2_8A


title: KAT6A_MGD1618 [RNA-seq]


title: Stage E6.5 embryo 1 section 6 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_6EP


title: Stage E7.25 embryo 2 section 7 region R2

description:
E7.25_2.txt
E7.25_2_7R2


title: KAT6A_MGD1191 [RNA-seq]


title: Stage E6.5 embryo 1 section 6 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_6EA


title: Stage E7.25 embryo 2 section 7 region R1

description:
E7.25_2.txt
E7.25_2_7R1


title: Stable MGUS patient_134

description:
S134
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 7 region P

description:
E7.25_2.txt
E7.25_2_7P


title: Stage E6.5 embryo 1 section 5 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_5P


title: Stable MGUS patient_133

description:
S133
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 6 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_6A


title: KAT6A_MGD1135 [RNA-seq]


title: Stable MGUS patient_132

description:
S132
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 8 region EP

description:
E7.25_2.txt
E7.25_2_8EP


title: Stable MGUS patient_131

description:
S131
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 7 region MP

description:
E7.25_2.txt
E7.25_2_7MP


title: KAT6A_MGD1094 [RNA-seq]


title: KAT6A_MGD1105 [RNA-seq]


title: Stage E6.5 embryo 1 section 5 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_5EP


title: Stage E7.25 embryo 2 section 8 region L1

description:
E7.25_2.txt
E7.25_2_8L1


title: Stage E6.5 embryo 1 section 5 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_5EA


title: Stage E7.25 embryo 2 section 7 region MA

description:
E7.25_2.txt
E7.25_2_7MA


title: Stable MGUS patient_130

description:
S130
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: RUNX1 ChIP-seq in MLL-AF4 KD SEM cells [SEM_MLL-AF4_KD_RUNX1]

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Leukemia cell line (SEM)

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

treatment_protocol: See sample table

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: chip antibody

value: Abcam ab23980

value: siRNA-mediated KD of MLL-AF4 for 48h


title: KAT6A_MGD1149 [RNA-seq]


title: Stage E6.5 embryo 1 section 5 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_5A


title: Stable MGUS patient_129

description:
S129
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_127

description:
S127
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: MAZ ChIP-seq in MLL-AF4 KD SEM cells [SEM_MLL-AF4_KD_MAZ]

value: Bethyl A301-652A


title: Stable MGUS patient_128

description:
S128
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 7 region L1

description:
E7.25_2.txt
E7.25_2_7L1


title: Stage E6.5 embryo 1 section 4 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_4P


title: ChIP-seq Input for MAZ and RUNX1 in MLL-AF4 KD SEM cells [SEM_MLL-AF4_KD_Input_TFs]


title: Stable MGUS patient_126

description:
S126
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 7 region EP

description:
E7.25_2.txt
E7.25_2_7EP


title: RUNX1 ChIP-seq in NT siRNA-transfected SEM cells [SEM_NT_RUNX1]

value: NT siRNA transfection for 48h


title: Stage E6.5 embryo 1 section 4 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_4EA


title: Stage E7.25 embryo 2 section 7 region EA

description:
E7.25_2.txt
E7.25_2_7EA


title: Stage E7.25 embryo 2 section 7 region A

description:
E7.25_2.txt
E7.25_2_7A


title: MAZ ChIP-seq in NT siRNA-transfected SEM cells [SEM_NT_MAZ]


title: Stage E6.5 embryo 1 section 4 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_4A


title: ChIP-seq Input for MAZ and RUNX1 in NT siRNA-transfected SEM cells [SEM_NT_Input_TFs]


title: Stage E7.25 embryo 2 section 7 region L2

description:
E7.25_2.txt
E7.25_2_7L2


title: Stable MGUS patient_125

description:
S125
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 6 region R

description:
E7.25_2.txt
E7.25_2_6R


title: Stable MGUS patient_124

description:
S124
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 3 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_3P


title: MLL ChIP-seq in MLL-AF4 KD SEM cells [SEM_MLL-AF4_KD_MLL]

value: Bethyl A300-086A


title: Stage E6.5 embryo 1 section 3 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_3EP


title: Stage E6.5 embryo 1 section 3 region EA

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_3EA


title: Stage E7.25 embryo 2 section 6 region MA

description:
E7.25_2.txt
E7.25_2_6MA


title: Stage E7.25 embryo 2 section 6 region MP

description:
E7.25_2.txt
E7.25_2_6MP


title: Stage E6.5 embryo 1 section 4 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_4EP


title: Stable MGUS patient_123

description:
S123
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells


title: Stable MGUS patient_121

description:
S121
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Stable MGUS


title: Stage E6.5 embryo 1 section 3 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_3A

value: embryo


title: Stable MGUS patient_122

description:
S122
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ChIP-seq Input for MLL in NT siRNA-transfected SEM cells [SEM_NT_Input_MLL]


title: Stage E7.25 embryo 2 section 6 region L

description:
E7.25_2.txt
E7.25_2_6L


title: Stable MGUS patient_120

description:
S120
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 6 region P

description:
E7.25_2.txt
E7.25_2_6P


title: Stage E7.25 embryo 2 section 6 region EP

description:
E7.25_2.txt
E7.25_2_6EP


title: Stage E6.5 embryo 1 section 2 region EP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_2EP


title: Stable MGUS patient_119

description:
S119
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_PBandRA_rep3_input

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
fastp 0.12.4 for adapter and quality trimming
Bowtie2 2.4.4 alignment to hg19 genome
Peaks called with MACS2 2.2.7.1 broadPeak mode with input sample reference
Differential Peaks were determined using DiffBind v3.4 on the consensus of broad peaks called in at least 2 of the 4 biological replicates
bigWig files were generated by deeptools with CPM normalisation and mean of the replicates generated with wiggletools
Assembly: hg19
Supplementary files format and content: broadPeak files generated from MACS2
Supplementary files format and content: bigwig files are normalised CPM per sample and the mean average of the 4 replicates
Supplementary files format and content: tables include differential H3K27ac marks for each condition compared to the DMSO control

growth_protocol: SK-N-BE(2)C cells were cultured in DMEM/F12 media with HEPES and l-glut supplemented with 10% FBS

extract_protocol:
cells were fixed for 10 minutes with 1% formaldehyde. 0.125 M Glycine (final) was subsequently used to quench the fixation. Chromatin was extracted from cells and subject to sonication. 80 ug of chromatin was incorporated into each ChIP that used 2 ug of H3K27ac antibody (ab4729). DNA fragments retrieved from ChIP were purified using GenElute™ Mammalian Genomic DNA Miniprep Kit
NEB Ultra II DNA library prep kit
H3K27ac ChIP-seq

treatment_protocol: 1uM palbociclib

value: neuroblastoma cell line

value: PBandRA

tag: chip type

value: input


title: Stage E7.25 embryo 2 section 6 region EA

description:
E7.25_2.txt
E7.25_2_6EA


title: Stable MGUS patient_118

description:
S118
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_PBandRA_rep2_input


title: ChIP-seq Input for MLL in MLL-AF4 KD SEM cells [SEM_MLL-AF4_KD_Input_MLL]


title: Stage E7.25 embryo 2 section 6 region A

description:
E7.25_2.txt
E7.25_2_6A


title: Stage E6.5 embryo 1 section 2 region A

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_2A


title: Stage E6.5 embryo 1 section 1 region EAP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_1EAP


title: MLL ChIP-seq in NT siRNA-transfected SEM cells [SEM_NT_MLL]


title: Stable MGUS patient_117

description:
S117
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_116

description:
S116
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 1 section 1 region AP

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_1AP


title: BE2C_PB_rep4_input

value: PB


title: BE2C_PBandRA_rep1_input


title: Stage E7.25 embryo 2 section 5 region P

description:
E7.25_2.txt
E7.25_2_5P


title: BE2C_PB_rep3_input


title: Stage E7.25 embryo 2 section 5 region R

description:
E7.25_2.txt
E7.25_2_5R


title: BE2C_PB_rep2_input


title: Stage E7.25 embryo 2 section 5 region M

description:
E7.25_2.txt
E7.25_2_5M


title: Stage E6.5 embryo 1 section 2 region P

description:
E6.5_1_FPKM_Filter_Log2.txt
E6.5_1_2P


title: Capture-C in dTag13-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_2

description:
3C library preparation followed by double oligonucleotide capture
SEM-SSRP1-FKBP_CapC_combined.gfc.gz

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Assembly: hg19
Supplementary files format and content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
Library strategy: Capture-C

extract_protocol:
Cells fixed with 2% formaldehyde and lysed on ice
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, pelleted and resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 2 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra II DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

treatment_protocol: see sample table

value: dTag-13 at 0.5 µM for 24h

tag: genes analysed

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, PROM1, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: Capture-C in dTag13-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_3


title: Stable MGUS patient_114

description:
S114
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_PB_rep1_input


title: Capture-C in dTag13-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_1


title: Stable MGUS patient_113

description:
S113
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 5 region EP

description:
E7.25_2.txt
E7.25_2_5EP


title: BE2C_PBandRA_rep4_input


title: Capture-C in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_3

value: DMSO for 24h


title: Stable MGUS patient_111

description:
S111
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_RA_rep4_input

value: RA


title: Capture-C in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_2


title: Stable MGUS patient_112

description:
S112
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_115

description:
S115
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 5 region EA

description:
E7.25_2.txt
E7.25_2_5EA


title: Stable MGUS patient_110

description:
S110
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_109

description:
S109
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 5 region A

description:
E7.25_2.txt
E7.25_2_5A


title: BE2C_RA_rep2_input


title: Stage E7.25 embryo 2 section 4 region R

description:
E7.25_2.txt
E7.25_2_4R


title: Stage E7.25 embryo 2 section 5 region L

description:
E7.25_2.txt
E7.25_2_5L


title: BE2C_RA_rep1_input


title: Stable MGUS patient_108

description:
S108
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_106

description:
S106
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Capture-C in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_3

description:
3C library preparation followed by double oligonucleotide capture
SEM-PAF1-FKBP_CapC_combined.gfc.gz


title: Capture-C in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_2


title: Stage E7.25 embryo 2 section 4 region P

description:
E7.25_2.txt
E7.25_2_4P


title: BE2C_DMSO_rep4_input

value: DMSO


title: BE2C_DMSO_rep3_input


title: BE2C_RA_rep3_input


title: Stage E7.25 embryo 2 section 4 region M

description:
E7.25_2.txt
E7.25_2_4M


title: Stable MGUS patient_107

description:
S107
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_DMSO_rep2_input


title: Stage E7.25 embryo 2 section 4 region EP

description:
E7.25_2.txt
E7.25_2_4EP


title: Capture-C in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_3


title: Capture-C in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_2


title: Capture-C in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_1


title: Stage E7.25 embryo 2 section 4 region L

description:
E7.25_2.txt
E7.25_2_4L


title: BE2C_DMSO_rep1_input


title: Capture-C in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate_1


title: Stage E7.25 embryo 2 section 3 region R

description:
E7.25_2.txt
E7.25_2_3R


title: BE2C_PBandRA_rep4_H3K27ac_ChIP


title: Stable MGUS patient_104

description:
S104
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Capture-C in MLL-AF4 KD SEM cells_replicate_3

description:
3C library preparation followed by double oligonucleotide capture
SEM_MLLAF4-KD_CapC_combined.gfc.gz

value: siRNA-mediated KD of MLL-AF4 for 96h


title: Stable MGUS patient_103

description:
S103
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_105

description:
S105
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_PBandRA_rep3_H3K27ac_ChIP


title: Capture-C in MLL-AF4 KD SEM cells_replicate_2


title: Stage E7.25 embryo 2 section 3 region P

description:
E7.25_2.txt
E7.25_2_3P


title: Stage E7.25 embryo 2 section 3 region M

description:
E7.25_2.txt
E7.25_2_3M


title: Stable MGUS patient_101

description:
S101
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_100

description:
S100
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Capture-C in MLL-AF4 KD SEM cells_replicate_1


title: BE2C_PBandRA_rep2_H3K27ac_ChIP


title: Capture-C in NT siRNA-transfected SEM cells_replicate_3

value: NT siRNA transfection for 96h


title: Stage E7.25 embryo 2 section 3 region L

description:
E7.25_2.txt
E7.25_2_3L


title: Stage E7.25 embryo 2 section 4 region EA

description:
E7.25_2.txt
E7.25_2_4EA


title: BE2C_PBandRA_rep1_H3K27ac_ChIP


title: BE2C_PB_rep4_H3K27ac_ChIP


title: BE2C_PB_rep3_H3K27ac_ChIP


title: Stage E7.25 embryo 2 section 3 region EA

description:
E7.25_2.txt
E7.25_2_3EA


title: Stage E7.25 embryo 2 section 3 region EP

description:
E7.25_2.txt
E7.25_2_3EP


title: Capture-C in NT siRNA-transfected SEM cells_replicate_1


title: ENL HT-ChIPmentation in RS4;11 cells

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Assembly: hg19
Supplementary files format and content: Peak calling and annotation using Homer v4.7
Supplementary files format and content: Bigwig generation using DeepTools

source_name: Leukemia cell line (RS4;11)

growth_protocol: Cells were continuously grown in IMDM (SEM) or RPMI (RS4;11) with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones and HT-CM) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (TFs). Cells were sonicated to give fragments of 100-300bp followed by IP.
IPed chromatin was tagmented by incubating in 29 µl Tagmentation Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 10% dimethylformamide) and adding 1 µl of transposase (Illumina) at 37 ˚C for 10 min. Tagmented DNA was amplified and indexed with NEBNext Ultra II Q5 Master Mix (NEB).

value: Pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: Bethyl A302-268A


title: BE2C_PB_rep2_H3K27ac_ChIP


title: Stage E7.25 embryo 2 section 3 region A

description:
E7.25_2.txt
E7.25_2_3A


title: Capture-C in NT siRNA-transfected SEM cells_replicate_2


title: Stable MGUS patient_97

description:
S097
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_PB_rep1_H3K27ac_ChIP


title: Stable MGUS patient_96

description:
S096
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_98

description:
S098
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_102

description:
S102
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_95

description:
S095
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_RA_rep4_H3K27ac_ChIP


title: Stage E7.25 embryo 2 section 2 region R

description:
E7.25_2.txt
E7.25_2_2R


title: Stable MGUS patient_99

description:
S099
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_94

description:
S094
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_RA_rep3_H3K27ac_ChIP


title: PAF1 HT-ChIPmentation in RS4;11 cells

value: Bethyl A300-172A


title: Capture-C in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate_1

description:
3C library preparation followed by double oligonucleotide capture
SEM-SSRP1-FKBP_CapC_combined.gfc.gz


title: PAF1 TOPmentation in RS4;11 cells


title: Stage E7.25 embryo 2 section 2 region M

description:
E7.25_2.txt
E7.25_2_2M


title: Stage E7.25 embryo 2 section 2 region L

description:
E7.25_2.txt
E7.25_2_2L


title: Stage E7.25 embryo 2 section 2 region P

description:
E7.25_2.txt
E7.25_2_2P


title: BE2C_RA_rep1_H3K27ac_ChIP


title: BE2C_RA_rep2_H3K27ac_ChIP


title: H3K79me3 TOPmentation in dTAG13-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: ENL TOPmentation in RS4;11 cells


title: Stable MGUS patient_92

description:
S092
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells

value: Stable MGUS


title: Stable MGUS patient_93

description:
S093
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_DMSO_rep4_H3K27ac_ChIP

value: neuroblastoma cell line


title: H3K79me3 TOPmentation in DMSO-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: Stage E7.25 embryo 2 section 2 region EP

description:
E7.25_2.txt
E7.25_2_2EP

value: embryo


title: BE2C_DMSO_rep3_H3K27ac_ChIP


title: Input for PAF1 TOPmentation in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stage E7.25 embryo 2 section 2 region A

description:
E7.25_2.txt
E7.25_2_2A


title: Stable MGUS patient_89

description:
S089
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_90

description:
S090
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_91

description:
S091
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_DMSO_rep2_H3K27ac_ChIP


title: PAF1 TOPmentation in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stage E7.25 embryo 2 section 1 region VE

description:
E7.25_2.txt
E7.25_2_1VE


title: Stable MGUS patient_88

description:
S088
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 1 region Epi

description:
E7.25_2.txt
E7.25_2_1Epi


title: Stable MGUS patient_87

description:
S087
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: BE2C_DMSO_rep1_H3K27ac_ChIP


title: H3K79me3 TOPmentation in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD3 TCR

city: Kiel

first: Ekaterina

last: Tikhonova

address: Arnold-Heller-Straße 3

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Comma-separated annotations of each high-confidence V(D)J contig from cell-associated barcodes

source_name: PMBC

extract_protocol:
PBMCs were stimulated with C. albicans, C. tropicalis and S. cerevisiae for 6 h in presence of 1 µg/mL CD40 and 1 µg/mL CD28 pure antibody (both Miltenyi Biotec). Cells were labeled with IFN-g and IL-17A catch reagent (Cytokine secretion assay, both Miltenyi Biotec) and incubated for additional 45 min in RMPI-1640 medium supplemented with 2% (v/v) human AB-serum under continuous rotation. Cells were further labeled with CD154-PE, IL-17A-APC and IFN-g-FITC followed by anti-PE MicroBeads and magnetically enriched by MS columns (all from Miltenyi Biotec). Cells were sorted into pre-coated low-bind collection tubes, containing sterile filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum. After sorting, cells were re-added to MS 18 columns to avoid cell loss during washing steps and stained on the column with 1µL hashtag antibodies (TotalSeq-C0251 anti-human Hashtag 1 (clone: LNH-94), TotalSeq-C0252 anti-human Hashtag 2 (clone: LNH-94), TotalSeq-C0253 anti-human Hashtag 3 (clone: LNH-94 in presence of Human TruStain FcX) (all BioLegend) in 50µL staining volume. Columns were washed twice, and cells were eluted with 500µL of sterile filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum.
Directly before loading, IL-17A+, IFN-g and CD154+ populations for each antigen were combined, centrifuged, and loaded on a Chromium Chip G (10x Genomics) according to the manufacturer’s instructions for processing with the Chromium Next GEM Single Cell 5´ Library and Gel Bead Kit v1.1. Between 5,000-12,000 cells were loaded for each reaction. TCR single-cell libraries were subsequently prepared from the same cells with the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell.

value: CD4+ T cells

value: PMBC

value: Crohn's disease


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD3 GEX


title: Input for PAF1 TOPmentation in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stage E7.25 embryo 2 section 2 region EA

description:
E7.25_2.txt
E7.25_2_2EA


title: PAF1 TOPmentation in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)

value: dTag-13 at 0.5 µM for 24h


title: Stable MGUS patient_85

description:
S085
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD3 TCR


title: MLL ChIP-seq in dTAG13-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)

value: dTag-13 at 0.5 microM for 24h

value: Bethyl A300-086A


title: Stage E7.25 embryo 2 section 12 region MP

description:
E7.25_2.txt
E7.25_2_12MP


title: Stable MGUS patient_84

description:
S084
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_86

description:
S086
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 12 region L

description:
E7.25_2.txt
E7.25_2_12L


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD3 TCR

value: C. albicans


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD3 GEX


title: MLL ChIP-seq in DMSO-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)

value: DMSO for 24h


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD3 GEX


title: Stage E7.25 embryo 2 section 12 region R

description:
E7.25_2.txt
E7.25_2_12R


title: ChIP-seq Input for MLL in DMSO-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: Stable MGUS patient_83

description:
S083
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 12 region P

description:
E7.25_2.txt
E7.25_2_12P


title: Stable MGUS patient_82

description:
S082
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 12 region EP

description:
E7.25_2.txt
E7.25_2_12EP


title: Stable MGUS patient_80

description:
S080
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: H3K79me3 TOPmentation in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: H3K27ac ChIP-seq in dTAG13-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)

value: Diagenode C15410196


title: Stable MGUS patient_81

description:
S081
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD2 TCR


title: Stage E7.25 embryo 2 section 12 region A

description:
E7.25_2.txt
E7.25_2_12A


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD2 TCR


title: Stage E7.25 embryo 2 section 11 region R2

description:
E7.25_2.txt
E7.25_2_11R2


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD2 GEX


title: H3K27ac ChIP-seq in DMSO-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: ChIP-seq Input for MLL in dTAG13-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: Stage E7.25 embryo 2 section 11 region R1

description:
E7.25_2.txt
E7.25_2_11R1


title: ChIP-seq Input for H3K27ac in DMSO-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD2 GEX


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD2 TCR


title: Stage E7.25 embryo 2 section 12 region EA

description:
E7.25_2.txt
E7.25_2_12EA


title: MLL ChIP-seq in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stable MGUS patient_77

description:
S077
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_79

description:
S079
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 11 region P

description:
E7.25_2.txt
E7.25_2_11P


title: Stage E7.25 embryo 2 section 11 region MA

description:
E7.25_2.txt
E7.25_2_11MA


title: Stage E7.25 embryo 2 section 11 region MP

description:
E7.25_2.txt
E7.25_2_11MP


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD2 GEX


title: Stable MGUS patient_78

description:
S078
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: MLL ChIP-seq in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD1 GEX


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD1 TCR


title: Stage E7.25 embryo 2 section 11 region L2

description:
E7.25_2.txt
E7.25_2_11L2


title: Stage E7.25 embryo 2 section 12 region MA

description:
E7.25_2.txt
E7.25_2_12MA


title: Stable MGUS patient_73

description:
S073
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ChIP-seq Input for MLL in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: ChIP-seq Input for MLL in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stable MGUS patient_74

description:
S074
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_76

description:
S076
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 11 region L1

description:
E7.25_2.txt
E7.25_2_11L1


title: H3K27ac ChIP-seq in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stable MGUS patient_75

description:
S075
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, Crohn's disease patient, S.cerevisiae-reactive CD4 T, CD1 TCR


title: Stable MGUS patient_72

description:
S072
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 11 region EP

description:
E7.25_2.txt
E7.25_2_11EP


title: PMBC, Crohn's disease patient, C.tropicalis-reactive CD4 T, CD1 GEX


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD1 TCR


title: H3K27ac ChIP-seq in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: ChIP-seq Input for H3K27ac in dTAG13-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: Stable MGUS patient_71

description:
S071
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ChIP-seq Input for H3K27ac in DMSO-treated SEM cells with PAF1 endogenously tagged with FKBP12(F36V)


title: PMBC, Crohn's disease patient, C.albicans-reactive CD4 T, CD1 GEX


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD3 TCR

value: healthy


title: Stable MGUS patient_69

description:
S069
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_70

description:
S070
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 10 region R2

description:
E7.25_2.txt
E7.25_2_10R2


title: PAF1 ChIP-seq in MLL-AF4 KD SEM cells

value: siRNA-mediated KD of MLL-AF4 for 96h


title: Stable MGUS patient_68

description:
S068
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_66

description:
S066
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ChIP-seq Input for H3K27ac in dTAG13-treated SEM cells with SSRP1 endogenously tagged with FKBP12(F36V)


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD3 GEX


title: Stage E7.25 embryo 2 section 10 region R1

description:
E7.25_2.txt
E7.25_2_10R1


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD3 TCR


title: PAF1 ChIP-seq in NT siRNA-transfected SEM cells

value: NT siRNA transfection for 96h

value: Bethyl A300-172A


title: Stage E7.25 embryo 2 section 10 region P

description:
E7.25_2.txt
E7.25_2_10P


title: Stable MGUS patient_67

description:
S067
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD3 GEX


title: Stage E7.25 embryo 2 section 10 region MP

description:
E7.25_2.txt
E7.25_2_10MP


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD3 TCR


title: ChIP-seq Input for PAF1 in MLL-AF4 KD SEM cells

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: Stage E7.25 embryo 2 section 10 region MA

description:
E7.25_2.txt
E7.25_2_10MA


title: Stage E7.25 embryo 2 section 11 region EA

description:
E7.25_2.txt
E7.25_2_11EA


title: Stage E7.25 embryo 2 section 11 region A

description:
E7.25_2.txt
E7.25_2_11A


title: H3K79me3 ChIP-seq in MLL-AF4 KD SEM cells

value: Diagenode pAb-068-050


title: Stage E7.25 embryo 2 section 10 region L2

description:
E7.25_2.txt
E7.25_2_10L2

value: embryo


title: ChIP-seq Input for H3K79me3 in MLL-AF4 KD SEM cells


title: Stable MGUS patient_64

description:
S064
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Stable MGUS


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD2 TCR

value: CD4+ T cells

value: PMBC


title: Stable MGUS patient_65

description:
S065
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_63

description:
S063
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD3 GEX


title: Stable MGUS patient_62

description:
S062
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 2 section 10 region L1

description:
E7.25_2.txt
E7.25_2_10L1


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD2 GEX


title: ChIP-seq Input for PAF1 in NT siRNA-transfected SEM cells


title: ChIP-seq Input for H3K79me3 in NT siRNA-transfected SEM cells


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD2 TCR


title: Stage E7.25 embryo 2 section 10 region EP

description:
E7.25_2.txt
E7.25_2_10EP


title: Stage E7.25 embryo 2 section 10 region A

description:
E7.25_2.txt
E7.25_2_10A


title: H3K27ac ChIP-seq in MLL-AF4 KD SEM cells


title: Stage E7.25 embryo 2 section 10 region EA

description:
E7.25_2.txt
E7.25_2_10EA


title: ChIP-seq Input for H3K27ac in MLL-AF4 KD SEM cells


title: Stage E7.25 embryo 1 section 9 region R2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9R2


title: H3K27ac ChIP-seq in NT siRNA-transfected SEM cells


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD2 GEX


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD2 GEX


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD2 TCR


title: Stable MGUS patient_59

description:
S059
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 9 region R1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9R1


title: ChIP-seq Input for H3K27ac in NT siRNA-transfected SEM cells


title: H3K79me3 ChIP-seq in NT siRNA-transfected SEM cells


title: Stable MGUS patient_56

description:
S056
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 9 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9P


title: SSRP1 ChIP-seq in SEM cells

value: Bethyl A303-067A


title: Stable MGUS patient_61

description:
S061
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 9 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9MP


title: Stable MGUS patient_55

description:
S055
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD1 GEX


title: ChIP seq Input for SSRP1 in SEM cells


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD1 TCR


title: TT-seq in dTag-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 3

description:
Nascent RNA
SEM-SSRP1-FKBP_TTseq_featureCounts.txt.gz
SEM-SSRP1-FKBP_TTseq_contrast_cpm.txt.gz

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: feature counts
Supplementary files format and content: contrast table

extract_protocol:
5e7 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. RNA was mildly fragmented by sonication. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).

value: dTag-13 at 0.5 microM for 24h


title: Stable MGUS patient_60

description:
S060
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: TT-seq in dTag-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 2


title: Stable MGUS patient_57

description:
S057
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD1 TCR


title: Stable MGUS patient_54

description:
S054
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_58

description:
S058
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 9 region L2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9L2


title: PMBC, healthy control, C.tropicalis-reactive CD4 T, HD1 GEX


title: TT-seq in dTag-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 1


title: Stable MGUS patient_53

description:
S053
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 9 region L1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9L1


title: PMBC, healthy control, C.albicans-reactive CD4 T, HD1 GEX


title: PMBC, healthy control, S.cerevisiae-reactive CD4 T, HD1 TCR


title: TT-seq in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 3


title: Stage E7.25 embryo 1 section 9 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9MA


title: Stable MGUS patient_51

description:
S051
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: TT-seq in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 2


title: Stage E7.25 embryo 1 section 9 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9EA


title: MCC_replicate_5

description:
3C library preparation followed by double oligonucleotide capture
FLT3_merged.bigWig
LMO4_merged.bigWig

library_source: other

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Assembly: hg19
Supplementary files format and content: bigWig showing the frequency of interactions with the Capture point

molecule: other

extract_protocol:
Cells fixed with 2% formaldehyde and lysed on ice
Briefly, 10^7 SEM cells were fixed with 2% formaldehyde for 10 min, then quenched with glycine and washed with PBS. Cells were permeabilized with 0.005% digitonin (Sigma Aldrich) for 15 min, then snap frozen. Thawed cells were pelleted and resuspended in reduced-calcium MNase buffer (10 mM Tris-HCl pH7.5, 1 mM CaCl2, then split into three aliquots. Cells were treated with a titration of different MNase (NEB) concentrations (typically 10-30 Kunitz U in an 800 µl volume) for 1h at 37 ˚C in a Thermomixer (Eppendorf) at 550 rpm. The reaction was stopped with addition of ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA) to 5 mM and 200 µl was removed to assess the extent of digestion. The remaining cells were pelleted, washed with PBS/EGTA, then processed for end repair, phosphorylation and ligation. Cell pellets were resuspended in DNA ligase buffer, supplemented with 400 µM dNTPs and 5 mM EDTA, before addition of DNA Polymerase I large (Klenow) fragment (NEB) to 100 U/µl, T4 polynucleotide kinase (NEB) to 200 U/µl and T4 DNA ligase (Thermo Scientific) to 300 U/µl. The reaction was incubated for 2h at 37 ˚C, then for 8h at 20 ˚C, at 550 rpm, then cooled to 4 ˚C overnight. Both the digested and ligated chromatin was decrosslinked at 65 ˚C in the presence of proteinase K, then DNA was purified using the Qiagen DNeasy Blood and Tissue Kit. Digestion and ligation efficiencies were assessed by TapeStation (Agilent D1000). 2 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra II DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the HyperCapture Target Enrichment Kit (Roche). The quality of the resulting captured library was assessed using the Agilent ScreenTape system.

treatment_protocol: Untreated cells

value: FLT3, LMO4


title: MCC_replicate_6


title: Stage E7.25 embryo 1 section 9 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9EP


title: Stage E7.25 embryo 1 section 9 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_9A


title: TT-seq in DMSO-treated SEM cells with endogenous SSRP1 tagged with FKBP12(F36V)_replicate 1


title: Stable MGUS patient_49

description:
S049
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: MCC_replicate_4


title: Stable MGUS patient_52

description:
S052
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 8 region R2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8R2


title: Stable MGUS patient_48

description:
S048
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: TT-seq in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 3

description:
Nascent RNA
SEM-PAF1-FKBP_TTseq_featureCounts.txt.gz
SEM-PAF1-FKBP_TTseq_contrast_cpm.txt.gz


title: MCC_replicate_3


title: TT-seq in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 2


title: Stage E7.25 embryo 1 section 8 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8P


title: Stable MGUS patient_50

description:
S050
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: MCC_replicate_1


title: TT-seq in dTag13-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 1


title: Stage E7.25 embryo 1 section 8 region R1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8R1


title: Stable MGUS patient_47

description:
S047
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_45

description:
S045
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 8 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8MP


title: TT-seq in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 3


title: Stage E7.25 embryo 1 section 8 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8MA


title: TT-seq in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 2


title: TT-seq in DMSO-treated SEM cells with endogenous PAF1 tagged with FKBP12(F36V)_replicate 1


title: sample159, Cluster 2

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.9) and multiqc (v1.6)
Alignment to the human genome using STAR (v2.7.9a)
Read count assessments using htseq-count (v0.11.3)
Assembly: GRCh38.104
Supplementary files format and content: count files, which are text files with counts per gene for each sample

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
2.5mL of whole blood was collected into PAXgene Blood RNA tubes (BD Biosciences; San Jose, CA, USA) and total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen; Germantown, MD, USA)
Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Ipswich, USA) and cDNA libraries were prepared using the NEBNext RNA First Strand Synthesis Module, NEBNext Ultra Directional RNA Second Strand Synthesis Module, and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB; Ipswich, USA)

value: Whole Blood

tag: location

value: Hospital

tag: endotype

value: Cluster 2

tag: batch

value: three

tag: additional metadata

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: Stable MGUS patient_44

description:
S044
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

tag: cell type


title: sample158, Cluster 1

value: Cluster 1


title: sample156, Cluster 3

value: Cluster 3


title: Stage E7.25 embryo 1 section 8 region L1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8L1


title: Stage E7.25 embryo 1 section 8 region L2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8L2


title: Stage E7.25 embryo 1 section 8 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8EP


title: RUNX1 TOPmentation seq for iALL patient sample 2

description: TOPmentation performed in MLL-AF4 patient blasts

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling and annotation using Homer v4.7
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

source_name: MLL-AF4 infant ALL patient 2 blasts

growth_protocol: Infant (<1 year old) and childhood ALL samples were obtained from Blood Cancer UK Childhood Leukemia Cell Bank, UK (REC: 16/SW/0219). All ALL samples were anonymized at source, assigned a unique study number and linked. Cryopreserved samples were thawed, and immediately processed.

extract_protocol:
Cells were washed with PBS and fixed in 2mM DSG for 30 minutes and 1% FA for 30 minutes. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

value: acute lymphoblastic leukemia (ALL)

tag: treatment

tag: individual

value: 1-year old MLL-AF4 ALL patient

value: Bone marrow aspirate

value: Cell Signaling 4334


title: MCC_replicate_2

description:
3C library preparation followed by double oligonucleotide capture
FLT3_merged.bigWig
LMO4_merged.bigWig


title: sample157, Cluster 2

tag: disease state


title: MLL TOPmentation seq for iALL patient sample 2

value: Bethyl A300-086A


title: Stable MGUS patient_46

description:
S046
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells

value: Stable MGUS


title: sample155, Cluster 2


title: Stage E7.25 embryo 1 section 8 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8EA

tag: developmental stage

value: embryo


title: sample154, Cluster 3


title: H3K79me2 TOPmentation seq for iALL patient sample 2

value: Millipore 04-835


title: Stage E7.25 embryo 1 section 8 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_8A

tag: strain


title: H3K4me3 TOPmentation seq for iALL patient sample 2

tag: tissue

value: Active Motif 39159


title: Stable MGUS patient_43

description:
S043
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_39

description:
S039
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_41

description:
S041
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample153, Cluster 1

value: Whole Blood


title: H3K4me1 TOPmentation seq for iALL patient sample 2

value: Diagenode pAb-194-050


title: Stable MGUS patient_38

description:
S038
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 7 region R2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7R2


title: Stable MGUS patient_37

description:
S037
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_36

description:
S036
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_40

description:
S040
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 7 region R1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7R1


title: Stage E7.25 embryo 1 section 7 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7P


title: Stable MGUS patient_42

description:
S042
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: H3K27ac TOPmentation seq for iALL patient sample 2

value: Diagenode C15410196


title: Stage E7.25 embryo 1 section 7 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7MA


title: sample150, Cluster 2

value: Discharged

value: Cluster 2

value: three


title: sample151, Cluster 1

value: Cluster 1

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: RUNX1 TOPmentation seq for chALL patient sample 3

source_name: MLL-AF4 childhood ALL patient 3 blasts

value: acute lymphoblastic leukemia (ALL)

value: 3-year old MLL-AF4 ALL patient


title: sample149, Cluster 3

value: Cluster 3


title: H3K27me3 TOPmentation seq for iALL patient sample 2

value: 1-year old MLL-AF4 ALL patient

value: Bone marrow aspirate

value: Millipore 07-449


title: PAF1 TOPmentation seq for chALL patient sample 3

value: Bethyl A300-172A


title: Stage E7.25 embryo 1 section 7 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7MP

value: embryo


title: Stage E7.25 embryo 1 section 7 region L2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7L2


title: sample152, Cluster 2


title: sample147, Cluster 3