title: Conventionally reared (Sample 1)

status: Public on Nov 20 2020

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

data_processing:
Cell Ranger v3.0 (10X Genomics) was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome
Genome_build: Ensembl GRCz11.96
Supplementary_files_format_and_content: TSV/MTX files

source_name: Dissociated intestines from conventionally reared fish

extract_protocol:
Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller
Chromium Single Cell 3′ Library & Gel Bead Kit v3

value: TL

value: Intestinal and associated tissue

value: 6 dpf larvae

value: conventionally reared


title: OR18

status: Public on Oct 14 2020

type: SRA

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

library_source: transcriptomic

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: total RNA extracted from mice lung

growth_protocol: Female CD-1 mice weighing 27-32 g were obtained from Charles River Laboratories Ltd. U.K. Prior to exposure, animals were habituated for 5 days. All mice were housed in filter-top cages in an enviromentally controled room and maintained at 21°C and 55% humidity. Lighting was set to mimic a 12/12 h dawn to dusk cycle. Animals had acess to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice were anesthetized by an interperitoneal injection of ketamine (1.9 mg/mouse) and xylazine (0.19 mg/mouse), and were intranasally (50 µl/nostril) intoxicated with crude ricin.

tag: treatment

value: NO TREATMENT

tag: strain

tag: tissue

value: lung


title: OR17


title: Sample 24_pioglitazone+gentamicin_24h_r3

status: Public on Sep 24 2020

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
BSSE_QGF_107425_HFJVLBGX7_1_3_8_24pg_r3_TAATACAG_ATATTCAC_S24
BSSE_QGF_107425_HF3KWBGX7_1_3_8_24pg_r3_TAATACAG_ATATTCAC_S24

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for reporting only one hit for multimapping reads ( outFilterMultimapNmax=10, outSAMmultNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

growth_protocol: 5-day-old (P5) C57BL/6N mice of both sexes were decapitated, and cochlear microdissections were performed under a light microscope to isolate the OC. OCs were incubated for 24 h in culture medium (Dulbecco’s Modified Eagle Medium, supplemented with 30 U/mL penicillin, 1% N1 supplement, 10% fetal calf serum, 25 mM HEPES) at 37°C and 5% CO2.

extract_protocol:
OCs for RNA isolation were stored in RNAlater (Cat #AM7020 Ambion, USA). RNA was isolated with a Direct-Zol RNA MiniPrep kit (Cat #R2071, Zymo Research, USA) according to the manufacturer’s instructions.
total RNA was used to generate sequencing libraries with the TruSeq Stranded RNA LT kit (Illumina). Sequencing was performed on an Illumina NextSeq 500 according to manufecturer specification.

treatment_protocol: Six OCs per condition were placed in separate wells of 12-well plates, and each experimental treatment was performed in triplicate. For whole-genome RNA sequencing, we used the 6-h and 24-h treatment time points. OCs were exposed to 50 µM gentamicin, 10 µM pioglitazone, or a combination of both. Control samples were incubated in parallel in culture medium without drugs.

tag: age

value: 5-day-old (P5)

value: organ of Corti (OC)

value: pioglitazone+gentamicin

tag: time in hours

tag: replicate


title: Sample 21_control_24h_r3

description:
BSSE_QGF_107422_HF3KWBGX7_1_3_5_24c_r3_GCACGGAC_GTCTCGCA_S21
BSSE_QGF_107422_HFJVLBGX7_1_3_5_24c_r3_GCACGGAC_GTCTCGCA_S21

value: control


title: Sample 22_gentamicin_24h_r3

description:
BSSE_QGF_107423_HF3KWBGX7_1_3_6_24g_r3_ATGTAAGT_ACTCTATG_S22
BSSE_QGF_107423_HFJVLBGX7_1_3_6_24g_r3_ATGTAAGT_ACTCTATG_S22

value: gentamicin


title: Sample 15_pioglitazone_24h_r1

description:
BSSE_QGF_107416_HF3KWBGX7_1_2_7_24p_r1_GACCTGAA_TTGGTGAG_S15
BSSE_QGF_107416_HFJVLBGX7_1_2_7_24p_r1_GACCTGAA_TTGGTGAG_S15

value: pioglitazone


title: Sample 16_pioglitazone+gentamicin_24h_r1

description:
BSSE_QGF_107417_HFJVLBGX7_1_2_8_24pg_r1_AGTTCAGG_CCAACAGA_S16
BSSE_QGF_107417_HF3KWBGX7_1_2_8_24pg_r1_AGTTCAGG_CCAACAGA_S16


title: Sample 17_control_24h_r2

description:
BSSE_QGF_107418_HFJVLBGX7_1_3_1_24c_r2_ATGAGGCC_GTTAATTG_S17
BSSE_QGF_107418_HF3KWBGX7_1_3_1_24c_r2_ATGAGGCC_GTTAATTG_S17


title: Sample 18_gentamicin_24h_r2

description:
BSSE_QGF_107419_HF3KWBGX7_1_3_2_24g_r2_GCAGAATT_ACCGGCCA_S18
BSSE_QGF_107419_HFJVLBGX7_1_3_2_24g_r2_GCAGAATT_ACCGGCCA_S18


title: Sample 20_pioglitazone+gentamicin_24h_r2

description:
BSSE_QGF_107421_HF3KWBGX7_1_3_4_24pg_r2_GGTACCTT_AAGACGTC_S20
BSSE_QGF_107421_HFJVLBGX7_1_3_4_24pg_r2_GGTACCTT_AAGACGTC_S20


title: Sample 19_pioglitazone_24h_r2

description:
BSSE_QGF_107420_HFJVLBGX7_1_3_3_24p_r2_AACGTTCC_GGAGTACT_S19
BSSE_QGF_107420_HF3KWBGX7_1_3_3_24p_r2_AACGTTCC_GGAGTACT_S19


title: Sample 14_gentamicin_24h_r1

description:
BSSE_QGF_107415_HFJVLBGX7_1_2_6_24g_r1_TCTCTACT_CGCGGTTC_S14
BSSE_QGF_107415_HF3KWBGX7_1_2_6_24g_r1_TCTCTACT_CGCGGTTC_S14


title: Sample 13_control_24h_r1

description:
BSSE_QGF_107414_HFJVLBGX7_1_2_5_24c_r1_CTCTCGTC_TATAACCT_S13
BSSE_QGF_107414_HF3KWBGX7_1_2_5_24c_r1_CTCTCGTC_TATAACCT_S13


title: OR20


title: Sample 12_pioglitazone+gentamicin_6h_r3

description:
BSSE_QGF_107413_HF3KWBGX7_1_2_4_6_pg_r3_CCAAGTCT_AAGGATGA_S12
BSSE_QGF_107413_HFJVLBGX7_1_2_4_6_pg_r3_CCAAGTCT_AAGGATGA_S12


title: Sample 11_pioglitazone_6h_r3

description:
BSSE_QGF_107412_HF3KWBGX7_1_2_3_6_p_r3_TTGGACTC_GGAAGCAG_S11
BSSE_QGF_107412_HFJVLBGX7_1_2_3_6_p_r3_TTGGACTC_GGAAGCAG_S11


title: Sample 10_gentamicin_6h_r3

description:
BSSE_QGF_107411_HF3KWBGX7_1_2_2_6_g_r3_GGCTTAAG_TCGTGACC_S10
BSSE_QGF_107411_HFJVLBGX7_1_2_2_6_g_r3_GGCTTAAG_TCGTGACC_S10


title: Germ free (Sample 2)

organism: Danio rerio

source_name: Dissociated intestines from germ-free fish

tag: genotype

tag: cell type

tag: developmental stage

value: germ-free


title: Myeloid cells sorted from tumor tissue

status: Public on Nov 16 2020

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

country: USA

institute: USCF Immunoprofiler

description: Droplet based Single cell RNAseq (10x genomics. 3 prime v2)

data_processing:
Alignement in human genome
Cell ranger processing
Geneation of Seurat object using Seurat V3
Genome_build: GRCh38
Supplementary_files_format_and_content: genes count and barcodes list
Supplementary_files_format_and_content: Matrix of genes and barcodes

organism: Homo sapiens

source_name: Kidney biopsy

value: tumor lesion


title: Sample 9_control_6h_r3

description:
BSSE_QGF_107410_HF3KWBGX7_1_2_1_6_c_r3_AATCCGGA_CTACAGTT_S9
BSSE_QGF_107410_HFJVLBGX7_1_2_1_6_c_r3_AATCCGGA_CTACAGTT_S9


title: Sample 1_control_6h_r1

description:
BSSE_QGF_107402_HF3KWBGX7_1_1_1_6_c_r1_TGGATCGA_GTGCGATA_S1
BSSE_QGF_107402_HFJVLBGX7_1_1_1_6_c_r1_TGGATCGA_GTGCGATA_S1


title: Sample 2_gentamicin_6h_r1

description:
BSSE_QGF_107403_HF3KWBGX7_1_1_2_6_g_r1_CAAGCTAG_ACATAGCG_S2
BSSE_QGF_107403_HFJVLBGX7_1_1_2_6_g_r1_CAAGCTAG_ACATAGCG_S2


title: Sample 7_pioglitazone_6h_r2

description:
BSSE_QGF_107408_HFJVLBGX7_1_1_7_6_p_r2_TTATAACC_GATATCGA_S7
BSSE_QGF_107408_HF3KWBGX7_1_1_7_6_p_r2_TTATAACC_GATATCGA_S7


title: Sample 8_pioglitazone+gentamicin_6h_r2

description:
BSSE_QGF_107409_HFJVLBGX7_1_1_8_6_pg_r2_CCGCGGTT_AGCGCTAG_S8
BSSE_QGF_107409_HF3KWBGX7_1_1_8_6_pg_r2_CCGCGGTT_AGCGCTAG_S8


title: Sample 4_pioglitazone+gentamicin_6h_r1

description:
BSSE_QGF_107405_HF3KWBGX7_1_1_4_6_pg_r1_ATCCACTG_AGGTGCGT_S4
BSSE_QGF_107405_HFJVLBGX7_1_1_4_6_pg_r1_ATCCACTG_AGGTGCGT_S4


title: Sample 6_gentamicin_6h_r2

description:
BSSE_QGF_107407_HF3KWBGX7_1_1_6_6_g_r2_GGACTTGG_CGCAGACG_S6
BSSE_QGF_107407_HFJVLBGX7_1_1_6_6_g_r2_GGACTTGG_CGCAGACG_S6


title: Sample 3_pioglitazone_6h_r1

description:
BSSE_QGF_107404_HF3KWBGX7_1_1_3_6_p_r1_GCTTGTCA_GAACATAC_S3
BSSE_QGF_107404_HFJVLBGX7_1_1_3_6_p_r1_GCTTGTCA_GAACATAC_S3


title: Sample 5_control_6h_r2

description:
BSSE_QGF_107406_HF3KWBGX7_1_1_5_6_c_r2_AAGTCCAA_TATGAGTA_S5
BSSE_QGF_107406_HFJVLBGX7_1_1_5_6_c_r2_AAGTCCAA_TATGAGTA_S5


title: Sample 23_pioglitazone_24h_r3

description:
BSSE_QGF_107424_HF3KWBGX7_1_3_7_24p_r3_CGGCGTGA_GCGCCTGT_S23
BSSE_QGF_107424_HFJVLBGX7_1_3_7_24p_r3_CGGCGTGA_GCGCCTGT_S23


title: 1104-3-03-A11_PAAD_3_Breg

status: Public on Aug 28 2020

city: Chapel Hill, NC

first: Yuliya

last: Pylayeva-Gupta

state: NC

address: 450 West Drive, CB 7295

department: Lineberger Comprehensive Center

institute: UNC

data_processing:
FASTQ files were aligned to the human reference genome using STAR v2.4.2
BAM output files were quantified using Salmon v0.8.2
FastQC v0.11.7 and MultiQC v1.5 were used to generate quality assurance reports.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt. Data matrix of Salmon quantified gene counts for each of the 2 samples. Genes are listed by NCBI gene ID, entrez #, and symbol

source_name: PBMCs

growth_protocol: No growth protocol. Sorted PBMCs were freshly isolated

extract_protocol:
Total RNA was extracted from FACS isolated B cells using Rneasy Plus Mini Kit according to manufacturers instructions.
Library was constructed with the Illumina TruSeq RNA Library prep kit v2 according to manufacturers instructions.

treatment_protocol: No treatment protocol. Sorted PBMCs were freshly isolated

tag: alias

value: Breg

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma (PAAD)


title: Bulk_SERIES_1: HSC_MTB_3

status: Public on Aug 13 2020

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

data_processing:
low-quality score bases (Phred score < 20) and adaptor sequences were trimmed using Trim Galore (v. 0.2.7)
Mapping of the resulting reads to the mouse genome reference sequence was done with kallisto (v0.43.0)
Genome_build: Ensembl GRCm38 release 81
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Hematopoietic stem cells

growth_protocol: Six to ten-week old C57BL/6J, Rag1-/, Ccr2/-, and CD45.1+ B6 mice were purchased from Jackson Laboratories or bred at the RI-MUHC, Montreal, QC, Canada. All experiments were performed with male mice, except parabiosis, which was performed on female mice. All animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860).

extract_protocol:
Bone marrow cells were harvested from femurs, tibiae, humeri and ilia, and incubated with the described biotin-conjugated antibodies against lineage-committed cells. Subsequently, the cells were incubated with MACS streptavidin conjugated microbeads (Miltenyi) for 30 minutes at 4°C. A depletion of the lineage-committed cells was performed using AutoMACS (Miltenyi) to reduce the contaminating total cell number. The remaining cells were incubated with the corresponding antibodies for HSCs vs MPPs cells.
Total RNA was extracted from the sorted HSCs and MPPs using Magmax-96 Total RNA isolation kit (life technologies, Ambion 1830M). RNA quality was evaluated spectrophotometrically, and quality was assessed with the Agilent 2100 Bioanalyzer
RNA-sequencing libraries were prepared using the SMARTer® Stranded RNA-Seq Kit (for HSCs) and sequenced with single-end 100bp reads on an Illumina HiSeq2500.

treatment_protocol: Throughout the study, mice were intravenously (iv) infected with Mtb H37Rv, Mtb H37Rv-ΔRD-1 or vaccinated with BCG-TICE with a dose of 1x106 single-suspended bacteria in 100µl PBS. 28 days after treatment, animals were sacrificed, and their BM extracted.

value: Hematopoietic stem cells (HSC)

value: MTB

tag: mouse id


title: Bulk_SERIES_1: HSC_MTB_2


title: Bulk_SERIES_1: MPP_MTB_1

source_name: Multi potent progenitors

value: Multi potent progenitors (MPP)


title: Bulk_SERIES_1: HSC_MTB_4


title: Bulk_SERIES_1: HSC_CTL_2

value: CTL


title: Bulk_SERIES_1: HSC_CTL_1


title: Bulk_SERIES_1: HSC_BCG_4

value: BCG


title: Bulk_SERIES_1: HSC_BCG_2


title: Bulk_SERIES_1: HSC_CTL_3


title: Gonadal white adipose tissue, fast, replicate 8

status: Public on Sep 01 2020

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.0).

label: biotin

source_name: Gonadal white adipose tissue, after 16hrs of fasting

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Animal studies were performed using 3 to 4-month-old pure-bred male mice on a C57Bl/6 background. The study was approved by the Local Animal Ethics Committee of Wageningen University.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Mice were fed, or fasted for 16 hours, prior to sacrifice. Gonadal white adipose tissue was collected for microarray analysis.

tag: sex (female=1, male=0)

value: 3-4 months

tag: nutritional status

value: Fast

tag: moment of sampling

value: morning

value: Gonadal white adipose tissue


title: Bulk_SERIES_1: HSC_BCG_3


title: Bulk_SERIES_1: MPP_BCG_3


title: Bulk_SERIES_1: MPP_MTB_2


title: Bulk_SERIES_1: MPP_BCG_4


title: Bulk_SERIES_1: MPP_MTB_4


title: Bulk_SERIES_1: HSC_MTB_1


title: Gonadal white adipose tissue, fed, replicate 8

source_name: Gonadal white adipose tissue, fed condition

value: Fed


title: Bulk_SERIES_1: MPP_BCG_1


title: Bulk_SERIES_1: MPP_CTL_4


title: 1104-3-03-A11_PAAD_3_Bcon

value: Bcon


title: Bulk_SERIES_1: MPP_BCG_2


title: EG_SERIES_3: PROG_BCG

data_processing:
Sample preprocessing was done using the count command of CellRanger.
We excluded cells that featured: (i) a high fraction of mitochondrial RNA reads (>5%), (ii) a low percentage of protein-coding genes (<95%) or (iii) a number of UMIs that was either too low (<5000) or too high (>40000)
we filtered out genes detected in less than five cells in all conditions
We used the function computeSumFactors, from the R package scran (Lun et al., 2016) to normalize the data
Genome_build: mm10 1.2.0
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: cKit+ Progenitors

extract_protocol:
Bone marrow cells were harvested from femurs, tibiae, humeri and ilia, and incubated with the described biotin-conjugated antibodies against lineage-committed cells. Subsequently, the cells were incubated with MACS streptavidin conjugated microbeads (Miltenyi) for 30 minutes at 4°C. A depletion of the lineage-committed cells was performed using AutoMACS (Miltenyi) to reduce the contaminating total cell number. The remaining cells were incubated with the corresponding antibodies for LKS+ and cKit+ progenitors
Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics).
Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (10x Genomics), according to the manufacturer’s instructions. Briefly, GEM-RT was performed in a thermal cycler: 53°C for 45 min, 85°C for 5 min. cDNA was cleaned up with DynaBeads MyOne Silane Beads (ThermoFisher Scientific) and amplified with a thermal cycler: 98°C for 3 min, cycled 12 x 98°C for 15 s, 67°C for 20s, 72°C for 1 min, and 72°C 1 min. After a cleanup with SPRIselect Reagent Kit, the libraries were constructed by performing the following steps: fragmentation, end-repair, A-tailing, SPRIselect cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR, and SPRIselect size selection. Libraries were sequenced on a NovaSeq S2 flowcell with 100 bp paired-end reads

treatment_protocol: mice were infected with approx.50-100 CFU of Mtb H37Rv in a nose-only aerosol exposure unit (Intox). 28 days after treatment, animals were sacrificed, and their BM extracted.

value: cKit+ Progenitors


title: Bulk_SERIES_1: MPP_CTL_2


title: Bulk_SERIES_1: MPP_CTL_3


title: EG_SERIES_3: PROG_PBS

value: PBS


title: EG_SERIES_3: PROG_MTB


title: Bulk_SERIES_1: MPP_CTL_1


title: EG_SERIES_3: LKS_MTB

source_name: LKS+ Hematopoietic stem cells

value: LKS+ Hematopoietic stem cells


title: Bulk_SERIES_1: HSC_BCG_1


title: EG_SERIES_3: LKS_BCG


title: Bulk_SERIES_1: MPP_MTB_3


title: EG_SERIES_3: LKS_PBS


title: P21_3 skin sample (wounded)

status: Public on Jul 01 2020

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

description: 10X Genomics scRNA-Seq v2

data_processing:
Cellranger version 3.0.2 pipeline to generate output folders
Velocyto 0.17.5 run10x function was used to make loom files
Genome_build: mm10
Supplementary_files_format_and_content: loom files

source_name: wounded skin

extract_protocol:
Cells were collected from dorsal skin (wounded or unwounded), single cells suspension according to protocol Jensen and Driskell 2010
scRNA libraries were constructed following 10X Genomics Protocol

treatment_protocol: 2mm circular full-thickness wound, collected 7dpw

value: dorsal skin

value: WT

tag: condition

value: 7 days post wounded 2mm


title: P2_1 skin sample (wounded)

description: 10X Genomics scRNA-Seq v2


title: AERO_SERIES_2: LKS_PBS

value: PBS aerosol


title: P21_1 skin sample (wounded)

description: 10X Genomics scRNA-Seq v2


title: AERO_SERIES_2: PROG_PBS


title: P2_3 skin sample (unwounded)

description: 10X Genomics scRNA-Seq v2

source_name: skin

value: unwounded


title: Aortic cells, 1_1

status: Public on Aug 04 2020

city: New York

first: Michele

last: Silvestro

state: NY

address: 550 1st Avenue

department: Surgery

institute: New York University Langone Medical Center

description: Single cell

data_processing:
Fastq files with I1 contains the sample index (8mer), the R1 files are the technical (contain the cell barcodes and UMI), the R2 files are biological
The Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at:  https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cloupe file was generated using the Cell Ranger 1.3 version. A description of the pipeline and instructions can be found at:  https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
Cell types were identified by their expression levels of gene provided that at least two copies of the transcript were found in the cell (cutoff: log2 fold-increased copies = 1 vs 1 copy only per cell). Loupe Cell Browser version 1.0.1 was then used to compare the transcriptome of each identified cluster corrected for False Discovery Rates, as applied in RNA sequencing. Excel files were exported from Loupe Cell Browser 1.0.1 analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file content K-mean clustering and t-SNE representation of 990 cells with 329,187 mean reads per cell and a median 2,330 genes per cell

source_name: Aortic cells

extract_protocol:
Aorta was collected and digested for 1 hour at 37°C in an enzymatic mix (10 mg/ml Collagenase type II (C6885, Sigma Aldrich) and 1mg/ml Elastase (LS002292, Worthington Biochemistry). Digested aortas were mechanically disrupted and immediately processed for single-cell RNA-sequencing. The cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single cell gel beads in emulsion (GEMs)
Libraries were prepared using the following kits: Chromium Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262, 10x Genomics)
Sequencing was performed on an Illumina HiSeq 4000 as 2 x 150 paired-end reads, one full lane per sample, for approximately >90% sequencing saturation. For alignment, barcode assignment and unique molecular identifiers (UMI) counting, the Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting (https://support.10xgenomics.com/single-cell-gene)

tag: disease

value: Abdominal aortic aneurysm

value: Apolipoprotein E deficient (ApoE-/-)

value: Angiotensin II perfusion 28 days

value: Aortic cells


title: KO.LPA.rep4

status: Public on Jun 23 2020

description: BSSE_QGF_135016_HJL3WDRXX_1_5_7_KO_4_LPA_CGTTAGAA_TTCAGGTC_S23_L001

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) using the multi-map settings '-outFilterMultimapNmax 10 --outSAMmultNmax 1'.
Mapped reads were assigned to genes based on the UCSC refGene annotation (downloaded 2015-Dec-18).
Specifically, the qCount function of the R/Bioconductor package QuasR was used to count the number of fragments overlapping with the exons of each gene assuming an exon union model.
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv; tab-separated values text file with columns: 1. Gene symbol, 2. gene name, 3. gene length (exon-union model), 4. ENTREZ ID, 5.-28. read counts

molecule: polyA RNA

growth_protocol: Bone marrow cells were cultured in adherent conditions in the presence of M-CSF to obtain BMDMs. The cells were grown for 7 days with medium change every 2-3 days.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to manufacturer's instructions.
TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA) were used for library preparation
Libraries were sequenced Paired-End 51 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NovaSeq 6000 instrument (Illumina) and the SP Flow-Cell loaded at a final concentration in Flow-Lane of 2pM and including 1% PhiX.

treatment_protocol: On day 7 of culture, the cells were given 10 µM LPA, 10 ng/mL LPS or were left untreated for 4 hours. After, the cells were lysed and collected in TRI Reagent (Zymo Research, R2050).

tag: strain background

tag: Sex

value: male

value: KO

value: bone marrow-derived macrophages (BMDM)

tag: treatment

value: LPA


title: GPR35-positive rep4

status: Public on Jun 25 2020

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) using the multi-map settings '--outFilterMultimapNmax 10 --outSAMmultNmax 1'
Read and alignment quality was evaluated using the qQCReport function of the R/Bioconductor package QuasR (R version 3.4.2, Bioconductor version 3.6)
Assignment of reads to genes employed the UCSC refGene annotation (downloaded 2015-Dec-18)
QuasR function qCount was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv.gz; tab-separated values text file with columns: 1.Entrez gene ID, 1. gene symbol, 3. gene name, 4. length (exon-union model), 5.-12. read counts

source_name: Intestinal macrophages

extract_protocol:
Intestines were removed, opened longitudinally and washed with PBS. Epithelial cells were removed by incubating in 5 mM EDTA 3x10 min at 37 C. The tissues were digested in RPMI 1640  containing 0.5 mg/ml Collagenase type VIII and 10 U/mL DNase 3x10 min at 37 C to obtain single cell suspension of lamina propria cells. GPR35-positive and -negative MHCII+CD64+ macrophages were sorted by FACS and lysed with trizol. RNA were extracted using Thermo Fisher PureLink RNA micro kit.
RNA was reverse transcribed and cDNA amplified with SMART-Seq v4 (Takara) and libraries prepared with Nextera XT (Illumina) according to manufacturer's instructions.

value: Intestinal macrophages

tag: group


title: GPR35-negative rep2


title: GPR35-negative rep3


title: GPR35-positive rep1


title: GPR35-positive rep2


title: GPR35-negative rep4


title: GPR35-positive rep3


title: AERO_SERIES_2: PROG_MTB

tag: strain

tag: tissue

value: cKit+ Progenitors

value: MTB aerosol


title: KO.LPS.rep4

description: BSSE_QGF_135017_HJL3WDRXX_1_5_8_KO_4_LPS_TACCGAGG_CCTGAACT_S24_L001

tag: genotype

value: LPS

tag: replicate


title: KO.Cont.rep4

description: BSSE_QGF_135015_HJL3WDRXX_1_5_6_KO_4_Cont_AGCCTCAT_AGTAGAGA_S22_L001

tag: cell type

value: Cont


title: GPR35-negative rep1


title: KO.LPS.rep3

description: BSSE_QGF_135014_HJL3WDRXX_1_5_5_KO_3_LPS_GATTCTGC_GACGAGAG_S21_L001


title: P2_1 skin sample (unwounded)

description: 10X Genomics scRNA-Seq v2

value: dorsal skin

value: WT


title: KO.LPA.rep3

description: BSSE_QGF_135013_HJL3WDRXX_1_5_4_KO_3_LPA_TCGTAGTG_AGACTTGG_S20_L001


title: KO.Cont.rep3

description: BSSE_QGF_135012_HJL3WDRXX_1_5_3_KO_3_Cont_CTACGACA_GAGTCCAA_S19_L001


title: KO.LPS.rep2

description: BSSE_QGF_135011_HJL3WDRXX_1_5_2_KO_2_LPS_TAAGTGGT_CTTAAGCC_S18_L001


title: KO.LPA.rep2

description: BSSE_QGF_135010_HJL3WDRXX_1_5_1_KO_2_LPA_CGGACAAC_TCCGGATT_S17_L001


title: P2_3 skin sample (wounded)

description: 10X Genomics scRNA-Seq v2

value: 7 days post wounded 2mm


title: AERO_SERIES_2: LKS_MTB

value: LKS+ Hematopoietic stem cells


title: P2_2 skin sample (wounded)

description: 10X Genomics scRNA-Seq v2


title: P21_2 skin sample (wounded)

description: 10X Genomics scRNA-Seq v2


title: P2_2 skin sample (unwounded)

description: 10X Genomics scRNA-Seq v2

value: unwounded


title: KO.LPA.rep1

description: BSSE_QGF_135007_HJL3WDRXX_1_4_6_KO_1_LPA_CTTGGTAT_CCAAGTCC_S14_L001


title: WT.LPA.rep4

description:
BSSE_QGF_135004_HJL3WDRXX_2_4_3_WT_4_LPA_TTACAGGA_TGACAAGC_S11_L002
BSSE_QGF_135004_HJL3WDRXX_1_4_3_WT_4_LPA_TTACAGGA_TGACAAGC_S11_L001


title: KO.Cont.rep1

description: BSSE_QGF_135006_HJL3WDRXX_1_4_5_KO_1_Cont_TCCAACGC_TTGGACTT_S13_L001


title: WT.LPS.rep4

description:
BSSE_QGF_135005_HJL3WDRXX_2_4_4_WT_4_LPS_CCGTGAAG_CAGTGGAT_S12_L002
BSSE_QGF_135005_HJL3WDRXX_1_4_4_WT_4_LPS_CCGTGAAG_CAGTGGAT_S12_L001


title: KO.LPS.rep1

description: BSSE_QGF_135008_HJL3WDRXX_1_4_7_KO_1_LPS_GTCGGAGC_GGTTATAA_S15_L001


title: KO.Cont.rep2

description: BSSE_QGF_135009_HJL3WDRXX_1_4_8_KO_2_Cont_ACTAAGAT_AACCGCGG_S16_L001


title: WT.Cont.rep4

description:
BSSE_QGF_135003_HJL3WDRXX_2_4_2_WT_4_Cont_GGCATTCT_CTAGCTTG_S10_L002
BSSE_QGF_135003_HJL3WDRXX_1_4_2_WT_4_Cont_GGCATTCT_CTAGCTTG_S10_L001


title: WT.LPA.rep1

description:
BSSE_QGF_134995_HJL3WDRXX_1_3_2_WT_1_LPA_GCAGAATT_ACCGGCCA_S2_L001
BSSE_QGF_134995_HJL3WDRXX_2_3_2_WT_1_LPA_GCAGAATT_ACCGGCCA_S2_L002


title: WT.LPA.rep3

description:
BSSE_QGF_135001_HJL3WDRXX_1_3_8_WT_3_LPA_TAATACAG_ATATTCAC_S8_L001
BSSE_QGF_135001_HJL3WDRXX_2_3_8_WT_3_LPA_TAATACAG_ATATTCAC_S8_L002


title: WT.LPS.rep1

description:
BSSE_QGF_134996_HJL3WDRXX_2_3_3_WT_1_LPS_AACGTTCC_GGAGTACT_S3_L002
BSSE_QGF_134996_HJL3WDRXX_1_3_3_WT_1_LPS_AACGTTCC_GGAGTACT_S3_L001


title: WT.Cont.rep2

description:
BSSE_QGF_134997_HJL3WDRXX_2_3_4_WT_2_Cont_GGTACCTT_AAGACGTC_S4_L002
BSSE_QGF_134997_HJL3WDRXX_1_3_4_WT_2_Cont_GGTACCTT_AAGACGTC_S4_L001


title: 120hpf_sibling control_1

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

description: ABNYU

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5, then quality trimmed using Trimmomatic. were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
Reads that passed quality control were mapped to Ref. geome GRCz10 by using bwa-mem
The resulting alignment files were then processed through PICARD tools to clean, sort and deduplicate (PCR and Optical duplicates)
Peaks calling was generated by MAC2 with BAMPE format, qvalue was set as 0.05.
Genome_build: mm10/GRCm38.p4
Supplementary_files_format_and_content: .bed called peaks

molecule: genomic DNA

source_name: embryo

extract_protocol:
10 sibling control or uhrf1 hi272 whole embryos at 5 dpf (120 hpf) zebrafish embryos were dissociated and from each embryo, 50,000 live cells were used per library preparation. ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the excpetion of dissociating the livers to get cell suspension was obtained using trypsin at 37 degree for 30 minutes. Strain ued: ABNYU
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.
Illumina NextSeq platform, 300 cycle, 2 X150 paired-end reads

value: sibling control larvae of uhrf1-hi272 mutants


title: WT.LPA.rep2

description:
BSSE_QGF_134998_HJL3WDRXX_1_3_5_WT_2_LPA_GCACGGAC_GTCTCGCA_S5_L001
BSSE_QGF_134998_HJL3WDRXX_2_3_5_WT_2_LPA_GCACGGAC_GTCTCGCA_S5_L002


title: WT.Cont.rep1

description:
BSSE_QGF_134994_HJL3WDRXX_2_3_1_WT_1_Cont_ATGAGGCC_GTTAATTG_S1_L002
BSSE_QGF_134994_HJL3WDRXX_1_3_1_WT_1_Cont_ATGAGGCC_GTTAATTG_S1_L001


title: WT.Cont.rep3

description:
BSSE_QGF_135000_HJL3WDRXX_1_3_7_WT_3_Cont_CGGCGTGA_GCGCCTGT_S7_L001
BSSE_QGF_135000_HJL3WDRXX_2_3_7_WT_3_Cont_CGGCGTGA_GCGCCTGT_S7_L002


title: WT.LPS.rep3

description:
BSSE_QGF_135002_HJL3WDRXX_2_4_1_WT_3_LPS_AATGCCTC_TCGATCCA_S9_L002
BSSE_QGF_135002_HJL3WDRXX_1_4_1_WT_3_LPS_AATGCCTC_TCGATCCA_S9_L001


title: 5 dpf liver exposed to 350 mM Ethanol - clutch 7

description: For library preparation, high quality of total RNA was QCed using a bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). Further, mRNA library was prepared using Illumina TruSeq V2 RNA sample Prep Kit (San Diego, CA) according to the manufacturer’s protocol. Briefly, 100 ng of total mRNA was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, end repair, addition of a single A base, TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 (Agilent Technologies). The quantities of the libraries required for RNA-seq were determined by real-time qPCR using a KAPA library quantification kit for the Illumina platform (Kapa Bio systems).

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignments of trimmed reads were performed using tophat2  v2.1.0, with the parameters “–no-novel-junctions” and “–G”
Accepted bam files were used for counting gene read numbers with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes

source_name: Liver

growth_protocol: Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection, embryos were divided into 30 mL plates, 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.

extract_protocol: Larvae were anesthetized with tricane and 20-35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026).RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc). RNA was quantified by Qubit flurometer.

treatment_protocol: At  96 hpf, 4 days after the embryos were collected, plates were treated with 1% and 2% Ethanol ( Sigma-Aldrich) for 24 hour exposure with untreated as control. At 5 dpf, 9 am the ethanol was washed out 3X  and treated with 500 uM tricaine (Ethyl 3- aminobenzoate methanesulfonate, Sigma-Aldrich, USA). Larvae were sorted for red liver positive and these fish were dissected in 3% methyl-cellulose.

tag: pool

tag: rna qbit concentration(ng/ul)


title: 5 dpf liver exposed to 175mM  Ethanol - clutch 7


title: 5 dpf liver exposed to 175mM  Ethanol - clutch 5


title: 5 dpf liver exposed to 350 mM Ethanol - clutch 5


title: 5 dpf liver exposed to 350 mM Ethanol - clutch 4


title: 5 dpf liver exposed to 350 mM Ethanol - clutch 1


title: 5 dpf Untreated liver - clutch 2

description: Larvae were anesthetized with tricane and 20-35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026).RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc). RNA was quantified by Qubit flurometer.

growth_protocol: At  96 hpf, 4 days after the embryos were collected, plates were treated with 1% and 2% Ethanol ( Sigma-Aldrich) for 24 hour exposure with untreated as control. At 5 dpf, 9 am the ethanol was washed out 3X  and treated with 500 uM tricaine (Ethyl 3- aminobenzoate methanesulfonate, Sigma-Aldrich, USA). Larvae were sorted for red liver positive and these fish were dissected in 3% methyl-cellulose.


title: 5 dpf Untreated liver - clutch 4


title: 5 dpf liver exposed to 175mM  Ethanol - clutch 2


title: 5 dpf liver exposed to 175mM  Ethanol - clutch 4

extract_protocol: At  96 hpf, 4 days after the embryos were collected, plates were treated with 1% and 2% Ethanol ( Sigma-Aldrich) for 24 hour exposure with untreated as control. At 5 dpf, 9 am the ethanol was washed out 3X  and treated with 500 uM tricaine (Ethyl 3- aminobenzoate methanesulfonate, Sigma-Aldrich, USA). Larvae were sorted for red liver positive and these fish were dissected in 3% methyl-cellulose.


title: 5 dpf liver exposed to 175 mM  Ethanol - clutch 1


title: 5 dpf Untreated liver - clutch 1

extract_protocol: 20-35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026).RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc). RNA was quantified by Qubit flurometer.


title: 5 dpf Untreated liver - clutch 7


title: AML11 high

status: Public on May 24 2020

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

data_processing:
RNA-seq reads were uniquely mapped to the hg19 reference genome using STAR, and subsequently normalized to RPKM values for all RefSeq genes using tag counting scripts. Visualization tracks were made using BamCoverage.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Primary Acute Myeloid Leukemia

extract_protocol:
The mononuclear cell (MNC) fraction from BM and/or PB was obtained by density gradient centrifugation using lymphoprep (PAA, Cölbe, Germany) according to standard procedures. For separation of ROSlow and ROShigh fractions following thawing of viably frozen MNCs, cells were washed and after overnight recovery on MS5 cells were stained for CD34+ and CellROX. Subsequently cells were sorted for CD34+, 15% low and 15% high ROS fraction. After sorting cells were lysed in TriZol for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell marker

value: Primary Acute Myeloid Leukemia

tag: ros phenotype

value: high

tag: patient id


title: AML6 low

value: low


title: 5 dpf Untreated liver - clutch 5


title: Nsd1KO3_Nsd1-N1918Q_Maintenance

status: Public on Apr 07 2020

description: Sample 11

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version STAR/2.5.2a-goolf-1.7.20) using the multi-map settings '--outFilterMultimapNmax 10 --outSAMmultNmax 1'.
The output was sorted and indexed with samtools (version SAMtools/1.7-goolf-1.7.20) and picard markDuplicates (version picard/2.9.2) was used to collapse samples run on different sequencing lanes.
The rsubread::featureCounts function was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: RefSeq genes downloaded from UCSC 2015, December 18).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file, first column contains EntrezGeneId, second column contains total number of base-pairs per gene (gene length) and remaining columns contain raw read counts.

source_name: Cultured erythroblast from bone marrow

growth_protocol: Either maintainance or differentiation medium, as indicated. Maintenance medium: StemSpan SFEM (StemCell Technologies, Vancouver, Canada), supplemented with 1%Pen/Strep, 0.4%cholesterol (Gibco, Thermo Fisher Scientific, Reinach, Switzerland), 2U/ml hEpo (Eprex 4000, 9096976, Pharmacy of University Hospital Basel), 100ng/ml mScf(Peprotech, London, UK), 10-6M dexamethasone (Calbiochem, Sigma Aldrich, Buchs, Switzerland) and 40ng/ml hIGF-1 (Peprotech, London, UK). Differentiation medium composed of IMDM (Gibco, Thermo Fisher Scientific, Reinach, Switzerland), 1%P/S, 10%FCS, 10%PFHMII (Gibco, Thermo Fisher Scientific, Reinach, Switzerland), 5%hPDS (0.45µM filtered, Blood donation service, University Hospital Basel), monothioglycerol (Sigma Aldrich, Buchs, Switzerland), 100ng/ml mSCF and 2U/ml hEpo

extract_protocol:
MACHEREY-NAGEL Nucleospin RNA Plus kit (Ref 740984.250)
TruSeq Stranded mRNA Library Prep Kit High Throughput (Cat # RS-122-2103, Illumine, San Diego, CA, USA)

treatment_protocol: Cell are NSD1 KO transduced with either wildtype Nsd1 or Nsd1N198Q with disrupted SET-domain

value: Cultured erythroblast from bone marrow

tag: add-back of nsd1

value: Maintenance

tag: time


title: AML1 high


title: Nsd1KO3_Nsd1-N1918Q_Differentiation

description: Sample 12

value: Differentiation


title: Nsd1KO4_Nsd1-N1918Q_Maintenance

description: Sample 14


title: WT.LPS.rep2

description:
BSSE_QGF_134999_HJL3WDRXX_2_3_6_WT_2_LPS_ATGTAAGT_ACTCTATG_S6_L002
BSSE_QGF_134999_HJL3WDRXX_1_3_6_WT_2_LPS_ATGTAAGT_ACTCTATG_S6_L001

value: male

value: bone marrow-derived macrophages (BMDM)


title: Nsd1KO4_Nsd1-wt_Maintenance

description: Sample 13


title: AML1 low


title: Nsd1KO2_Nsd1-N1918Q_Maintenance

description: Sample 7


title: Nsd1KO3_Nsd1-wt_Maintenance

description: Sample 9


title: Nsd1KO2_Nsd1-N1918Q_Differentiation

description: Sample 8


title: Nsd1KO2_Nsd1-wt_Differentiation

description: Sample 6


title: Nsd1KO2_Nsd1-wt_Maintenance

description: Sample 5


title: Nsd1KO1_Nsd1-N1918Q_Maintenance

description: Sample 3


title: Nsd1KO1_Nsd1-N1918Q_Differentiation

description: Sample 4


title: Nsd1KO1_Nsd1-wt_Differentiation

description: Sample 2


title: AML7 low


title: 16_MYB_Control

status: Public on Apr 14 2020

data_processing:
Reads were mapped to the hg19 reference genome using BWA14 and further processed using MACS for peak calling and bam2bw for visualization.
Genome_build: NCBI build37
Supplementary_files_format_and_content: bigwig

source_name: THP1_shSCR control

growth_protocol: Human THP1 cells were purchased from the ATCC and authenticated by short tandem repeat profiling using the PowerPlex 16 system (Promega, Southampton, UK) and mycoplasma negative status confirmed using the MycoAlert Mycoplasma Detection Kit (Lonza, Verviers, Belgium) and cultured in RPMI supplemented with 10% FCS, L-glutamine and penicillin/streptomycin.

extract_protocol:
25x106 shSCR or shRUVBL2 transduced THP1 cells were cross-linked with 2 mM DSG for 30 minutes at room temperature. After washing the samples 3 times with PBS, cells were fixed with 1% formaldehyde for 15 minutes at room temperature and the reaction quenched by adding glycine to final concentration 0.25 M for 5 minutes at room temperature. Fixed cells were washed twice with cold PBS, and then sequentially in lysis buffer A (0.25% TritonX100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6]) and lysis buffer B (150 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6] ), incubating for 10 minutes on ice each time. Cells were finally resuspended in incubation buffer (0.15% SDS, 1% TritonX100, 150 nM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6] ) plus protease inhibitors (Sigma Aldrich) and incubated for 30 minutes on ice. Lysates were then sonicated for 6 cycles (30 sec on / 30 sec off) in the Bioruptor® Pico water bath sonicator (Diagenode, Liege, BE). Cleared supernatant was stored at -80°C. 500 μl of sonicated chromatin were diluted 10 times in ChIP Dilution Buffer (0.01% SDS, 1% Triton X-100, 1.2 mM EDTA [pH 8], 16.7 mM Tris-HCl pH 8 and 167 mM NaCl) and were incubated rotating at 4°C overnight, with protein A/G magnetic beads (Merck Millipore) and 2-10 μg of anti-MYB (1-1, Merck Millipore; and D-7, Santa Cruz Biotechnology) or anti-H3K27Ac (ab4729, Abcam) antibodies. Beads were washed for 10 minutes once in low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl), in high salt buffer (0.1% SDS, 1% TritonX100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl), LiCl Buffer (0.25 M LiCl, 1% NP-40, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and in TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). DNA was eluted from the ChIP samples by two 1 hour incubations at 55°C with elution buffer (1% SDS, 100 mM NaHCO3). Chromatin was reverse-crosslinked and subjected to RNase and proteinase K digestion, and extracted by using the MinElute PCR purification kit (Qiagen). Libraries were prepped from 1ng of ChIP DNA using the NEBNext DNA Ultra II assay (New England Biolabs, Hitchin, UK) with bead based size selection for 200 bp fragments and 12 cycles of amplification. Samples were then sequenced on an Illumina NextSeq 500, using a 43bp, paired end configuration.
Libraries were prepped from 1ng of ChIP DNA using the NEBNext DNA Ultra II assay (New England Biolabs, Hitchin, UK) with bead based size selection for 200 bp fragments and 12 cycles of amplification. Samples were then sequenced on an Illumina NextSeq 500, using a 43bp, paired end configuration.

treatment_protocol: For constitutive shRNA expression used in ChIP-seq analysis, the MISSION® pLKO.1 shRNA constructs containing non-silencing control shSCR (SHC002) or shRUVBL2 (Clone ID:NM_006666.1-1102s1c1) shRNA were purchased from Sigma Aldrich.

tag: cell line

value: acute myeloid leukemia (AML) cell line

tag: genotype/variation

value: shSCR transduced

tag: chip antibody

value: MYB (1-1, Merck Millipore and D-7, Santa Cruz Biotechnology)


title: 6_H3K27ac_shRVBL2

value: shRVBL2 transduced

value: H3K27ac (ab4729, Abcam)


title: 17_MYB_shRVBL2


title: Nsd1KO1_Nsd1-wt_Maintenance

description: Sample 1


title: AML6 high


title: AML7 high


title: AML11 low


title: Nsd1KO_Nsd1-N1918Q_Maintainance_H3K36me3_rep2

description: matching input sample: Nsd1KO_Nsd1-N1918Q_Maintainance_Input_rep2

data_processing:
Reads were aligned with bowtie2 to the mouse genome (UCSC version mm10). The output was sorted and indexed with samtools.
Duplicated reads were marked with picard. Coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the bioconductor package bamsignals.
These window counts were exported in bigWig format using the bioconductor package rtracklayer.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file with FPKM counts per bin

extract_protocol:
Pull-down beads were Protein G sepharose (Sigma-Aldrich, P3296). Washes were done with the low salt, high salt, li-Cl wash buffers according to EZ-Magna CHIP A/G kit protocol from Millipore. DNA elution was done with the IPURE Kit V2 (Diagenode, Cat.No. C03010012). Antibodies: GATA1 ab11862 10 ug per ChIP Abcam; H3K36me3: ab9050-11 10 ug per ChIP Abcam; H3K27ac: ab4729 10 ug per ChIP Abcam
ChIP protocol was adapted from the EZ-Magna ChIPTM A/G kit protocol (Millipore, Merck KGaA, Darmstadt, Germany). Cells (Nsd1 WT and Nsd1 Set in maintenance as well as 24h differentiation) were fixed with 1% formaldehyde, lysed with Cell Lysis and then Nuclear Lysis buffers to a concentration of 20^106 cells per mL, and finally sonicated (20-min cycle on Covaris apparatus; KBioscience). Sheared chromatin was immunoprecipitated overnight using the following antibodies: anti-GATA1 (Abcam, ab11852), anti-H3K36me3 (Abcam, ab9050-100), anti-H3K27ac (Abcam, ab4729). 1/10 of the sheared chromatin was used as a reference (Input). Immune complex collection was performed using Protein G Sepharose (Sigma-Aldrich, P3296) for 1h30 at 4°C. Rinses were done according to Magna ChIPTM kit protocol with Low salt, High salt and LiCL immune complex wash buffers. Finally, elution was performed according the IPure Kit protocol (Diagenode, Cat.No. C03010012) following manufacturer’s instructions. Two independent ChIP-seq experiments were conducted for Gata1, H3K27ac and H3K36me3.

value: Maintainance

tag: antibody


title: Nsd1KO_Nsd1-N1918Q_Differentiation_H3K36me3_rep2

description: matching input sample: Nsd1KO_Nsd1-N1918Q_Differentiation_Input_rep2


title: 5_H3K27ac_Control


title: Nsd1KO_Nsd1-N1918Q_Differentiation_H3K36me3_rep1

description: matching input sample: Nsd1KO_Nsd1-N1918Q_Differentiation_Input_rep1


title: Nsd1KO_Nsd1-wt_Maintainance_H3K36me3_rep2

description: matching input sample: Nsd1KO_Nsd1-wt_Maintainance_Input_rep2


title: Nsd1KO_Nsd1-wt_Differentiation_H3K36me3_rep2

description: matching input sample: Nsd1KO_Nsd1-wt_Differentiation_Input_rep2


title: Nsd1KO3_Nsd1-wt_Differentiation

description: Sample 10


title: Nsd1KO_none_Maintainance_H3K36me3_rep2

description: matching input sample: Nsd1KO_none_Maintainance_Input_rep2


title: Nsd1KO_Nsd1-wt_Maintainance_H3K36me3_rep1

description: matching input sample: Nsd1KO_Nsd1-wt_Maintainance_Input_rep1


title: Nsd1KO_none_Maintainance_H3K36me3_rep1

description: matching input sample: Nsd1KO_none_Maintainance_Input_rep1


title: Nsd1KO_Nsd1-N1918Q_Maintainance_H3K36me3_rep1

description: matching input sample: Nsd1KO_Nsd1-N1918Q_Maintainance_Input_rep1


title: Nsd1KO_Nsd1-N1918Q_Maintainance_H3K27ac_rep2

value: H3K27ac (Abcam ab4729)


title: Nsd1KO_Nsd1-wt_Differentiation_H3K36me3_rep1

description: matching input sample: Nsd1KO_Nsd1-wt_Differentiation_Input_rep1


title: Nsd1KO_Nsd1-N1918Q_Maintainance_Gata1_rep2

value: Gata1 (Abcam ab11862)


title: Nsd1KO_Nsd1-wt_Maintainance_Input_rep2

value: Input


title: Nsd1KO_Nsd1-wt_Maintainance_H3K27ac_rep2


title: Nsd1KO_Nsd1-N1918Q_Maintainance_Input_rep2


title: Nsd1KO_Nsd1-N1918Q_Differentiation_Gata1_rep2


title: Nsd1KO_Nsd1-wt_Maintainance_Gata1_rep2


title: Nsd1KO_Nsd1-wt_Differentiation_Gata1_rep1


title: Nsd1KO_Nsd1-N1918Q_Differentiation_H3K27ac_rep1


title: Nsd1KO_Nsd1-wt_Differentiation_H3K27ac_rep2


title: Nsd1KO_Nsd1-N1918Q_Differentiation_Gata1_rep1


title: Nsd1KO_Nsd1-wt_Differentiation_H3K27ac_rep1


title: Nsd1KO_Nsd1-wt_Differentiation_Input_rep1


title: Nsd1KO_Nsd1-N1918Q_Differentiation_Input_rep1


title: Nsd1KO_Nsd1-wt_Differentiation_Input_rep2


title: Nsd1KO_Nsd1-N1918Q_Differentiation_Input_rep2


title: Nsd1KO_Nsd1-wt_Differentiation_Gata1_rep2


title: Nsd1KO_Nsd1-N1918Q_Maintainance_H3K27ac_rep1


title: Nsd1KO_Nsd1-N1918Q_Maintainance_Input_rep1


title: Nsd1KO_Nsd1-wt_Maintainance_Input_rep1


title: Nsd1KO_Nsd1-N1918Q_Maintainance_Gata1_rep1


title: Nsd1KO_Nsd1-wt_Maintainance_H3K27ac_rep1


title: Nsd1KO_Nsd1-wt_Maintainance_Gata1_rep1


title: Nsd1KO_none_Maintainance_Input_rep2


title: Nsd1KO_none_Maintainance_H3K27ac_rep2


title: Nsd1KO_none_Maintainance_Gata1_rep2


title: Nsd1KO_Nsd1-N1918Q_Differentiation_H3K27ac_rep2


title: Nsd1KO_none_Maintainance_Input_rep1


title: Nsd1_KO5

description: Sample 8

source_name: Bone marrow

extract_protocol:
Qiagen total RNAEasy extraction kit (Cat #. 74104)
mRNAseq - Dynal mRNA Direct kit Oligo-dT beads pulling polyA. GTAC Washington University

value: Bone marrow

tag: Sex

value: Female


title: Nsd1_KO4

description: Sample 7


title: Nsd1_KO3

description: Sample 6

value: Male


title: Nsd1_KO2

description: Sample 5


title: Nsd1KO_none_Maintainance_Gata1_rep1

value: Cultured erythroblast from bone marrow


title: Nsd1_KO1

description: Sample 4


title: CONTROL3

description: Sample 3


title: CONTROL2

description: Sample 2


title: CONTROL1

description: Sample 1


title: ATAC_FL_D24_rep1

status: Public on Mar 31 2020

data_processing:
Reads were aligned with bowtie2 to the pig genome (UCSC version susScr11).
Coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the R/Bioconductor package bamsignals.
Windows falling in ENCODE blacklist regions as well as chrM were excluded.
These window counts were transformed to RPKM values (i.e. divided by library size and window size, multiplied by 1e9) and exported in bigWig format using the R/Bioconductor package rtracklayer.
Genome_build: susScr11
Supplementary_files_format_and_content: bigWig tracks generated with export function of R/Biocondictor rtracklayer package; scores represent RPKM values

organism: Sus scrofa

source_name: forelimb buds

growth_protocol: Domestic pig (Sus scrofa domesticus) embryos of day 21 (D21) and day 24 (D24) of development were produced by hormonal synchronization of recipient sows followed by artificial insemination. Date of insemination was considered gestational day zero (D0) and pregnancy was assessed via ultrasound scans.

extract_protocol:
Per biological replicate, dissected left and right forelimb buds from the same embryo were pooled and dissociated in PBS (Gibco 14040-117) at 4ºC using a 2ml glass tissue grinder (Sigma-Aldrich D8938; 20 strokes with pestle A followed by 20 strokes with pestle B).
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi:10.1002/0471142727.mb2129s109. ATAC-seq libraries corresponding to the two biological replicates per developmental stage were sequenced (PE41) using one lane of a NextSeq500 system (Illumina).

tag: developmental stage


title: ATAC_FL_D21_rep1


title: ATAC_FL_D24_rep2


title: ATAC_FL_D21_rep2


title: ATAC_FL_E11.5_rep2

data_processing:
Reads were aligned with bowtie2 to the mouse genome (UCSC version mm10).
Coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the R/Bioconductor package bamsignals.
Windows falling in ENCODE blacklist regions as well as chrM were excluded.
These window counts were transformed to RPKM values (i.e. divided by library size and window size, multiplied by 1e9) and exported in bigWig format using the R/Bioconductor package rtracklayer.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks generated with export function of R/Biocondictor rtracklayer package; scores represent RPKM values

growth_protocol: Wild-type NMRI mice were maintained in the animal facility under normal conditions. Date of vaginal plug was scored as embryonic day (E) 0.5 and pregnancy was confirmed by palpation.

tag: strain

value: NMRI


title: ATAC_FL_E11.5_rep1


title: ATAC_FL_E10.5_rep1


title: RS019

status: Public on Mar 17 2020

data_processing:
For expression analyses, the hg19 reference genome index was first generated using STAR aligner with UCSC gene annotation. Paired-end reads were mapped to the indexed genome in two-pass mode with default parameters, to increase alignment accuracy and sensitivity. Stranded gene-level read counts were enumerated at the same time. Expression quantification for each RefSeq gene was performed by Cuffnorm function in Cufflinks, to estimate Fragments Per Kilobase per Million aligned reads value (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level read counts were enumerated by STAR tool. bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage

extract_protocol:
The mononuclear cell (MNC) fraction from BM and/or PB was obtained by density gradient centrifugation using lymphoprep (PAA, Cölbe, Germany) according to standard procedures. For separation of different cell fractions, following thawing of viably frozen MNCs, cells were washed and stained with a panel of antibodies and sorted for purification of different cell fractions. Blast fraction was defined as CD34 positive. Sorting purity was defined as ≥95% and confirmed by reanalysis.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RS020


title: RS011


title: RS008


title: RS006


title: RS005


title: RS001


title: Nsd1KO_none_Maintainance_H3K27ac_rep1

tag: genotype


title: S09_SI_CU_C

status: Public on Mar 16 2020

description: Sample 8

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm9, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in July 2013) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm9
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: Cultured ILC3

growth_protocol: Intestinal ILC3s were cultured in 24-well plates (0.5-1 x 10^6 cells/well) in IMDM medium (IMDM powder, Sigma Aldrich), containing 3.02 g/L NaHCO3 (Sigma Aldrich), 1 % Penicillin Streptomycin (Thermo Fisher Scientific), 1 % Ciproxine Perfusion 0.2g (Bayer), 0.1 % Kanamycin (Sigma Aldrich), 1 % Insulin Transferrin Selenium (Thermo Fisher Scientific), 0.3 % Primatone (Sigma Aldrich), 1 % MEM-NEAA (Thermo Fisher Scientific), 0.1 % 2-mercaptoethanol (Thermo Fisher Scientific), 5 % FBS, 5 % IL-2 cell culture supernatant, IL-7 (30 ng/mL, Preprotech) and SCF (20 ng/mL, Preprotech) for 7 days at 37 °C, 10% CO2.

extract_protocol:
RNA was isolated with the PicoPure RNA isolation kit (Thermo Fisher Scientific-Cat#KIT0204) and whole transcriptome RNA was amplified with the Ovation® RNA-Seq System V2 kit (NuGen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell suspensions of spleen (SP) and small intestine (SI) were prepared as previously described (von Burg et al., Proc Natl Acad Sci USA 2014). In brief the SI was opened longitudinal, incubated with 30 mM EDTA in 1 x PBS and washed several times with 1 x PBS to remove feces and mucus. Tissue pieces were digested in DMEM (Thermo Fisher Scientific) containing 0.025 mg/mL DNase I (Roche) and 1mg/mL collagenase D (Roche) for 15 min at 37°C. Supernatant was collected after washing with DMEM. Digestion steps were repeated 3 times with remaining tissue. After digestion SI cells were purified by Percoll density gradient (40/80%) centrifugation. The SP was cut into pieces and digested as the SI with DMEM containing DNase I and Collagenase D in 4 steps, each 15 min at 37°C. Afterwards erythrolysis was performed. Splenocytes were depleted of B and T cells according to standard protocols with MACS technology (Miltenyi Biotec).  ILC3  (CD117+, Thy1.2+, KLRG1-, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1)) were sort purified from cell suspensions.

tag: tissue

value: Small Intestine

tag: age

value: 8-12 weeks


title: S07_SI_CU_A

description: Sample 7


title: S06_SI_C

description: Sample 6

source_name: Freshly isolated ILC3


title: S05_SI_B

description: Sample 5


title: S03_SP_C

description: Sample 3

value: Spleen


title: S02_SP_B

description: Sample 2


title: S04_SI_A

description: Sample 4


title: SI_B

description: Sample 5

source_name: NCR- ILC3

extract_protocol:
RNA was isolated with the PicoPure RNA isolation kit (Thermo Fisher Scientific) and whole transcriptome RNA was amplified with the Ovation® RNA-Seq System V2 kit (NuGen)
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell suspensions of spleen (SP) and small intestine (SI) were prepared as previously described (von Burg et al., Proc Natl Acad Sci USA 2014). In brief the SI was opened longitudinal, incubated with 30 mM EDTA in 1 x PBS and washed several times with 1 x PBS to remove feces and mucus. Tissue pieces were digested in DMEM (Thermo Fisher Scientific) containing 0.025 mg/mL DNase I (Roche) and 1mg/mL collagenase D (Roche) for 15 min at 37°C. Supernatant was collected after washing with DMEM. Digestion steps were repeated 3 times with remaining tissue. After digestion SI cells were purified by Percoll density gradient (40/80%) centrifugation. The SP was cut into pieces and digested as the SI with DMEM containing DNase I and Collagenase D in 4 steps, each 15 min at 37°C. Afterwards erythrolysis was performed. Splenocytes were depleted of B and T cells according to standard protocols with MACS technology (Miltenyi Biotec). NCR- ILC3  (CD117+, Thy1.2+, eYFP+, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1, NKp46)) were sort purified from cell suspensions.

value: Small intestine

value: C57BL/6 - RORc(gamma_t)-Cretg Rosa26ReYFP/+


title: Sp_C

description: Sample 4


title: S01_SP_A

description: Sample 1


title: SI_C

description: Sample 6


title: SI_A

description: Sample 3


title: Sp_B

description: Sample 2


title: ATAC_FL_E10.5_rep2


title: SU86_2

status: Public on Mar 01 2020

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequence files were merged across lanes according to sample and subjected to a first round of quality control using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina universal adapters were trimmed from all samples using Trim Galore ([www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and samples were then subjected to a second round of quality control
Reads were mapped to the human Hg38 reference genome using Bowtie2
The edgeR package with Limma/Voom was used for linear modeling, empirical Bayes smoothing, TMM normalization, generation of Log2(CPM), and statistical analysis
Genome_build: Hg38
Supplementary_files_format_and_content: Log2(Normalized Counts per Million + 1)

source_name: pancreatic cancer cell line

growth_protocol: All cells were maintained according to respective ATCC recommended culture conditions

extract_protocol:
Total RNA was extracted from each cell line using the Maxwell 16 LEV automation system and simplyRNA purification kit (Promega, Cat. No. 1280) according to the manufacturer’s protocol. The extracted RNA was quantified by spectrophotometry using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) to ensure a reading of OD260/OD280 between 1.8 and 2.0.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: Cells were not drug treated

tag: disease state

value: cancer

value: Pancreas


title: PANC2_2


title: PANC1_3


title: SU86_1


title: Sp_A

description: Sample 1


title: PANC2_1


title: PANC1_2


title: PANC2_3


title: PANC1_1


title: MIAPACA_1

value: MIA PaCa-2


title: MIAPACA_3


title: SU86_3


title: MIAPACA_2


title: HPNE_1

source_name: non-cancerous pancreatic cell line

value: normal

value: hTERT-HPNE


title: HPNE_2


title: HPNE_3


title: HPAF_3


title: HPAF_2


title: HPAF_1


title: CFPAC1_3


title: CAPAN2_3


title: CAPAN2_2


title: CFPAC1_2


title: ASPC1_1


title: CAPAN2_1


title: CFPAC1_1


title: ASPC1_2


title: HIF2_GFP_8509

status: Public on Feb 04 2020

data_processing:
Sequencing reads were aligned to the human genome hg19 using bwa and bam2bw was used for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files

growth_protocol: The (human) erythromyeloblastoid leukemia cell line K562 was cultured in RPMI 1640 (containing L-glutamine) supplemented with 10% FCS and 1% penicillin/streptomycin (PAA Laboratories).

extract_protocol:
K562 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature at a concentration of 15x106 cells/ml. The fixed cells were sonicated for 4 minutes (30 sec on; 30 sec off) using the Diagnode Bioruptor and centrifuged at maximum speed for 10 minutes. Chromatin of about 5x105 cells was incubated overnight in dilution buffer (167mM NaCl, 16,7 mM Tris (pH 8), 1,2mM EDTA, 1% Triton X-100) with 1 µg antibody at 4C. ProtA/G beads were blocked and incubated with the chromatin-Ab for one hour at 4C. Beads were washed with three different wash buffers and chromatin was eluted from the beads. DNA-proteins were de-crosslinked (200mM NaCl and 4 µl proteinase K (10mg/ml)), by incubation for four hours at 65C and samples were purified using the Qiaquick MinElute PCR purification kit according manufacturer’s protocol.
Sequencing samples were prepared according to the manufacturer's protocol (Illumina). End repair was performed using the precipitated DNA using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ~300 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR and used for cluster generation on the NextSeq500 genome analyzer. The 50 bp tags were mapped to the human genome HG19 using BWA (Li and Durbin, 2009). For processing and manipulation of SAM/BAM files SAMtools was used (Li et al., 2009). For each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window and visualized in the UCSC genome browser (Kent et al., 2002).

treatment_protocol: K562 cells were transduced with the lentiviral GFP-fusion vectors encoding HIF1α and HIF2α and EGFP positive cells were sorted

value: anti-GFP (ab290, Abcam)

tag: treatment

value: untreated

tag: sample collection (day)


title: HIF1_GFP_8510


title: ME_ChIP_RUNX1-KD

status: Public on Jan 22 2020

data_processing:
ChIP-seq: After reads mapping to the hg19 reference genome using BWA14, peak calling of CBFβ-MYH11 fusion, RUNX1, EZH2 and RING1B ChIP-seq was conducted using MACS1.3.3 at a p-value cutoff of 10-6. RNA-seq:  RNA-seq reads were uniquely mapped to the hg19 reference genome using STAR, and subsequently normalized to RPKM values for all RefSeq genes using tag counting scripts.
Genome_build: NCBI build37
Supplementary_files_format_and_content: bigwig

growth_protocol: ME-1 cells were routinely cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37℃. ME-1 shRNA stable cell lines were cultured in tet-free FBS, and shRNA expression was induced for 72 h for ChIP-seq and RNA-seq by adding 600 ng/ml doxycycline (Dox). Engrafted cells from inv(16) AMLs were isolated and directly used for ChIP-seq.

extract_protocol:
ChIP-seq: Purified cells were first cross-linked with 1% formaldehyde for 20 min at room temperature, quenched with 0.125 M glycine and washed with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6. Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6) and sonicated using a Diagenode Bioruptor sonicator for 20 min at high power (30 seconds ON and 30 seconds OFF cycle). Sheared chromatin was centrifuged at maximum speed for 10 min and then incubated overnight at 4℃ in incubation buffer supplemented with 0.1% BSA with protein A/G-Sepharose beads (Santa Cruz) and 1 µg of antibody. Beads were washed sequentially with four different wash buffers at 4℃: two times with a solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, TEE (10 mM Tris pH 8.0, 0.1 mM EDTA and 0.5 mM EGTA), one time with a similar buffer but now with 500 mM NaCl, one time with a solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, TEE and two times with TEE. Precipitated chromatin was eluted from the beads with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature for 20 minutes. Protein-DNA crosslinks were reversed at 65℃ for 4 hours in the presence of 200 mM NaCl, after which DNA was isolated by Qiagen column. RNA-seq: Total RNA was isolated with the RNeasy RNA extraction kit with on-column DNaseI treatment (Qiagen), and the concentration was measured with a Qubit fluorometer (Invitrogen). Ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit (Epicentre) according to manufacturer instructions.
ChIP-seq: ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the HiSeq 2000 or NextSeq (Illumina). RNA-seq: Total RNA was isolated with the RNeasy RNA extraction kit with on-column DNaseI treatment (Qiagen), and the concentration was measured with a Qubit fluorometer (Invitrogen). Ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit (Epicentre) according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5× fragmentation buffer (200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94℃ for exactly 90 s. After ethanol precipitation, fragmented RNA was mixed with 5 µg random hexamers, followed by incubation at 70℃ for 10 min and chilling on ice. We synthesized the first-strand cDNA with this RNA primer mix by adding 4 µl 5× first-strand buffer, 2 µl 100 mM DTT, 1 µl 10 mM dNTPs, 132 ng of actinomycin D, 200 U SuperScript III, followed by 2 h incubation at 48℃. First strand cDNA was purified by Qiagen mini elute column to remove dNTPs and eluted in 34 µl elution buffer. Second-strand cDNA was synthesized by adding 91.8 µl, 5 µg random hexamers, 4 µl of 5× first-strand buffer, 2 µl of 100 mM DTT, 4 µl of 10 mM dNTPs with dTTP replaced by dUTP, 30 µl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymer¬ase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubated at 16℃ for 2 h followed by incubation with 10 U T4 polymerase at 16℃ for 10 minutes. Double-stranded cDNA was purified by Qiagen mini elute column and used for library preparation as described in the KAPA HyperPrep protocol.

treatment_protocol: shRNA expression to knockdown CBFB-MYH11 was induced for 72 h for ChIP-seq and RNA-seq by adding 600 ng/ml doxycycline (Dox)

tag: cell type

value: acute myeloid leukemia (AML) cell line

value: harbouring a dox inducible CBFB-MYH11 knockdown construct

value: 600 ng/ml doxycycline

value: RUNX1 ab23980 (abcam)


title: ME_ChIP_RUNX1_Con

value: no dox


title: ME_ChIP_RING1B_KD

value: RING1B D139-3 MBL Life Science


title: ASPC1_3


title: ME_6_RNA_noind


title: ME_ChIP_RING1B_Con


title: PDX1-RING1B

source_name: patient

value: engrafted primary inv(16) AMLs

value: no


title: ME_ChIP_MYH11_KD

value: MYH11 ( Novus Biologicals)


title: ME_ChIP_MYH11_Con


title: PDX2-RING1B


title: ME_ChIP_EZH2-KD

value: EZH2 39901 Active Motif


title: PDX2-EZH2


title: ME_ChIP_EZH2-Con


title: ME_6_RNA_ind


title: ME_5_RNA_noind


title: PDX1-MYH11


title: ME_5_RNA_ind


title: PDX2-MYH11


title: control_colon3

status: Public on Jan 21 2020

description: UMIsMatrix.txt.gz

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). Because the mouse strain includes a fluorescent reporter gene, a generic EYFP sequence obtained from https://www.addgene.org/browse/sequence_vdb/6394/ was added to the reference transcriptome before mapping.
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R (v3.5.0). The UMI matrix was filtered to included only cells with a count of at least 100 genes detected, giving a total of 5,949 cells (16,889 genes), and is provided as file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (1.8.4) and scatter (1.8.4) Bioconductor packages, and following the simpleSingleCell  Bioconductor workflow (version 1.2.1). Expression values of 11,947 genes for 3,213 cells were obtained after quality filtering and normalization, and used for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-colon1")

source_name: colon monocytes and macrophages from corn oil CD98ΔCX3CR1 control mouse

growth_protocol: Mice were hold in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from suspensions of lamina propria of eight individual CD98ΔCX3CR1 female mice
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for Cd11b+ and Ccr2+/Cd64+ expression.
Around 3000 cells per sample were loaded into each well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: 100µl tamoxifen (20mg/ml) per mouse was i.p. injected daily over 5 consecutive days. Readout at day 7 (optimum of Cd98 silencing).

value: colon

value: monocytes and macrophages

value: control

value: female


title: control_colon1

description: UMIsMatrix.txt.gz


title: Cd98 KO_colon7

description: UMIsMatrix.txt.gz

source_name: colon monocytes and macrophages from tamoxifen induced Cd98 KO (CD98ΔCX3CR1) mouse

value: Cd98 KO


title: Cd98 KO_colon8

description: UMIsMatrix.txt.gz


title: Cd98 KO_colon6

description: UMIsMatrix.txt.gz


title: Day40_ind_H3K27ac

status: Public on Jan 14 2020

data_processing:
RNA-Seq:The sequencing reads were mapped to the human genome assembly hg19 using Tophat2 (bowtie) and bam2bw was used for visualization.
ChIP-Seq: Sequencing reads were aligned to the human genome hg19 using bwa, peak calling of H3K27ac and H3K4me3 ChIP-Seq was conducted using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files

source_name: Differentiated iPSC suspension cells

growth_protocol: The iPSCs were cultured in E8 medium supplemented with 1% Penicillin/Streptomycin on vitronectin coated plates at 37°C. Cells were split as colonies every 3-4 days on fresh vitronectin coated plates using ReLeSR.

extract_protocol:
ChIPmentation:The purified cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature at a concentration of 15x106 cells/ml. The fixed cells were sonicated for 5 minutes (30 sec on; 30 sec off) using the Diagenode Bioruptor and centrifuged at maximum speed for 10 minutes. Chromatin of 2x105 cells was incubated overnight in dilution buffer (167mM NaCl, 16,7 mM Tris (pH 8), 1,2mM EDTA, 1% Triton X-100) with 1 µg H3K4me3 antibody at 4C. ProtA/G beads were blocked with dilution buffer (+0,15% SDS) and incubated with the chromatin-Ab for one hour at 4C. Beads were washed with three different wash buffers and the DNA library was prepared using the Nextera DNA sample prep kit  ChIP-Seq: Control and AML1-ETO iMonocyte and iGranulocyte suspensions were crosslinked with 1% formaldehyde for 10 minutes at room temperature at a concentration of 15x106 cells/ml. The fixed cells were sonicated for 4 minutes (30 sec on; 30 sec off) using the Diagnode Bioruptor and centrifuged at maximum speed for 10 minutes. Chromatin of about 5x105 cells was incubated overnight in dilution buffer (167mM NaCl, 16,7 mM Tris (pH 8), 1,2mM EDTA, 1% Triton X-100) with 1 µg H3K27ac antibody at 4C. ProtA/G beads were blocked and incubated with the chromatin-Ab for one hour at 4C. Beads were washed with three different wash buffers and chromatin was eluted from the beads. DNA-proteins were de-crosslinked (200mM NaCl and 4 µl proteinase K (10mg/ml)), by incubation for four hours at 65C and samples were purified using the Qiaquick MinElute PCR purification kit according manufacturer’s protocol. The procedure was performed according the Blueprint Histone ChIP protocol RNA-Seq:imonocytes and igranulocytes were purified by MACS sort using CD14 and CD16 beads (Miltenyi Biotec). Total RNA was isolated from 1x106 purified CD14+ imonocytes and CD16+ igranulocytes as well as from control and AML1-ETO imonocytes and igranulocytes using the RNeasy mini kit (Qiagen) and performing on-column DNaseI treatment. Ribosomal RNA was depleted from 500ng of RNA by using the ribo-zero rRNA removal kit according manufacturer’s protocol (Illumina)
Libraries were generated from precipitated DNA of 5 million cells using the Kapa hyper prep kit. End repair and A-tailing was performed on the double strand DNA using end repair and A-tailing buffer. Subsequently, the adapters were ligated and a post-ligation cleanup was performed using Agencourt AMPure XP reagent. The libraries were amplified by PCR using the Kapa Hifi hotstart readymix and primer mix for 10 cycles. Samples were purified using the Qiaquick MinElute PCR purification kit and 300 bp fragments were selected from E-gel and the size was checked on the agilent bioanalyzer. Samples were sequenced on the Illumina HiSeq 2000, generating 42 bp single end reads.

treatment_protocol: Differentiation was initiated by plating iPSCs on geltrex-coated plates in E8 medium till colonies reach a size of 500 uM. The medium was replaced by stemline II medium supplemented with 20 ng/ml BMP4, 40 ng/ml VEGF, 50 ng/ml bFGF cytokines. On day 6 the cytokines were replaced with a specific cytokine cocktail to induce monocyte (50 ng/ml SCF, 50 ng/ml FLT3-L, 50 ng/ml IL-3, 50 ng/ml M-CSF and 10 ng/ml TPO) and granulocyte (50 ng/ml SCF, 50 ng/ml IL-3, 50 ng/ml G-CSF, 5 ng/ml TPO) differentiation

value: Differentiated iPSC suspension cells

value: H3K27ac #A1723-0041d (Diagenode)

value: 14 ng/ml dox


title: Mega_iPSC

source_name: iPSC

value: iPSC


title: Day40_ctrl_H3K27ac


title: CD16_ChIP_H3K4me3

source_name: iGranulocytes

value: iGranulocytes

value: H3K4me3 #HS0010 (Diagnode)


title: PDX1-EZH2


title: Day40_ctrl

value: no dox


title: CD14_ChIP_H3K4me3

source_name: iMonocytes

value: iMonocytes


title: Day31_ctrl


title: Day30_ind

source_name: Differentiated iPSC adherent cells

value: Differentiated iPSC adherent cells


title: Day40_ind


title: Day30_ctrl


title: control_colon4

description: UMIsMatrix.txt.gz


title: Day10_ctrl


title: Day5_ctrl


title: Day10_ind


title: Day5_ind


title: Day20_ctrl


title: Day0_ctrl

source_name: iPSC adherent cells

value: iPSC adherent cells


title: Cd98 KO_colon5

description: UMIsMatrix.txt.gz


title: control_colon2

description: UMIsMatrix.txt.gz


title: CD45_iPSC

source_name: iLeukocytes

value: iLeukocytes


title: CD16_iPSC_9763


title: Day0_ind


title: CD16_iPSC_8801


title: CD14_iPSC_9762


title: CD14_iPSC_8285


title: Day31_ind


title: Day20_ind


title: Control Grey Matter 9371242006_K

status: Public on Jan 13 2020

description: Control Grey Matter

hyb_protocol: standard Illumina protocol

scan_protocol: Beadchips were scanned by the iScan Array scanner (Illumina, San Diego, Ca, USA)

data_processing: The R/Bioconductor packages beadarray (version 2.30.0) and illuminaHumanv4.db (version 1.26.0) were used for reading-in data files and for probe annotation (probes n=48107). Between-array normalization was performed by variance stabilizing transformation followed by a quantile normalization using functions from the Bioconductor package lumi (version 2.32.0).

source_name: Cortex, Frontal

label_protocol: Gene expression profiling was done using the Illumina cDNA-mediated annealing, selection, extension, and ligation (DASL) assay according to the manufacturer’s protocol (Fan et al., 2004) (Part No. 15018210, Revision history D, April 2012, Illumina, San Diego, Ca, USA)

extract_protocol: Total RNA from grey matter tissue was isolated using the Zymo ZR RNA Microprep Kit. RNA quality was controlled by using the Nanodrop Spectrophotometer (Thermo Scientific, Wilmington, USA) and the RNA 6000 Nano total RNA Kit on an Agilent 2100 Bioanalyzer. Degraded (RIN < 6) and/or contaminated (260/280 nm ratio < 1.8; 230/280 nm ratio < 1.8) samples were excluded from the study.

tag: patient id

value: F

tag: age at death

tag: post mortem interval

tag: pm simple

value: medium

tag: ms type

tag: disease duration

value: Grey Matter

tag: tissue region

value: Frontal

tag: block

tag: sample

tag: rin

tag: hla status

value: Other


title: MS Grey Matter 9371242014_J

description: MS Grey Matter

source_name: Cortex, Parietal

tag: Sex

value: short

value: SPMS

tag: tissue

value: Parietal


title: MS Grey Matter 9371242014_I

description: MS Grey Matter

value: long


title: Control Grey Matter 9371242014_D

description: Control Grey Matter

value: M


title: Control Grey Matter 9371242014_H

description: Control Grey Matter


title: Control Grey Matter 9371242006_L

description: Control Grey Matter


title: Control Grey Matter 9371242006_I

description: Control Grey Matter


title: Control Grey Matter 9371242014_K

description: Control Grey Matter


title: MS Grey Matter 9371242006_F

description: MS Grey Matter

value: PRMS


title: Control Grey Matter 9371242002_G

description: Control Grey Matter


title: MS Grey Matter 9371242014_L

description: MS Grey Matter

value: PPMS


title: MS Grey Matter 9371242006_D

description: MS Grey Matter


title: Control Grey Matter 9371242002_K

description: Control Grey Matter


title: MS Grey Matter 9371242006_G

description: MS Grey Matter


title: MS Grey Matter 9371242014_A

description: MS Grey Matter


title: Control Grey Matter 9371242002_J

description: Control Grey Matter


title: MS Grey Matter 9371242014_G

description: MS Grey Matter


title: MS Grey Matter 9371242006_C

description: MS Grey Matter


title: MS Grey Matter 9371242002_I

description: MS Grey Matter


title: MS Grey Matter 9371242014_E

description: MS Grey Matter


title: MS Grey Matter 9371160141_J

description: MS Grey Matter


title: Control Grey Matter 9371242002_H

description: Control Grey Matter


title: MS Grey Matter 9371160141_L

description: MS Grey Matter


title: MS Grey Matter 9371242002_C

description: MS Grey Matter


title: MS Grey Matter 9371242006_E

description: MS Grey Matter


title: MS Grey Matter 9371242002_D

description: MS Grey Matter


title: MS Grey Matter 9371242002_F

description: MS Grey Matter


title: MS Grey Matter 9371242002_L

description: MS Grey Matter


title: MS Grey Matter 9371242002_B

description: MS Grey Matter


title: Control Grey Matter 9371242006_A

description: Control Grey Matter


title: MS Grey Matter 9371160141_I

description: MS Grey Matter


title: Control Grey Matter 9371160141_C

description: Control Grey Matter


title: Control Grey Matter 9371160141_F

description: Control Grey Matter


title: Control Grey Matter 9371160141_G

description: Control Grey Matter


title: MS Grey Matter 9371160140_K

description: MS Grey Matter


title: MS Grey Matter 9371160140_A

description: MS Grey Matter


title: Control Grey Matter 9371160141_E

description: Control Grey Matter


title: MS Grey Matter 9371160141_D

description: MS Grey Matter


title: Control Grey Matter 9371160140_B

description: Control Grey Matter


title: MS Grey Matter 9371160140_F

description: MS Grey Matter


title: MS Grey Matter 9371160141_A

description: MS Grey Matter


title: Control Grey Matter 9371160140_I

description: Control Grey Matter


title: MS Grey Matter 9371160138_H

description: MS Grey Matter


title: Control Grey Matter 9371160138_I

description: Control Grey Matter


title: Control Grey Matter 9371160138_F

description: Control Grey Matter


title: Control Grey Matter 9371160138_D

description: Control Grey Matter


title: MS Grey Matter 9371160140_J

description: MS Grey Matter


title: MS Grey Matter 9371160140_L

description: MS Grey Matter


title: Control Grey Matter 9371160133_H

description: Control Grey Matter


title: Control Grey Matter 9371160138_A

description: Control Grey Matter


title: MS Grey Matter 9371160133_F

description: MS Grey Matter


title: MS Grey Matter 9371160138_J

description: MS Grey Matter


title: MS Grey Matter 9371160138_G

description: MS Grey Matter


title: Control Grey Matter 9371160133_K

description: Control Grey Matter


title: MS Grey Matter 9371160133_I

description: MS Grey Matter


title: MS Grey Matter 9371160141_B

description: MS Grey Matter


title: MS Grey Matter 9371160133_G

description: MS Grey Matter


title: MS Grey Matter 9371160138_C

description: MS Grey Matter


title: MS Grey Matter 9371160140_E

description: MS Grey Matter


title: Control Grey Matter 9371160140_H

description: Control Grey Matter


title: Control Grey Matter 9371160133_D

description: Control Grey Matter


title: Control Grey Matter 9371160121_K

description: Control Grey Matter


title: Control Grey Matter 9371160121_L

description: Control Grey Matter


title: MS Grey Matter 9371160133_A

description: MS Grey Matter


title: MS Grey Matter 9371160121_F

description: MS Grey Matter


title: Control Grey Matter 9371160121_E

description: Control Grey Matter


title: Control Grey Matter 9371160121_D

description: Control Grey Matter


title: Control Grey Matter 9371160121_C

description: Control Grey Matter


title: MS Grey Matter 9371160121_A

description: MS Grey Matter


title: MS Grey Matter 9371160121_H

description: MS Grey Matter


title: MS Grey Matter 9371160121_J

description: MS Grey Matter


title: MS Grey Matter 9371160121_I

description: MS Grey Matter


title: MS Grey Matter 9371160120_K

description: MS Grey Matter


title: Control Grey Matter 9371160111_F

description: Control Grey Matter


title: MS Grey Matter 9371160120_I

description: MS Grey Matter


title: Control Grey Matter 9371160120_J

description: Control Grey Matter


title: Control Grey Matter 9371160120_B

description: Control Grey Matter


title: MS Grey Matter 9371160120_A

description: MS Grey Matter


title: MS Grey Matter 9371160111_G

description: MS Grey Matter


title: MS Grey Matter 9371160120_C

description: MS Grey Matter


title: Control Grey Matter 9371160111_I

description: Control Grey Matter


title: MS Grey Matter 9371160111_E

description: MS Grey Matter


title: MS Grey Matter 9371160121_G

description: MS Grey Matter


title: Control Grey Matter 9371160111_D

description: Control Grey Matter


title: MS Grey Matter 9371160120_E

description: MS Grey Matter


title: MS Grey Matter 9371160111_H

description: MS Grey Matter


title: Control Grey Matter 9371160090_L

description: Control Grey Matter


title: MS Grey Matter 9371160120_H

description: MS Grey Matter


title: MS Grey Matter 9371160120_D

description: MS Grey Matter


title: MS Grey Matter 9371160090_F

description: MS Grey Matter


title: MS Grey Matter 9371160090_H

description: MS Grey Matter


title: Control Grey Matter 9371160090_G

description: Control Grey Matter


title: MS Grey Matter 9371160111_L

description: MS Grey Matter


title: Control Grey Matter 9371160090_J

description: Control Grey Matter


title: MS Grey Matter 9371160090_K

description: MS Grey Matter


title: MS Grey Matter 9371160090_I

description: MS Grey Matter


title: MS Grey Matter 9371160090_C

description: MS Grey Matter


title: Control Grey Matter 9371160090_B

description: Control Grey Matter


title: Control Grey Matter 9371160079_G

description: Control Grey Matter


title: Control Grey Matter 9371160120_G

description: Control Grey Matter


title: MS Grey Matter 9371160079_B

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242047_G

description: MS Grey Matter Lesion

value: Grey Matter Lesion

value: 01 allele status:15:01


title: MS Grey Matter 9371160079_L

description: MS Grey Matter


title: MS Grey Matter 9371242047_A

description: MS Grey Matter


title: Control Grey Matter 9371160090_A

description: Control Grey Matter


title: MS Grey Matter Lesion 9371242047_E

description: MS Grey Matter Lesion

value: 01 allele status:Other


title: MS Grey Matter Lesion 9371242047_B

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242031_J

description: MS Grey Matter


title: MS Grey Matter 9371160079_K

description: MS Grey Matter


title: MS Grey Matter 9371160079_A

description: MS Grey Matter


title: MS Grey Matter 9371242047_I

description: MS Grey Matter


title: MS Grey Matter 9371160079_F

description: MS Grey Matter


title: MS Grey Matter 9371242047_L

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242031_L

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242047_C

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242047_H

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242031_K

description: MS Grey Matter


title: MS Grey Matter 9371242047_D

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242031_H

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242031_E

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242020_I

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242020_H

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242031_I

description: MS Grey Matter


title: MS Grey Matter 9371242047_K

description: MS Grey Matter


title: MS Grey Matter 9371242020_G

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242020_K

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242031_B

description: MS Grey Matter


title: MS Grey Matter 9371242020_J

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242031_A

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242020_B

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242020_D

description: MS Grey Matter


title: MS Grey Matter 9371242020_E

description: MS Grey Matter


title: MS Grey Matter 9371242031_D

description: MS Grey Matter


title: MS Grey Matter 9371242015_H

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242015_C

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242015_D

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242015_A

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242009_K

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242015_K

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242009_I

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242015_L

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242020_A

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242015_G

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242015_E

description: MS Grey Matter


title: MS Grey Matter 9371242009_J

description: MS Grey Matter


title: MS Grey Matter 9371242020_C

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242020_F

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242015_J

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242009_D

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242004_L

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242009_B

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242009_F

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242004_J

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242009_G

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242004_I

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242004_H

description: MS Grey Matter


title: MS Grey Matter 9371242004_B

description: MS Grey Matter


title: MS Grey Matter 9371160135_L

description: MS Grey Matter


title: MS Grey Matter 9371242004_C

description: MS Grey Matter


title: MS Grey Matter Lesion 9371242009_C

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371160135_I

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371242004_K

description: MS Grey Matter Lesion


title: MS Grey Matter 9371160135_K

description: MS Grey Matter


title: MS Grey Matter Lesion 9371160135_J

description: MS Grey Matter Lesion


title: MS Grey Matter 9371242004_G

description: MS Grey Matter


title: MS Grey Matter 9371160135_F

description: MS Grey Matter


title: MS Grey Matter 9371160135_H

description: MS Grey Matter


title: MS Grey Matter 9371160116_I

description: MS Grey Matter


title: MS Grey Matter 9371242020_L

description: MS Grey Matter


title: MS Grey Matter Lesion 9371160135_E

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371160116_J

description: MS Grey Matter Lesion


title: MS Grey Matter 9371160116_L

description: MS Grey Matter


title: MS Grey Matter 9371242004_F

description: MS Grey Matter


title: MS Grey Matter Lesion 9371160135_B

description: MS Grey Matter Lesion


title: MS Grey Matter 9371160116_H

description: MS Grey Matter


title: MS Grey Matter Lesion 9371160116_F

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371160135_D

description: MS Grey Matter Lesion


title: Clone c7 from Donor4

data_processing:
Reads were aligned to the human genome (UCSC hg19) using the spliced
read aligner STAR (version 2.5.0c). Sequencing and mapping quality was assessed by
the qQCReport function of the R package QuasR (R version 3.2.3, QuasR version 1.10.1). Gene expression was
quantified by the qCount function of QuasR using an exon-union model
of hg19 RefSeq genes (downloaded from UCSC 2015-02-09).
Genome_build: hg19
Supplementary_files_format_and_content: gene_counts.csv; comma separated values; columns correspond to: 1. ENTREZ ID, 2. gene symbol, 3. gene name, 4. gene length (exon-union model), 5.-38. raw counts per sample

source_name: Bone marrow derived mesenchymal cells

growth_protocol: expansion in aMEM, 10%FBS, 5ng/mL FGF2 for 28 days

extract_protocol:
column-based quick-RNA min-prep (ZymoResearch)
TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (Illumina)

tag: gender

value: female

tag: age

tag: chondrogenic capacity (bern score)

tag: proliferation rate (doublings/day)


title: Clone c5 from Donor4


title: MS Grey Matter 9371160116_E

description: MS Grey Matter

tag: patient id


title: Clone c24 from Donor4


title: Clone c31 from Donor4


title: MS Grey Matter Lesion 9371160116_D

description: MS Grey Matter Lesion

tag: age at death


title: Clone c3 from Donor3


title: Clone c15 from Donor4


title: Clone c2 from Donor3


title: Clone c5 from Donor3


title: MS Grey Matter 9371160116_G

description: MS Grey Matter

tag: post mortem interval


title: Clone c15 from Donor3


title: Clone c12 from Donor3


title: MS Grey Matter Lesion 9371160116_A

description: MS Grey Matter Lesion


title: Clone c11 from Donor3


title: Clone c10 from Donor3


title: Clone c1 from Donor3


title: MS Grey Matter 9371160116_B

description: MS Grey Matter


title: Clone c7 from Donor2

value: male


title: Clone c4 from Donor4


title: Clone c5 from Donor2


title: Clone c4 from Donor2


title: Clone c3 from Donor2


title: Clone c1 from Donor2


title: Clone c18 from Donor2


title: Clone c50 from Donor1


title: Clone c9 from Donor1


title: Clone c49 from Donor1


title: Clone c48 from Donor1


title: Clone c44 from Donor1


title: Clone c35 from Donor1


title: Clone c34 from Donor1


title: Clone c16 from Donor1


title: Clone c22 from Donor1


title: Clone c19 from Donor1


title: Clone c26 from Donor1


title: Clone c17 from Donor1


title: Clone c12 from Donor1


title: MS Grey Matter Lesion 9371242004_E

description: MS Grey Matter Lesion


title: MS Grey Matter Lesion 9371160116_C

description: MS Grey Matter Lesion

value: F


title: Clone c28 from Donor1


title: C-1.Cortex.HI.P10

description: Gene expression data from rat microglia

hyb_protocol: The labeled, fragmented cDNA (5.5µg ) was hybridized to the GeneChip Rat Transcriptome Array 1.0 (Affymetrix, Santa Clara, CA) for 16 hours in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) at 45° C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA)

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed with the R/Bioconductor package oligo. The function rma was used for array normalization. The package affycoretools was used for probe annotation. Only unique probe sets with an ENTREZ ID were retained for further analysis. In case of several probe sets mapping to the same ENTREZID the one with the highest variance as measured by the interquartile range was retained.

organism: Rattus norvegicus

source_name: Rat microglia from cortex region Cortex

label_protocol: Biotin labeling was performed using the GeneChip WT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's protocol from 500 pg total RNA per sample.

extract_protocol: Total RNA was extracted from CD11b+ purified cells with the Arcturus PicoPure RNA isolation kit (ThermoFisher Scientific, Waltham, MA) including DNAse treatment. The concentration, purity and integrity of RNA were assessed for each sample using the  2100 Bioanalyzer with the RNA 6000 Pico LabChips (Agilent, Santa Clara, CA). In sample CH14DIVUSBR100337 and CH50DIVUSBR100077, RIN values could repeatedly not been calculated (RIN value: “NA”), but the graphical assessment of the electropherogram indicated a similar RNA integrity as compared to samples with RIN > 8.4).

treatment_protocol: P7 Sprague-Dawley rats were subjected to sham surgery (exposure of the right [ipsilateral] common carotid artery) or HI surgery (temporary occlusion of the ipsilateral common carotid artery and exposure to hypoxia). Animals were transcardially perfused with NaCl 0.9% at either P10 or P20. The anterior dorsolateral SVZ (ipsilateral in HI animals, ipsi- and contralateral in sham animals) and the contralateral M2 supplementary motor cortex (CX) were microdissected. SVZ and CX tissue was collected separately in individual rats and dissociated by papain / DNAse treatment. Microglia were purified by anti-CD11b magnetic bead sorting (Miltenyi Biotec, San Diego, CA).

tag: animal id

value: Cortex

tag: treatment

value: HI


title: B-3.SVZ.Sham.P20

description: Gene expression data from rat microglia

source_name: Rat microglia from cortex region SVZ

value: SVZ

value: Sham


title: A-2.SVZ.Sham.P10

description: Gene expression data from rat microglia


title: B-2.Cortex.Sham.P20

description: Gene expression data from rat microglia