title: dc-cd8a_3

city: Augsburg

first: Stephen

last: Krämer

address: Alter Postweg 101

institute: University of Augsberg

description: bisulfite converted genomic DNA

data_processing:
Sequence alignment was performed using an updated version of the workflow published in (Wang et al., Nat. Prot., 2013). The workflow was implemented as a Roddy Workflow  (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows). Alignment was performed against the mm10 reference genome extended with the PhiX and lambda phage sequences. Briefly, before alignment, trimmomatic was used for adapter trimming and reads were in silico converted (C>T for the first read in the pair, G>A for the second). Alignments of the individual libraries were performed against the concatenated C>T and G>A in silico converted reference genomes using bwa mem with default parameters. After alignment, reads were converted back to their original state.
PCR duplicate removal was performed per library using Picard MarkDuplicates before merging reads from all libraries.
At each cytosine position, reads that maintain the cytosine status were considered methylated, and the reads that have cytosine converted to thymine were considered unmethylated.
Only reads with a mapping quality >= 25 and bases with Phred-scaled quality score ≥25 were considered for methylation calling.
At least the first 9 bp of the second read and last 9 bp before the adapter in the first read were excluded from methylation calling. The in silico conversion and methylation calling steps were performed using bistro (https://github.com/stephenkraemer/bistro).
Genome_build: mm10
Supplementary_files_format_and_content: QC-filtered methylation calls for all autosomal CpGs in BED6+3 format, with the following columns: chrom, start, end, motif, score, strand, beta_value, n_meth, n_total. The two cytosines in a CpG motif were merged, and the CpG position is given on the plus strand. The score column holds no information (always '.').

source_name: cDC CD8a+

extract_protocol:
All populations were isolated from 8- to 12-week-old C57BL/6J mice by fluorescence activated cell sorting. The following hematopoietic cell populations were isolated from bone marrow cells: MDPs, CDPs, cMoPs and monocytes. Monocytes were sorted from total bone morrow.  MDPs, CDPs and cMoPs were sorted from lineage negative cells. Lineage depletion of mature hematopoietic cell lineages was performed using Sheep anti-Rat IgG magnetic beads and rat IgG isotype lineage antibodies. The following hematopoietic cell populations were isolated from splenic cell suspensions: pDC, cDC CD8a+, cDC CD11b+. DNA was isolated from snap-frozen cell pellets (10.000 - 25.000 sorted cells) using the QIAamp DNA Micro Kit (Qiagen) according to the manufacturer’s instructions.
Tagmentation-based whole-genome bisulfite sequencing (TWGBS) libraries were prepared as described previously (Wang et al., Nat. Prot., 2013). We used 10-30 ng genomic DNA as input.

tag: cell type

value: cDC CD8a+

tag: cell marker

value: MHC II+ CD11c+ (high) CD8a


title: D7_EX1A3_TLR

status: Public on Nov 03 2021

type: SRA

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

description: processed data file: RSEM_Gene_VST_D0-D7LPS.TLR.BCR.txt.gz

library_source: transcriptomic

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Genome_build: GRCm38.p6/mm10 (Gencode release M20)
Supplementary_files_format_and_content: Tab separated sheets containing DESeq2 rLog transformed data

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Spleen tissue was harvested from sex- and age-matched C57BL/6, Blimp-1-Venus19 or Prdm1Δex1A mice16 (provided by E. Bikoff, University of Oxford) between 6-12 weeks old that had been maintained in specific-pathogen-free (SPF) conditions. All procedures were performed under the approved UK Home Office project license in line with the Animal (Scientific Procedures) Act 1986 and in accordance with the UK National Cancer Research Institute Guidelines for the welfare of animals. Single cell suspensions were obtained after density centrifugation using lympholyte-M (Cedarlane). The EasySep™ mouse B-cell isolation kit (STEMCELL Technologies) containing anti-CD43 was used to isolate B2 cells. Following isolation, B cells were phenotyped to ensure >95% purity before culture
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).
RNA samples were quantified with a Qubit HS RNA assay kit (Thermo Fisher Scientific) and the quality was assessed by RNA HS assay using the TapeStation system (Agilent). Sequencing libraries were generated by using a TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina) according to the manufacturer’s protocol. Library performance was checked on the TapeStation followed by picogreen quantification. Equimolar pooling was performed across all the libraries and the final pool was sequenced on a NextSeq 500 platform (Illumina) using 76-bp single-end sequencing.

treatment_protocol:
isolation-conditions: Spleen tissue was harvested from sex- and age-matched C57BL/6, Blimp-1-Venus19 or Prdm1Δex1A mice (provided by E. Bikoff, University of Oxford) between 6-12 weeks old that had been maintained in specific-pathogen-free (SPF) conditions. All procedures were performed under the approved UK Home Office project license in line with the Animal (Scientific Procedures) Act 1986 and in accordance with the UK National Cancer Research Institute Guidelines for the welfare of animals. Single cell suspensions were obtained after density centrifugation using lympholyte-M (Cedarlane). The EasySep™ mouse B-cell isolation kit (STEMCELL Technologies) containing anti-CD43 was used to isolate B2 cells. Following isolation, B cells were phenotyped to ensure >95% purity before culture
culture-conditions: Day 0:  for BCR signalling, isolated B-cells were seeded in 24 well plates at 2.5x10^5 cells/mL (0.5mL/well; 1.25x10^5 cells/well) with irradiated CD40L expressing murine L cells (0.5mL/well; 6.25x10^4/well), 12µg/mL F(ab’)2 anti-IgM/IgG (Jackson Immunoresearch), 50ng/mL IL-4 and 50ng/mL IL-5 (Miltenyi) for 2 days. For TLR signalling, B-cells were seeded at the same density as above with CD40L expressing murine L cells, 5µg/mL LPS (0111:B4, Sigma-Aldrich), IL-4 and IL-5. Day 2: On subsequent days, both mechanisms followed the same steps. At day 2, cells were removed from the CD40L cells and transferred across to new 24 well plates. Day 4: On day 4, plasmablasts were re-seeded in 10ng/mL IL-6 (Miltenyi), 100ng/mL APRIL (Caltag), MEM amino acids and Lipid Mixture 1 (Sigma-Aldrich) at 5x105 cells/mL in 96 well plates (0.2mL/well; 1x105 cells/well). Cells were fed with fresh media every 3-4 days containing APRIL, IL-6, amino acids and lipids. Feeding was carried out until elective termination.

tag: strain background

tag: genotype/variation

tag: Sex

value: female

tag: age

value: 9 weeks old

tag: tissue

value: spleen

tag: time point

value: Plasmablast


title: KO2_Riboseq

city: New York

first: Jennifer

last: Blaze

state: New York

address: 1470 Madison Ave 9-202

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Riboseq processed data.xlsx
4618_Riboseq

data_processing:
Library strategy: Ribo-seq
The adapters in the sequencing reads were removed using cutadapt (v3.1) with options ‘--trimmed-only -m 15 -a AGATCGGAAGAGCAC ’. The PCR duplicates in the reads were collapsed using CLIPflexR v0.1.19. The Unique Molecule Identifiers (UMIs) for each read were extracted using umi_tools v1.1.1 with the options 'extract --bc-pattern=NN' for the 5' end and options 'extract --3prime --bc-pattern=NNNNN ' for the 3' end.  Reads corresponding to rRNA and other non-nuclear mRNA were removed by aligning out the reads using Bowtie2 v2.4.2 on a depletion reference (rRNA, tRNA and mitochondrial RNA sequences). This depletion reference was built from the non-coding transcriptome for Mus musculus (Ensembl release v96). The reads that did not align to the depletion reference were aligned to the Mus Musculus mRNA transcriptome using Bowtie2 with options '--sensitive --end-to-end --norc'. The mRNA transcriptome was built using the cDNA longest CDS reads of Mus Musculus downloaded from Ensembl release v96. The resulting reads were converted to bam files and then sorted using samtools v1.11. The duplicate reads in the sorted files were removed using umi_tools v1.1.1 with options 'dedup'.  The quality check and downstream processing of the processed reads was performed using Ribolog v0.0.0.9. After quality check, the psite information was converted to codon counts in Ribolog. The codon reads resulting from stalling were corrected using the CELP (Consistent Excess of Loess Preds) method in Ribolog. After median normalization and removal of transcripts with 0 counts, the translational efficiency testing was performed in Ribolog as well.

source_name: Mouse cortex

extract_protocol:
Cortical tissue was homogenized in lysis buffer (containing cycloheximide) and cleared for 10 minutes at 20,000 x g at 4oC.  Monosomes obtained by RNase I digestion were purified using spin-column chromatography. Briefly, MicroSpin S-400 HR columns (Cytiva) were equilibrated with 3 mL of Polysome buffer by gravity flow, then spun down 4 mins at 600 g. 100 µl of RNase I digested lysate was loaded onto the column and spun 2 mins at 600 g. The flow through was collected and the RNA was extracted using RNA Clean & Concentrator-25 kit (Zymo). The rRNA depletion was performed onto linker ligated RPFs using riboPOOLs (siTOOLs).  RNAseq libraries were constructed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara), as recommended by the manufacturer. RiboSeq and RNAseq libraries were sequenced on HiSeq4000 (Illumina) at the Center for Advanced Technology (UCSF).
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

tag: tissue type

value: Cortex

tag: strain

value: Nsun2 floxed, Camk2a-Cre pos.

tag: developmental stage

value: Adult

tag: molecule

value: Ribosome-protected mRNA


title: WT1_Riboseq

description:
Riboseq processed data.xlsx
4612_Riboseq

value: Nsun2 floxed, Camk2a-Cre neg.


title: h1hESC_EC-EQ_27

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

description:
EQ_ExpectedCounts.csv
EC-EQ_27

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads trimmed to have length 51 bp using seqtk 1.0
Sequencing reads were mapped to GRCh38 Ensembl using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts csv

organism: Homo sapiens

source_name: differentiated human embryonic stem cells

growth_protocol: Cells were grown as in GSE75748. EC: H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days. TB: H1 were seeded in E7 (E8 minus FGF2) with 50ng/ml BMP4 and SB431542.

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system. For EQ, EQ-Vary and EQ-75%, we retrieved the harvested cDNA, which are amplified full-length single-cell cDNAs identical to those in GSE75748.
For the EQ and EQ-75% experiments, 2.0 µL of the amplified/tagmented cDNA were used for pooling. In the EQ-Vary experiment, a single scaling factor was applied to generate variable amounts of the pooling volume. These pooled single-cell libraries were used in an AMpure XP Bead-based Dual Bead Cleanup and Size Selection reaction (Agencourt AMPure XP PCR Purification modified Instructions for Use, Beckman Coulter). In both bead cleanup reactions, 90% of AMPure XP beads were added to the amplified single-cell libraries to select for an approximate size range of 150-700 bp and incubated for 15 minutes at room temperature. Libraries bound to beads were then placed on a magnet for 5 minutes, washed twice with 70% Ethanol, eluted with Suspension Buffer (Nextera XT DNA Sample Preparation Index Kit, Illumina), and transferred to a new tube.  Final amplified and pooled single-cell libraries were quantified with the Qubit dsDNA HS Assay Kit (Q32854, Thermofisher) and Bioanalyzer High Sensitivity DNA Analysis Kit (5067-4626, Agilent).Libraries were multiplexed with 96 samples per lane and sequenced on an Illumina HiSeq3000 with paired-end 65 or 78 bp reads.
Single-cell RNA-Seq

tag: cell line

value: H1 hESC cell line

tag: sample type

value: EC

tag: equilization amt

value: equalized


title: h1hESC_EC-EQ_18

description:
EQ_ExpectedCounts.csv
EC-EQ_18


title: h1hESC_EC-EQ_17

description:
EQ_ExpectedCounts.csv
EC-EQ_17


title: dc-cd8a_2

country: Germany

description: bisulfite converted genomic DNA

library_source: genomic

molecule: genomic DNA


title: CdCl2 18weeks Rep2

city: Chicago

first: Malek

last: El Muayed

state: IL

address: 303 E. Chicago Ave Tarry 15

department: Endocrinology, Metabolism, and Molecular Medicine

institute: Northwestern University Feinberg School of Medicine

description: CdCl2 18weeks Rep2

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: pancreatic islet

extract_protocol:
Pancreatic islets were isolated and purified using Biocoll density gradient.  Total RNA was extracted using Trizol reagent followed by phase separation with chloroform. Total RNA was quantified using Nanodrop spectrophotometer and sent to the Genomics Core Facility for library preparation and  sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

value: male

tag: genotype

value: WT

tag: treatment

value: 1mM CdCl2

tag: duration of treatment

value: 18 weeks treatment in vivo


title: D7_EX1A1_TLR

value: female


title: D7_M2_BCR

description: processed data file: RSEM_Gene_VST_D0-D10TLR.BCR.txt.gz

value: wild type

value: 7 weeks old


title: CdCl2 18weeks Rep5

description: CdCl2 18weeks Rep5


title: D7_M1_BCR

value: spleen

value: Plasmablast


title: h1hESC_EC-EQ_14

description:
EQ_ExpectedCounts.csv
EC-EQ_14


title: Vehicle 18weeks Rep6

description: Vehicle 18weeks Rep6

value: vehicle


title: h1hESC_EC-EQ_10

description:
EQ_ExpectedCounts.csv
EC-EQ_10


title: D7_M3_TLR


title: CdCl2 18weeks Rep4

description: CdCl2 18weeks Rep4


title: D7_M2_TLR


title: h1hESC_EC-EQ_13

description:
EQ_ExpectedCounts.csv
EC-EQ_13


title: Vehicle 18weeks Rep4

description: Vehicle 18weeks Rep4


title: D7_M1_TLR


title: h1hESC_EC-EQ_11

description:
EQ_ExpectedCounts.csv
EC-EQ_11


title: pdc_3

description: bisulfite converted genomic DNA

source_name: pDCs

tag: cell type

value: pDCs

tag: cell marker

value: PDCA+ CD11c+


title: D7_EX1A3_LPS

tag: strain background

tag: genotype/variation

value: 9 weeks old


title: D7_M3_BCR

tag: Sex

tag: age


title: Vehicle 18weeks Rep3

description: Vehicle 18weeks Rep3

tag: tissue


title: dc-cd8a_1

description: bisulfite converted genomic DNA

value: cDC CD8a+

value: MHC II+ CD11c+ (high) CD8a


title: D7_EX1A2_TLR

tag: time point


title: CdCl2 18weeks Rep3

description: CdCl2 18weeks Rep3

tag: strain


title: CdCl2 18weeks Rep1

description: CdCl2 18weeks Rep1


title: pdc_2

description: bisulfite converted genomic DNA


title: D7_EX1A2_LPS


title: h1hESC_EC-EQ_6

description:
EQ_ExpectedCounts.csv
EC-EQ_6

value: H1 hESC cell line

value: EC

value: equalized


title: dc-cd11b_3

description: bisulfite converted genomic DNA

source_name: cDC CD11b+

value: cDC CD11b+

value: MHC II+ CD11c+ (high) CD11b +


title: h1hESC_EC-EQ_5

description:
EQ_ExpectedCounts.csv
EC-EQ_5


title: Vehicle 18weeks Rep2

description: Vehicle 18weeks Rep2

value: pancreatic islets

value: male

value: WT

value: 18 weeks treatment in vivo


title: D7_EX1A1_LPS

value: female

value: spleen


title: dc-cd11b_1

description: bisulfite converted genomic DNA


title: dc-cd11b_2

description: bisulfite converted genomic DNA


title: CdCl2 6weeks Rep4

description: CdCl2 6weeks Rep4

value: 1mM CdCl2

value: 6 weeks treatment in vivo


title: h1hESC_EC-EQ_9

description:
EQ_ExpectedCounts.csv
EC-EQ_9


title: h1hESC_EC-EQ_4

description:
EQ_ExpectedCounts.csv
EC-EQ_4


title: h1hESC_EC-EQ_12

description:
EQ_ExpectedCounts.csv
EC-EQ_12


title: D7_M2_LPS

value: wild type

value: Plasmablast


title: D7_M1_LPS

value: 9 weeks old


title: h1hESC_EC-EQ_2

description:
EQ_ExpectedCounts.csv
EC-EQ_2


title: h1hESC_TB-EQ_13

description:
EQ_ExpectedCounts.csv
TB-EQ_13

value: TB


title: Vehicle 18weeks Rep5

description: Vehicle 18weeks Rep5

value: vehicle


title: pdc_1

description: bisulfite converted genomic DNA

value: pDCs

value: PDCA+ CD11c+


title: D4_Ex1A3_BCR


title: D7_M3_LPS


title: h1hESC_EC-EQ_7

description:
EQ_ExpectedCounts.csv
EC-EQ_7

value: H1 hESC cell line

value: EC

value: equalized


title: Vehicle 6weeks Rep5

description: Vehicle 6weeks Rep5

value: pancreatic islets

value: male


title: cmop_2

description: bisulfite converted genomic DNA

source_name: cMoPs

value: cMoPs


title: cmop_1

description: bisulfite converted genomic DNA


title: monos_3

description: bisulfite converted genomic DNA

source_name: Monocytes

value: Monocytes

value: B220- CD5- CD8a- Ter119- CD11b+ Ly6Chi SiglecF- Ly6G- FceRI-


title: CdCl2 96hours Rep4

description: CdCl2 96hours Rep4

value: WT

value: 0.5uM CdCl2

value: 96 hours treatment ex vivo


title: D4_M3_BCR

value: wild type

value: 7 weeks old

value: spleen

value: Plasmablast


title: CdCl2 96hours Rep3

description: CdCl2 96hours Rep3


title: cdp_2

description: bisulfite converted genomic DNA

source_name: CDPs

value: CDPs

value: Lin- cKit  Flt3+ CD115+


title: Vehicle 6weeks Rep3

description: Vehicle 6weeks Rep3

value: vehicle

value: 6 weeks treatment in vivo


title: monos_2

description: bisulfite converted genomic DNA


title: D4_Ex1A2_BCR

value: female

value: 9 weeks old


title: D4_M2_BCR

value: male


title: h1hESC_EC-EQ_8

description:
EQ_ExpectedCounts.csv
EC-EQ_8

value: H1 hESC cell line

value: EC

value: equalized


title: CdCl2 96hours Rep2

description: CdCl2 96hours Rep2

value: pancreatic islets

value: WT


title: Vehicle 18weeks Rep1

description: Vehicle 18weeks Rep1

value: 18 weeks treatment in vivo


title: Vehicle 6weeks Rep2

description: Vehicle 6weeks Rep2


title: cdp_4

description: bisulfite converted genomic DNA


title: mdp_2

description: bisulfite converted genomic DNA

source_name: MDPs

value: MDPs


title: D4_Ex1A3_TLR


title: Vehicle 96hours Rep5

description: Vehicle 96hours Rep5

value: 96 hours treatment ex vivo


title: mdp_1

description: bisulfite converted genomic DNA


title: Vehicle 96hours Rep4

description: Vehicle 96hours Rep4


title: h1hESC_EC-EQ_3

description:
EQ_ExpectedCounts.csv
EC-EQ_3


title: cdp_3

description: bisulfite converted genomic DNA


title: CdCl2 6weeks Rep3

description: CdCl2 6weeks Rep3

value: 1mM CdCl2


title: CdCl2 6weeks Rep2

description: CdCl2 6weeks Rep2


title: ColGFP rep3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
cutadapt was run with options :-q 0,13 -u 3 -u -0--trim-n -m 20
tophat was run with options: --b2-very-sensitive --no-coverage-search --library-type fr-unstranded -I 500000 --transcriptome-only
htseq was run with options: -f bam -s no -m intersection-nonempty
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text of raw counts

source_name: lung

extract_protocol:
Lungs were harvested, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung


title: cdp_1

description: bisulfite converted genomic DNA

value: CDPs


title: DBL rep4


title: h1hESC_EC-EQ_1

description:
EQ_ExpectedCounts.csv
EC-EQ_1


title: CdCl2 6weeks Rep1

description: CdCl2 6weeks Rep1


title: Vehicle 96hours Rep2

description: Vehicle 96hours Rep2


title: D4_Ex1A1_TLR

value: spleen

value: Plasmablast


title: D4_M3_TLR

value: wild type

value: 7 weeks old


title: CdCl2 96hours Rep5

description: CdCl2 96hours Rep5

value: 0.5uM CdCl2


title: Vehicle 96hours Rep1

description: Vehicle 96hours Rep1

value: male

value: vehicle


title: Vehicle 6weeks Rep4

description: Vehicle 6weeks Rep4

value: 6 weeks treatment in vivo


title: TDonly rep2


title: D4_M1_BCR


title: monos_1

description: bisulfite converted genomic DNA

value: Monocytes

value: B220- CD5- CD8a- Ter119- CD11b+ Ly6Chi SiglecF- Ly6G- FceRI-


title: DBL rep3


title: CdCl2 96hours Rep1

description: CdCl2 96hours Rep1

value: pancreatic islets

value: WT


title: D4_M1_TLR


title: D4_Ex1A1_BCR

value: female

value: 9 weeks old


title: ColGFP rep2


title: Vehicle 6weeks Rep1

description: Vehicle 6weeks Rep1


title: TET2KO_Input_DIPseq_Rep3

city: Miami

last: Nimer

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Base calling using Illumina RTA 2.4.11
Reads were trimmed using cutadapt (–m25), aligned using bowtie2 (v2.0.5) to the mouse mm10 genome build, quality filtered (mapq > 30), and deduplicated using Picard Markduplicates.
Peaks were called using macs2 (-g mm --nomodel --extsize 200 –B) and differential peaks were determined using macs2 bdgdiff from the intermediate lambda and pileup bedgraphs generated from macs2 callpeaks.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig files contain fold change signal over input generated from macs2.

source_name: HSPCs

growth_protocol: Genomic DNA from sorted HSPCs was isolated using the AllPrep DNA/RNA Plus micro kit (Qiagen)

extract_protocol:
Approximately 200 ng of genomic DNA was sonicated followed by end-repair, A-tailing and adaptor ligation using standard Illumina protocols. 10% of the volume was retained for Input.
Immunoprecipitation with anti-5- hmC antibodies (1 μg/ml, Active Motif) was performed at 4°C overnight and immunoprecipitated DNA was recovered using protein G magnetic beads (Invitrogen). After proteinase K digestion, DNA was purified from all input and immunoprecipitated samples, and amplified by PCR for library preparation.
Single-End, 100bp sequenced on an Illumina HiSeq 2500.

value: HSPCs

tag: dip antibody

value: input


title: TET2KO_Input_DIPseq_Rep2


title: CD11c-YFP rep1

city: Taipei

first: Tyng-An

last: Zhou

state: Taiwan

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Paired-end sequencing. Read1 used to read cell and molecule barcodes and Read2 contained cDNA sequences.
bcl2fastq v2.20 for base-calling.
Sequenced reads were mapped to GRCm39 mouse genome using STAR 2.7.9a with parameters --limitOutSJcollapsed 5000000 --outFilterMultimapNmax 1 --quantMode GeneCounts --soloType CB_UMI_Simple --soloUMIlen 12 --soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloUMIfiltering MultiGeneUMI; CB whitelist was obtained from Cell Ranger of 10x Genomics (3M-february-2018.txt).
Count matrices were read and downsampled by DropletUtils (Morgan M, et al., Nat Methods, 2020) and analyzed SingleCellExperiment (Robert R.A, et al., Nat Methods, 2019) workflow.
Genes were annotated by biomaRT (Durinck S, et al., Nat Protoc, 2009); cell-level and feature-level QC were done by Scater (McCarthy DJ, et al., Bioinformatics, 2017).
Normalized expression values were calculated by Scran (Lun ATL, et al., F1000Research, 2016)
Genome_build: GRCm39 (mm39)
Supplementary_files_format_and_content: matrix.mtx files of count matrices.
Supplementary_files_format_and_content: features.tsv files of gene ID correspond to row indices of matrix.
Supplementary_files_format_and_content: barcodes.tsv files of barcode sequences correspond to column indices of matrix.

source_name: Thymus

growth_protocol: All mice were maintained under specific pathogen-free conditions.

extract_protocol:
For myeloid cell isolation, mouse thymuses were cut into small pieces and digested with 0.2 mg/mL DNase I (Roche) and 0.2 mg/mL collagenase P (Roche) in complete DMEM for 20 min at 37˚C with frequent agitation.Thymic myeloid cells were enriched by 57% Percoll PLUS (GE Healthcare) discontinuous gradient centrifugation at 4˚C, 1800 rpm, for 20 min without brake. Cells at the interface were collected and washed with PBS to remove residual silica particles. GFP+ and YFP+ cells were then sorted on BD FASC Melody.  The sorted  cells were resuspended in PBS with 0.5% BSA (HM Biological), filtered through 70 µm filter, and used for encapsulation and library preparation.
RNA libraries were prepared for sequencing follow the Single Cell 3' v3 Gene Expression Library protocol of 10x Genomics.

treatment_protocol: Mice were sacrified by CO2.

value: thymus

value: myeloid cell

value: Itgax-Venus

value: Mice were sacrified by CO2


title: D4_Ex1A2_TLR

value: spleen

value: Plasmablast


title: TET2KO_Input_DIPseq_Rep1


title: TDonly rep3

value: lung


title: D4_Ex1A2_LPS


title: MaFIA rep2


title: Vehicle 96hours Rep3

description: Vehicle 96hours Rep3

value: male

value: vehicle

value: 96 hours treatment ex vivo


title: P300KO_TET2KO_Input_DIPseq_Rep3

value: p300 Tet2 KO


title: ColGFP rep1


title: P300KO_TET2KO_Input_DIPseq_Rep2


title: MaFIA rep1


title: P300KO_TET2KO_Input_DIPseq_Rep1


title: D4_M2_TLR

value: wild type

value: 7 weeks old


title: CD11c-YFP rep2


title: P300KO_Input_DIPseq_Rep1


title: D4_Ex1A3_LPS

value: female


title: D4_M1_LPS

value: 9 weeks old


title: Transgenic C3

city: Davis

first: Abijeet

middle: Singh

last: Mehta

state: California

address: Tupper hall

department: Dermatology

institute: University of California

description: ExpC

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were mapped to dm6 using TopHat aligner.
Partek Genomics Suite was applied for gene quantification based on RefSeq transcript models.
Genome_build: dm6
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw read count and RPKM normalized counts for each sample.

organism: Drosophila melanogaster

source_name: 3rd instar larvae

extract_protocol:
Tissue was homogenized in TRIzol to extract RNA that was then purified using RNA clean and ConcentratorTM (Zymo research, Cat. No. R1080) columns.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA with Ribo-Zero kit. Barcoded libraries were pooled and paired-end (2X100) sequenced on an Illumina HiSeq 2500.

treatment_protocol: For this experiment we had 1 control, and 5 experimental samples. Control is Tubulin Gal-4/S-T Drosophila stock. And 5 experimental treatments are five transgenic flies that are as follows: ExpA: Candidate 1, ExpB: Candidate 2, ExpC: Candidate 3, ExpD: Candidate 4, ExpE: Candidate 5 respectively.

value: Candidate 3 (C3)

value: Tublin Gal4; UAS-C3

value: Whole Larvae

tag: developmental stage

value: 3rd instar larvae

tag: time

value: 4th day after egg laying


title: D0_M3_None

value: Bcell


title: WT_Input_DIPseq_Rep1

value: WT

value: HSPCs

value: input


title: TDonly rep1

value: lung


title: Transgenic C1

description: ExpA

value: Candidate 1 (C1)

value: Tublin Gal4; UAS-C1


title: D4_Ex1A1_LPS

value: spleen

value: Plasmablast


title: P300KO_Input_DIPseq_Rep2


title: DBL rep1


title: D0_M1_None

value: wild type

value: male

value: 7 weeks old


title: D4_M3_LPS

value: female

value: 9 weeks old


title: Wild Type

description: Control

value: Tublin Gal4/S-T

value: Whole Larvae


title: P300_TET2KO_5hmc_DIPseq_Rep2

value: p300 Tet2 KO

value: 5hmc (Acitve Motif #39791)


title: WT_IgG

data_processing:
Base calling using Illumina RTA 2.4.11
Reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18).
Fastq files were aligned to mouse mm10 using BWA (v0.7.13 aln -q 5 -l 32 -k 2).
Aligned files were deduplicated using Picard Mark Duplicates (v2.10.6).
Genome_build: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig fold enrichment signal files were generated using Macs2 (v2.1.1.20160309) using IgG as control.
Supplementary_files_format_and_content: narrowPeaks were called using Macs2 using IgG as a control.

source_name: Lin- bone marrow cells

growth_protocol: 25 million mouse bone marrow Lin- cells (purity >80%) obtained using the Direct Lineage Cell depletion kit (Miltenyi Biotec, 140-110-470).

extract_protocol:
Cells pellets were suspended in buffer (0.1% SDS, 1% Triton, 1 mM EDTA, 16.7 mM Tris pH 8.1, 167 mM NaCl) and were sonicated for 14 cycles  (30s on/off) using Diagenode Bioruptor Pico. 1 ug of chromatin samples were used in each IP with 1.5 ug of antibody against Myb or rabbit normal IgG, and 20 ul of Protein A beads (NEB, S1425S).
The washed beads were tagged with 2ul of TDE1 from Illumina (FC-121-1030) in a 30 ul reaction. The beads were reversed cross-linked overnight at 65 degree. The DNA was amplified for 12 cycles with Illumina primers.
Libraries were sequenced single-end in an Illumina Nextseq 500

value: WT

value: Lin- bone marrow cells

tag: chip antibody

value: Cell Signaling, 2729S


title: Cardiomyocytes, NRVM-NC3

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was done using  Illumina with 50bp paired end reads.
For bulk RNA-seq, the reads were mapped with STAR 2.5.3a to the mouse genome (mm10 or rn6). The counts for each gene were obtained by using –quantMode GeneCounts commands in STAR, and the other parameters during alignment were set to default.
For scRNA-seq, raw reads were aligned to the mouse genome (mm10) and the digital expression matrix was generated using cellranger count.
Genome_build: mm10 and rn6
Supplementary_files_format_and_content: csv file with raw expression values

source_name: Cardiomyocytes

growth_protocol: (1) Immortalized CFs were seeded at low density at approximately 20-30% confluency in 24 well plates in high glucose DMEM  supplemented with 10%FBS  and 1% penicillin and streptomycin and cultured for 24 hours (500 μL/well). Cells were then washed with PBS and maintained for another 24 hours in serum-free DMEM/ITS medium which was made with high glucose DMEM supplemented with 0.1% Insulin-Transferrin-Selenium (ITS) and 1% penicillin and streptomycin. After 24 hours, DMEM/ITS medium was replaced by conditioned medium and then cells incubated for 24 or 48 hours. (2). NRVMs were seeded at low density at approximately 20-30% confluency in 24 well plates in high glucose DMEM  supplemented with 10%FBS  and 1% penicillin and streptomycin and cultured for 24 hours (500 μL/well). Cells were then washed with PBS and maintained for another 24 hours in serum-free DMEM/ITS medium which was made with high glucose DMEM supplemented with 0.1% Insulin-Transferrin-Selenium (ITS) and 1% penicillin and streptomycin. After 24 hours, DMEM/ITS medium was replaced by conditioned medium and then cells incubated for 24 hours.

extract_protocol:
Total RNA from cells was extracted using RNA mini Kit (BioRad, 7326830). For heart tissue RNA extraction, the uninjured and injured regions of the heart were harvested and homogenized in lysis buffer and then extracted using RNA mini kit. cDNA was synthesized by using iScript cDNA Synthesis Kit (BioRad, 1708890)
RNA libraries were prepared for sequencing using standard Illumina protocols
bulk RNA-seq and scRNA-seq

treatment_protocol: (1). Immortalized cardiac fibroblasts were treated with conditioned medium and extract RNA after 24 hours and 48 hours. (2). NRVMs were treated with conditioned medium and extract RNA after 24 hours. (3). Harvest cardiac non-myocyte population in Control or ENPP1 CKO at 7 days following myocardial infarction.

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley

value: Vehicle conditioned medium

value: 24 hours


title: P300_TET2KO_5hmc_DIPseq_Rep1

value: HSPCs


title: D4_M2_LPS

value: wild type

value: spleen

value: Plasmablast


title: Transgenic C5

description: ExpE

value: Candidate 5 (C5)

value: Tublin Gal4; UAS-C5

value: 3rd instar larvae

value: 4th day after egg laying


title: WT_Myb

value: Abcam ab76009


title: Transgenic C4

description: ExpD

value: Candidate 4 (C4)

value: Tublin Gal4; UAS-C4

value: Whole Larvae


title: Cardiomyocytes, NRVM-ENPP1-plus-ATP-3

value: ENPP1+ATP conditioned medium


title: Cardiomyocytes, NRVM-NC2

value: Neonatal rat ventricular myocytes


title: Cardiomyocytes, NRVM-ENPP1-2

value: Sprague-Dawley

value: ENPP1 conditioned medium


title: TET2KO_H3K27me3_Rep1

data_processing:
Base calling using Illumina RTA 2.4.11
Reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18).
Fastq files were aligned to mouse mm10 using BWA (v0.7.13 aln -q 5 -l 32 -k 2).
Aligned files were deduplicated using Picard Mark Duplicates (v2.10.6).
Genome_build: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig fold enrichment signal files were generated using Macs2 (v2.1.1.20160309) using H3 as control.
Supplementary_files_format_and_content: narrowPeaks were called using Macs2 for H3K27ac, H3K4me1 and H3K4me3 using H3 as a control.

growth_protocol: 25 million mouse bone marrow Lin- cells (purity >80%) obtained using the Direct Lineage Cell depletion kit (Miltenyi Biotec, 140-110-470) were crosslinked and processed with the ChIP-IT High Sensitivity kit (Active Motif 53040) following manufacturer’s instructions

extract_protocol:
5 ug of chromatin from Lin- cells and 1 ug of antibody were combined with 10 ng of chromatin from Drosophila melanogaster S2 cells (Active Motif 53083) as spike-in control.
Libraries were generated using NEBNExt Ultra II DNA library prep kit for Illumina
Libraries were sequenced single-end in an Illumina Nextseq 500

value: Tet2 Knockout

value: Lin- bone marrow cells


title: Cardiomyocytes, NRVM-NC1

value: wild type

value: Vehicle conditioned medium

value: 24 hours


title: WT_Input_DIPseq_Rep2

value: WT

value: HSPCs

value: input


title: P300KO_TET2KO_H3K27me3_Rep1

value: p300 Tet2 Knockout


title: M1_585B1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
The human genome sequence (GRCh38.p2, chromosomes 1 to 22 and X) was obtained from the NCBI ftp site (ftp://ftp.ncbi.nlm.nih.gov/). The transcript annotation (gencode.v25.annotation.gff3) was obtained from the GENCODE site (https://www.gencodegenes.org/).
Paired-end reads were aligned using Tophat v2.1.0/Bowtie2 v2.2.7 with the “‐no‐coverage‐search” option (Kim et al., 2013; Langmead and Salzberg, 2012), followed by cufflinks v2.2.1 with the “-compatible-hits-norm”, “-library-type fr-firststrand”, and “-max-mle-iterations 50000” options (Trapnell et al., 2010) to estimate fragments per kbp of transcript per million mapped reads (FPKM) per gene.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hiPSC

growth_protocol: The human iPSC lines (Table S1) were maintained under a feeder-free condition (StemFit AK03 or AK03N [Ajinomoto] medium on recombinant LAMININ511 [iMatrix-511; Nippi]-coated cell culture plates) (Nakagawa et al., 2014). For single-cell dissociation for the passage, the cells were treated with 0.5x TryPLE Select (Life Technologies) solution in 0.5 mM EDTA/PBS for 8-10 min at 37˚C and harvested with cell scrapers. 10 uM of Rho-associated coiled-coil forming kinase (ROCK) inhibitor (Y-27632; Wako Pure Chemical Industries) was added and the treatment was continued for 24 h after seeding.

extract_protocol:
Total RNA was extracted from harvested iPSCs (~4 × 10^5) by using RNeasy Micro Kit columns (QIAGEN) following the manufacturer’s guidelines.
RNA-seq libraries were prepared using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

tag: cell line

value: Human induced pluripotent stem cells (hiPSCs)


title: WT_Input_DIPseq_Rep3

tag: genotype


title: Cardiomyocytes, NRVM-ATP-3

tag: treatment

value: ATP conditioned medium


title: Transgenic C2

description: ExpB

value: Candidate 2 (C2)

value: Tublin Gal4; UAS-C2

value: 3rd instar larvae

value: 4th day after egg laying


title: P300_TET2KO_5hmc_DIPseq_Rep3

value: p300 Tet2 KO

value: 5hmc (Acitve Motif #39791)


title: Cardiomyocytes, NRVM-ENPP1-plus-ATP-2

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley

value: ENPP1+ATP conditioned medium


title: D0_M2_None

source_name: Spleen

value: wild type

value: male

value: 7 weeks old

value: spleen

value: Bcell


title: TET2KO_5hmc_DIPseq_Rep1

value: HSPCs


title: Cardiomyocytes, NRVM-ENPP1-plus-ATP-1

value: 24 hours


title: WT_H3K27me3_Rep1

value: WT

value: Lin- bone marrow cells


title: Cardiomyocytes, NRVM-ATP-1

value: ATP conditioned medium


title: M2_1383D6

value: Human induced pluripotent stem cells (hiPSCs)


title: Cardiomyocytes, NRVM-ENPP1-3

value: ENPP1 conditioned medium


title: P300KO_TET2KO_H3Kme3_Rep1

value: p300 Tet2 Knockout


title: F4_L_1390G3


title: TET2KO_5hmc_DIPseq_Rep3

value: 5hmc (Acitve Motif #39791)


title: Cardiomyocytes, NRVM-ENPP1-1

value: Neonatal rat ventricular myocytes


title: TET2KO_5hmc_DIPseq_Rep2


title: F4_M_1390G3


title: F5_M_1390C1


title: Cardiomyocytes, NRVM-AMP-2

value: Sprague-Dawley

value: AMP conditioned medium


title: P300KO_H3K27me3_Rep1

value: p300 Knockout


title: WT_5hmc_DIPseq_Rep3


title: Cardiomyocytes, NRVM-ATP-2

value: wild type


title: F3_L_1381B1


title: F5_E_1390C1


title: P300KO_5hmc_DIPseq_Rep3


title: Cardiac fibroblasts, 48h-NC-2

source_name: Cardiac fibroblast

value: Immortalized cardiac fibroblast

value: Vehicle conditioned medium

value: 48 hours


title: P300KO_5hmc_DIPseq_Rep2

value: HSPCs


title: F5_L_1390C1


title: TET2KO_H3Kme1_Rep1

value: Tet2 Knockout

value: Diagenode Cat#15410194 lot#A1862D


title: F4_E_1390G3


title: Cardiomyocytes, NRVM-AMP-3

value: 24 hours


title: Cardiomyocytes, NRVM-AMP-1


title: P300KO_H3Kme3_Rep1

value: Lin- bone marrow cells


title: WT_H3Kme3_Rep1

value: WT


title: WT_5hmc_DIPseq_Rep2


title: P300KO_H3Kme1_Rep1


title: Cardiac fibroblasts, 48h-E-A-2

value: ENPP1+ATP conditioned medium


title: WT_5hmc_DIPseq_Rep1


title: TET2KO_H3Kme3_Rep1


title: F3_E_1381B1

value: Human induced pluripotent stem cells (hiPSCs)


title: P300KO_TET2KO_H3Kme1_Rep1

value: p300 Tet2 Knockout


title: F3_M_1381B1


title: Cardiac fibroblasts, 48h-ENPP1-1

value: ENPP1 conditioned medium


title: Cardiac fibroblasts, 48h-NC-1


title: F2_CTCF_rep1

data_processing:
Paired-end reads were processed using the Cutadapt v1.9.1 (https://cutadapt.readthedocs.io/) to obtain 50 bp reads uniformly. The GC content per read was analyzed using the FastQC v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The truncated reads were aligned to the human genome (GRCh38.p2, chromosome 1 to 22 and X) using Bowtie2 v2.2.6 with the “-very-sensitive” option (Langmead & Salzberg, 2012).
Duplicate reads were removed using the MarkDuplicates command of Picard-tools v2.1.0 (https://broadinstitute.github.io/picard/) with the “REMOVE_DUPLICATES = true” option, and proper paired reads were extracted using SAMtools v1.3 (Li et al., 2009) with the “-f 0x2” option.
BigWig files were created from the same BAM files using IGVTools v2.3.52 (Robinson et al., 2011) and the wigToBigWig tool (http://hgdownload.cse.ucsc.edu/admin/exe/), with normalization by million mapped reads.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: BigWig

extract_protocol:
The ChIP experiment was performed as previously described (Lee et al., 2006) with minor modifications. Harvested iPSCs were crosslinked with 1% formaldehyde (methanol-free; Thermo Scientific) in PBS for 10 min at room temperature and quenched with 125 mM glycine. Crosslinked cells were incubated in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% TritonX-100, proteinase inhibitors) for 10 min at 4˚C. After centrifugation, the pellets were resuspended and incubated in lysis buffer 2 (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, proteinase inhibitors) for 10 min at 4˚C. After centrifugation, the pellets were resuspended and incubated in lysis buffer 3 (50 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, proteinase inhibitors) for 10 min at 4˚C. Chromatin was sonicated using a Picoruptor (Diagenode) to achieve a mean DNA fragment size of around 200~400 base pairs. 1/10 volume of Triton X-100 was added and the supernatants (sonicated chromatin) after centrifugation were used for immunoprecipitation. Sonicated chromatin was diluted in lysis buffer 3 to an optimal volume for antibody reaction and pre-cleared for 35 min at 4˚C using Dynabeads M-280 Sheep anti-Mouse IgG beads (Invitrogen) or Dynabeads Protein A beads (Invitrogen) blocked with 0.5% BSA in PBS. Pre-cleared chromatin was then incubated with antibody that was pre-incubated with the appropriate Dynabeads in 0.5% BSA in PBS overnight at 4˚C. After the incubation for 6 h at 4˚C, the beads were washed 4 times in wash buffer 1 (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 0.1% SDS), twice in wash buffer 2 (20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.1% SDS), and twice in wash buffer 3 (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 1% Na-Deoxycholate, 1% NP-40). The washed beads were eluted in 10 mM Tris-HCl pH 8, 5 mM EDTA, 300 mM NaCl, 1% SDS, and crosslinks were reversed overnight at 65 ˚C. Input samples (chromatin equivalent of 2 × 10^5 cells) were treated in a similar manner. The following day, IP and Input samples were incubated with RNase A (Thermo Scientific) for 25 min at 37˚C, and Proteinase K (Thermo Scientific) for 40 min at 55˚C. IP or Input DNA was purified using the QIA quick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using a KAPA Hyper Prep Kit (Roche) following the manufacturer’s guidelines. An adapter kit (FastGene) was used for the sample indexes. The average size and concentration of library samples were analyzed using LabChIP GX (PerkinElmer) and KAPA Library Quantification Kit (Roche), respectively.

value: anti-CTCF (rabbit monoclonal, CST, D31H2)

tag: controled by


title: MN_CHIA_PET

first: Michael

last: Closser

institute: Columbia University

data_processing:
Library strategy: ChIA-PET
MACS/GEM for ChIP peak calling
CID for ChIA-PET interaction calls
STAR/Cufflinks for RNA quatification
bedtools for cell specific genomic features
Genome_build: mm10
Supplementary_files_format_and_content: all files are tab demilited text. tpm for expression, peak calls with ChIP/ATAC, interaction calls for ChIA-PET

source_name: ESC derived motor neuron

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on a monolayer of Mitomycin-C–treated mouse embryonic fibroblasts (GlobalStem) in EmbryoMax D-MEM (Life Technologies) supplemented with 15% Knockout serum replacement (Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM β-mercaptoethanol and 100 U ml−1 leukemia inhibitory factor (Millipore), 1.25uM GSK3i (Selleckchem), and 100nM FRI (Gift from Austin Smith).

extract_protocol: ChIA-PET experiments were performed similar to previously described (Fullwood et al., 2009; Li et al., 2012). Briefly, on the appropriate day of differentiation, embryoid bodies were dissociated in trypsin into single cell suspension. Cells were cross-linked using 2mM DSG for 15 mins followed by 1% formaldehyde for 15 mins. Fixation was quenched with 2M Glycine (125mM final concentration) for 10 mins at room temp. Cross-linked chromatin was fragmented by sonication to a size of approximately 300bp. Chromatin complexes were immunoprecipitated with monoclonal anti-RNAPII (Covance, 8WG16) coated protein G Dynabeads (Life Technologies). To prepare ChIA-PET libraries DNA was end polished with T4 DNA polymerase and then ligated with biotinylated half linker fragments with T4 DNA Ligase (Life Technologies). Next ligation was performed under dilute conditions to promote intramolecular ligation events and avoid inter-ligation products from distinct chromatin complexes. Following ligation, DNA was purified by reverse crosslinking followed by phenol-chloroform extraction and ethanol precipitation. Ligation products were released via Mme1 restriction digest followed by purification on streptavidin beads. Finally adapters were ligated and PET constructs were amplified and subjected to Illumina 40bp PE sequencing.

treatment_protocol: Motor neuron differentiation was performed as previously described6,12. Briefly, mESCs were dissociated with .05% trypsin (Invitrogen) and seeded in single cell suspension at 5-7 × 105 cells per ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout Serum Replacemtn (vol/vol), Pen/Strep, 2 mML-glutamine, and 0.1 mM 2- mercaptoethanol) to initiate formation of embryoid bodies (EBs) (day 0). Medium was exchanged on day 2 of differentiation and motor neuron identity was induced by supplementing media with 1 μM all-trans retinoic acid (RA) to caudalize and 500nM Sonic Hedgehog agonist (SAG) to ventralize EBs for directed differentiation or 1 μM RA and 1ug/ml doxycycline to induce programming factor expression for direct programming.

tag: cell type

value: ESC derived motor neuron

tag: background

value: 129/Ola embryonic motor neurons

tag: conditions

value: Cultured in ADFNK for 2 days followed by RA/DOX for 2 days to induce motor neuron differntiation

tag: purification

value: pure population


title: P300KO_5hmc_DIPseq_Rep1

value: 5hmc (Acitve Motif #39791)


title: Cardiac fibroblasts, 48h-ENPP1-2

value: Immortalized cardiac fibroblast

value: wild type

value: 48 hours


title: F2_K4me3_rep2

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: F2_1205A


title: F1_201B7


title: F2_Input_2


title: Cardiac fibroblasts, 48h-ATP-2

value: ATP conditioned medium


title: WT_H3Kme1_Rep1

value: Lin- bone marrow cells

value: Diagenode Cat#15410194 lot#A1862D


title: MN_ChIPinput_1

data_processing:
MACS/GEM for ChIP peak calling
CID for ChIA-PET interaction calls
STAR/Cufflinks for RNA quatification
bedtools for cell specific genomic features
Genome_build: mm10
Supplementary_files_format_and_content: all files are tab demilited text. tpm for expression, peak calls with ChIP/ATAC, interaction calls for ChIA-PET

extract_protocol:
Chromatin immunoprecipitation experiments were performed as previously described6. Briefly, on the appropriate day of differentiation approximately 20-30 million cells were dissociated with trypsin into single cell suspension from EBs and crosslinked with 1% formaldehyde for 15 min at room temperature. Cells were lysed, chromatin pellets were isolated then solubilized and fragmented by sonication to 200-500bp length. Fragmented chromatin was then subject to immunoprecipitation using Protein G coated Dynabeads (Life Technologies) and antibodies (~5 μg) against the protein of interest (Isl1, the Developmental Studies Hybridoma Bank, clone numbers 39F7 and 4D5, gifts from T. Jessell and Susan Morton; V5, Abcam, ab15828; RNA Pol2, Covance, 8WG16; H3K27ac, Abcam, ab4729; Med1, Bethyl Labs, A300-793A; Smc1a, Bethyl Labs, A300-055A; p300, Santa Cruz, sc-584, Lot# I2712). After washing the beads to remove un-bound proteins and DNA, ChIP-seq samples were eluted from the magnetic beads and crosslinks were reversed overnight. Finally, protein and RNA were digested and DNA was purified by phenol chloroform extraction followed by ethanol precipitation. ChIP-Seq libraries were prepared following Illumina Tru-Seq ChIP Library Preparation Kit and sequenced by 40bp single-end sequencing on either Illumina HiSeq 2000 or NextSeq 500. All sequencing data were aligned to build version NCBI38/mm10 assembly of the mouse genome using Bowtie246. Peak calling was performed using the GEM peak caller47 for transcription factors and MACS248 for histone modifications.
Standard Illumina protocols for Tru-Seq


title: P300KO_Input_DIPseq_Rep3

value: HSPCs

value: input


title: multiple myeloma patient 65

type: genomic

city: Catanzaro

first: Mariamena

last: Arbitrio

address: via Tommaso Campanella, 115

country: Italy

institute: Institute of Biomedical Research and Innovation (IRIB), National Council of Research (CNR)

description: Hybridized to Affymetrix DMET array

hyb_protocol: DNA was PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip Command Console Software (AGCC version 4.0). Genotypes were extracted from CEL files using DMET Console software version 1.1.
Genotype Call (SNP call): AA, AB, BB, possible rare allele, and NoCall

label: Biotin

source_name: multiple myeloma patient 65

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood mononuclear cells of multiple myeloma patients at diagnosis using the Perfect Pure DNA Blood kit (5 Prime). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease

value: multiple myeloma

tag: disease stage

value: at diagnosis


title: F3_CTCF_rep1

value: Human induced pluripotent stem cells (hiPSCs)

value: anti-CTCF (rabbit monoclonal, CST, D31H2)


title: F3_K4me3_rep2


title: MN_CHIP_h3k27ac_2

value: ESC derived motor neuron

value: 129/Ola embryonic motor neurons


title: multiple myeloma patient 64

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 64


title: MN_CHIP_h3k27ac_1

value: Cultured in ADFNK for 2 days followed by RA/DOX for 2 days to induce motor neuron differntiation

value: pure population


title: Cardiac fibroblasts, 48h-AMP-2

value: Immortalized cardiac fibroblast

value: AMP conditioned medium


title: MN_ChIPinput_2


title: multiple myeloma patient 63

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 63


title: multiple myeloma patient 62

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 62


title: F1_CTCF_rep1


title: multiple myeloma patient 61

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 61


title: Cardiac fibroblasts, 24h-NC-1

value: wild type

value: Vehicle conditioned medium

value: 24 hours


title: Cardiac fibroblasts, 24h-ENPP1-2

value: ENPP1 conditioned medium


title: multiple myeloma patient 60

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 60


title: MN_CHIP_Lhx3_2


title: F3_Input_2


title: F1_K9me3_rep2

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: MN_CHIP_Lhx3_1


title: MN_CHIP_Med1_1


title: Cardiac fibroblasts, 24h-ENPP1-1


title: MN_CHIP_Med1_2


title: Cardiac fibroblasts, 48h-AMP-1

value: 48 hours


title: Cardiac fibroblasts, 24h-E-A-2

value: ENPP1+ATP conditioned medium


title: multiple myeloma patient 59

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 59

value: multiple myeloma


title: MN_CHIP_Isl1_2


title: F1_K27ac_rep2

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: F1_K4me3_rep2

value: Human induced pluripotent stem cells (hiPSCs)

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: Cardiac fibroblasts, 24h-NC-2


title: Cardiac fibroblasts, 48h-E-A-1


title: MN_CHIP_Isl1_1

value: ESC derived motor neuron


title: F1_K27me3_rep2

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: Cardiac fibroblasts, 24h-E-A-1


title: multiple myeloma patient 57

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 57

value: at diagnosis


title: F1_Input_2


title: e14.5_sn_atac_3

source_name: Trkc::mCherry e14.5 sensory neuron

extract_protocol:
ATAC-seq libraries were prepared as described previously13. Approximately 20,000- 50,000 cells were lysed in hypotonic buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to isolate nuclei and pelleted at 800g for 6 min. The nuclear pellet was resuspended in 50 μL of the transposase reaction mix (Illumina DNA Library Preparation Kit, FC-121-1030) containing 2.5 μL Tn5 transposase, 25 μL 2xTD buffer, 22.5 uL nuclease-free water, and then incubated for 30 min at 37°C. Following transposition reaction DNA was purified using DNA-5 purification kit (Zymo Research). The purified DNA was PCR amplified with sequencing adaptors, purified using AMPure XP beads (Beckman Coulter), and sequenced by 38bp paired- end sequencing on an Illumina NextSeq 500. ATAC-Seq data was aligned using Bowtie2 to build version NCBI38/mm10 assembly of the mouse genome. Peaks were called using MACS248. Cell specific and shared ATAC peaks were identified using intersectBED from bedtools52.
Standard Illumina protocols for Tru-Seq

value: Trkc::mCherry e14.5 sensory neuron

value: mouse embryonic day 14.6

value: FACS purified RFP+


title: Cardiac fibroblasts, 24h-ATP-2

value: Immortalized cardiac fibroblast

value: wild type

value: ATP conditioned medium


title: multiple myeloma patient 54

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 54


title: multiple myeloma patient 55

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 55


title: Cardiac fibroblasts, 24h-ATP-1

value: 24 hours


title: multiple myeloma patient 56

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 56


title: Cardiac fibroblasts, 24h-AMP-2

value: AMP conditioned medium


title: Cardiac fibroblasts, 24h-AMP-1


title: multiple myeloma patient 53

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 53


title: F5e_K4me3_rep1


title: F5e_CTCF_rep1

value: anti-CTCF (rabbit monoclonal, CST, D31H2)


title: F5e_K27me3_rep1


title: F5e_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: F5e_K27ac_rep1


title: multiple myeloma patient 52

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 52

value: multiple myeloma


title: e13.5_mn_atac_2

source_name: Chat::nucGFP e13.5 motor neuron

value: Chat::nucGFP e13.5 motor neuron

value: mouse embryonic day 13.5

value: FACS purified GFP+


title: e13.5_mn_atac_1


title: e14.5_sn_atac_2

value: mouse embryonic day 14.5


title: e10.5_mn_atac_3

source_name: Hb9::GFP e10.5 motor neuron

value: Hb9::GFP e10.5 motor neuron

value: mouse embryonic day 10.5


title: e14.5_sn_atac_1

value: Trkc::mCherry e14.5 sensory neuron


title: LIPA mouse on FPC diet 39

city: Minneapolis

first: Douglas

last: Mashek

state: MINNESOTA

address: 321 Church St. SE, Suite 6-155

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.1.0) using the mouse genome (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Genome_build: mm10

source_name: liver

growth_protocol: Mice were fed a control or FPC diet for 16 weeks

extract_protocol:
Samples were extracted using a combined TRIzol/RNAeasy prep
total RNA samples were converted to Illumina sequencing libraries using Illumina’s (San Diego, CA) TruSeq RNA Sample Preparation Kit (Cat. # RS-122-2001 or RS-122-2002) or Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2101).

treatment_protocol: Mice were injected with an AAV to overexpress GFP or LIPA 1 week before diet started

tag: overexpression

value: LIPA

tag: diet

value: FPC diet


title: multiple myeloma patient 58

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 58

value: at diagnosis


title: Cardiac fibroblasts, 48h-ATP-1

source_name: Cardiac fibroblast

value: Immortalized cardiac fibroblast

tag: strain

value: wild type

value: 48 hours


title: e10.5_mn_atac_2


title: F4e_CTCF_rep1

value: Human induced pluripotent stem cells (hiPSCs)


title: multiple myeloma patient 50

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 50


title: e10.5_mn_atac_1


title: LIPA mouse on FPC diet 34


title: F4e_K27me3_rep1

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: multiple myeloma patient 49

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 49


title: multiple myeloma patient 48

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 48


title: invitro_mn_atac.2

source_name: ESC derived motor neuron

value: ESC derived motor neuron

value: 129/Ola embryonic motor neurons

value: Cultured in ADFNK for 2 days followed by RA/DOX for 2 days to induce motor neuron differntiation

value: pure population


title: multiple myeloma patient 47

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 47

value: multiple myeloma


title: LIPA mouse on FPC diet 31


title: invitro_mn_atac.1


title: LIPA mouse on FPC diet 33


title: F4e_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: GFP mouse on FPC diet 20

value: GFP


title: e14.5_sn_rna_2

extract_protocol:
For mESC and mESC-derived motor neurons total RNA was extracted from approximately 200k cells using TRIzol reagent (Life Technologies) followed by isopropanol precipitation. RNA was treated with DNase-I to ensure no DNA contamination followed by acidic- phenol:chloroform extraction and another precipitation. Following RNA quality control on BioAnalyzer ribosomal RNA was depleted using the Illumina Ribo-Zero rRNA Removal Kit (MRZH116). RNA-seq libraries were prepared for sequencing using total RNA following standard Illumina protocols for 150nt kit, and sequenced by 76bp paired end sequencing on Illumina HiSeq 2000 or NextSeq500. FACS sorted primary neuron samples were prepared similarly, except RNA was purified from approximately 50k-100k cells and ribosomal RNA was depleted using Kapa Ribo Erase. Sequencing data was aligned to build version NCBI38/mm10 assembly of the mouse genome using in the STAR (Spliced Transcripts Alignment to a Reference) alignment algorithm version2.3.143. The relative abundances of transcripts were computed using the Cufflinks package release 2.2.144. Differential expression analysis was performed using the edgeR package45. For differential expression genes were required to have a minimum average gene expression value of FPKM>=1 in at least one condition, p-value <.01 and logFC > |2|.
Standard Illumina protocols for Tru-Seq

value: mouse embryonic day 14.5

value: FACS purified RFP+


title: F5e_Input_1


title: multiple myeloma patient 51

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 51


title: LIPA mouse on FPC diet 36

value: LIPA


title: e14.5_sn_rna_1

source_name: Trkc::mCherry e14.5 sensory neuron

value: Trkc::mCherry e14.5 sensory neuron


title: multiple myeloma patient 46

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 46

value: at diagnosis


title: F4e_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: F4e_K27ac_rep1

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: F4e_Input_1


title: M0 macrophage co-culture

city: Baltimore

first: Lei

last: Zheng

state: Maryland

address: 1650 Orleans Street, CRB I Rm 351

department: Department of Oncology

institute: Johns Hopkins University

description: M0 macrophages+ Panc 10.05

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina’s Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing: Data were extracted using Methylation Module of GenomeStudio v1.0 Software.

label: Cy3, Cy5

source_name: human PBMC derived macrophges

label_protocol: Standard Illumina Protocol

extract_protocol: Lysates were clarified from macrophages and genomic DNA was isolated by a QIAamp DNA Micro Kit (Qiagen). Genomic DNA quality was assessed by low concentration agarose gel (0.6%) electrophoresis and fluorescent spectrometry with PicoGreen DNA Kit(Life Technologies).

tag: tissue

value: peripheral blood

tag: individual

value: Healthy donor

value: PBMC-derived macrophages

tag: phenotype

tag: culture type

value: co-culture


title: e13.5_mn_rna_2

value: Chat::nucGFP e13.5 motor neuron

value: mouse embryonic day 13.5

value: FACS purified GFP+


title: multiple myeloma patient 45

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 45

value: multiple myeloma


title: F5_CTCF_rep1

tag: cell line

value: Human induced pluripotent stem cells (hiPSCs)

tag: chip antibody

value: anti-CTCF (rabbit monoclonal, CST, D31H2)


title: e13.5_mn_rna_1


title: GFP mouse on FPC diet 13

value: GFP

value: FPC diet


title: multiple myeloma patient 43

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 43


title: GFP mouse on FPC diet 12


title: F5_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: F5_K27me3_rep1

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: GFP mouse on purified diet 8

value: purified control diet


title: F5_K27ac_rep1


title: multiple myeloma patient 44

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 44

value: at diagnosis


title: multiple myeloma patient 41

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 41


title: GFP mouse on FPC diet 11


title: e10.5_mn_rna_1

source_name: Hb9::GFP e10.5 motor neuron

value: Hb9::GFP e10.5 motor neuron

value: mouse embryonic day 10.5


title: e10.5_mn_rna_3


title: e10.5_mn_rna_2


title: M2-like macrophage co-culture

description: M2-like macrophages+ Panc 10.05

value: peripheral blood

value: Healthy donor


title: F5_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: M0 macrophage single culture

description: M0 macrophages

value: PBMC-derived macrophages

value: single culture


title: M2-like macrophage single culture

description: M2-like macrophages


title: multiple myeloma patient 40

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 40


title: invitro_mn_rna.3

value: ESC derived motor neuron

value: 129/Ola embryonic motor neurons

value: Cultured in ANDFK for 2 days followed by RA/DOX for 2 days to induce motor neuron differntiation

value: pure population


title: multiple myeloma patient 42

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 42

value: multiple myeloma


title: M1-like macrophage co-culture

description: M1-like macrophages+ Panc 10.05

value: co-culture


title: GFP mouse on FPC diet 19

source_name: liver

value: GFP

value: FPC diet


title: GFP mouse on FPC diet 16


title: GFP mouse on purified diet 7

value: purified control diet


title: multiple myeloma patient 39

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 39

value: at diagnosis


title: LIPA mouse on FPC diet 37b

value: LIPA


title: F5_Input_1

value: Human induced pluripotent stem cells (hiPSCs)


title: multiple myeloma patient 38

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 38


title: GFP mouse on purified diet 6


title: M2_CTCF_rep1

value: anti-CTCF (rabbit monoclonal, CST, D31H2)


title: M2_K27me3_rep1

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: multiple myeloma patient 37

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 37


title: multiple myeloma patient 36

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 36


title: M2_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: GFP mouse on purified diet 3


title: invitro_mn_rna.2

source_name: ESC derived motor neuron


title: invitro_mn_rna.1


title: es_rna.3

source_name: mESC

value: mESC

value: 129/Ola embryonic stem cells

value: Cultured in 2i + LIF


title: multiple myeloma patient 35

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 35


title: es_rna.2


title: M2_K27ac_rep1

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: GFP mouse on purified diet 1


title: GFP mouse on purified diet 2


title: P300KO_TET2KO_H3_ChIPseq_Rep1

data_processing:
Base calling using Illumina RTA 2.4.11
Reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18).
Fastq files were aligned to mouse mm10 using BWA (v0.7.13 aln -q 5 -l 32 -k 2).
Aligned files were deduplicated using Picard Mark Duplicates (v2.10.6).
Genome_build: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig fold enrichment signal files were generated using Macs2 (v2.1.1.20160309) using H3 as control.

source_name: Lin- bone marrow cells

extract_protocol:
5 ug of chromatin from Lin- cells and 1 ug of H3K27ac antibody (Diagenode #15410196 lot#A1723-0041D) or H3 total antibody (Abcam ab24834 lot#GR174196-14) were combined with 10 ng of chromatin from Drosophila melanogaster S2 cells (Active Motif 53083) as spike-in control.
Libraries were generated using NEBNExt Ultra II DNA library prep kit for Illumina
Libraries were sequenced single-end in an Illumina Nextseq 500

tag: genotype

value: p300 Tet2 Knockout

value: Lin- bone marrow cells


title: Sample_135687_d

first: Vibha

middle: N.

last: Lama

state: Michigan

address: 1150 W. Medical Center Drive

department: Internal Medicine

data_processing:
10x Genomics Cell Ranger 3.0.0
The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (part number 1000268) following the manufacturer’s protocol.
The libraries were run on an Agilent TapeStation 4200 (part number G2991BA) for library quality control before sequencing.
Libraries were sequenced on a NovaSeq6000 with the following run configuration: Read 1 - 150 cycles; i7 index read - 8 cycles; Read 2 - 150 cycles. The total number of cells recovered was 11,118.
Genome_build: mm10
Supplementary_files_format_and_content: differential_expression.csv: table indicating which features are differentially expressed in each cluster relative to all other clusters
Supplementary_files_format_and_content: metrics_summary.csv: summary of Number of Cells,Mean Reads per Cell, etc
Supplementary_files_format_and_content: html file containing summary of the processed data
Supplementary_files_format_and_content: Cell Ranger output for cell level counts

source_name: CD45neg CD31neg cells

growth_protocol: Tamoxifen-dosed Gli1CreERT2/WT;Rosa26mTmG/WT B6D2F1/J mice of age ~8 weeks were used.

extract_protocol:
Single Cell 3' v3
RNA libraries were prepared for sequencing using single cell gene expression (3/ GEX); Cell Ranger Version 3.0.0

treatment_protocol: Lungs from Gli1CreERT2/WT;Rosa26mTmG/WT B6D2F1/J mice were harvested, sorted for CD45neg CD31neg cells

value: Gli1_Cre_ERT2/WT; Rosa_mTmG/WT mouse

value: lung

tag: age

value: 8 weeks


title: Sample_135687_c


title: multiple myeloma patient 34

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 34

value: multiple myeloma


title: M2_Input_1

tag: cell type

tag: controled by


title: Sample_135687_b


title: TET2KO_H3_ChIPseq_Rep1

value: Tet2 Knockout


title: F4_CTCF_rep1


title: multiple myeloma patient 32

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 32

value: at diagnosis


title: Sample_135687_a


title: multiple myeloma patient 31

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 31


title: F4_K27me3_rep2


title: es_rna.1

tag: background

tag: conditions

value: pure population


title: multiple myeloma patient 30

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 30

tag: disease


title: hashpool 2

city: Copenhagen N

first: Morten

last: Dall

address: BLEGDAMSVEJ 3B, BLDG. 7.7

country: Denmark

institute: University of Copenhagen

description:
Hashpool for sample identification (pooled)
HTO_count_matrix.csv

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000.
Fastq files were generated using cellranger 5.0.1.
Reads were mapped with Alevin onto the GRCm38 mouse genome assembly, with the GENCODE version M25 gene model
Raw data were filtered to retain nHTOcounts with more than 100 and less than 1250 counts. Counts were HTO normalized and demultiplexed, and negatives were removed. Singles were subset, and data were further subset by RNA features, where singles with more than 0 and less than 5500 features were retained. Data were normalized using the SCTransform function.
Genome_build: m38
Supplementary_files_format_and_content: csv files containing a count matrix, a matrix of counts following SCTransformation, and a HTO count matrix used to assess cell origin.

source_name: Liver

extract_protocol:
Tissue was crushed on liquid nitrogen and a small amount was transferred to a non-stick Eppendorph tube and was added 1.5 mL lysis buffer (Pure lysis buffer (L9286-180ml, Sigma) w. 0.1% DTT (43816-10ml, Sigma) and 1% Triton (T1565-1.7ml, Sigma)). Samples were incubated on ice for 5 min and were carefully pipetted up and down during the incubation. Samples were centrifuged for 5 min at 750 g at 4 °C and the supernatant was removed. Pellet was resuspended in 1 mL nuclei buffer (PBS, w/o MgCl₂ and CaCl₂ (20012068, Invitrogen), 1% BSA (SRE0036-25ml, Sigma), 2 mM MgCl2 (M1028-100ml, Sigma) and 0.1 % Protector RNase inhibitor 40U/µl (3335399001, Sigma), and solution was passed through a 40 µm strainer (43-10040-40, Pluriselect). Samples were incubated for 10 min on ice and centrifuged for 5 min at 750 g at 4 °C. Supernatant was removed and the pellet was resuspended in 110 µL nuclei buffer. For each sample, the remaining 100 µL were added 1 µL of individual TotalSeq™-A antibodies (BioLegend, San Diego, CA) from 0.5 µg/µl stocks to enable multiplexing . Samples were incubated for 30 min on ice, and each sample was added 1 mL nuclei buffer. Samples were centrifuged 10 min at 1000 g at 4 °C, and the supernatants were discarded. Pellets were resuspended in 200 µL Nuclei Freeze Buffer (EZ Nuclei Storage Buffer (NUC101, Sigma), 0.1% BSA (SRE0036-25ml, Sigma) and 2 mM MgCl2 (M1028-100ml, Sigma)) and were stored at -80 °C until sorting.
Using a SH800S Cell Sorter (SONY) 4,250 nuclei from each of the 6 samples was sorted and pooled for generation of libraries for snRNA-seq using the 10x Genomics Chromium single-cell 3′ reagent kits (version 3.1).

value: Liver

tag: genotypes

value: C57BL6/BomTac Nampt cKO (wildtype) and C57BL6/BomTac Alb-Cre Nampt cKO (knockout)


title: multiple myeloma patient 33

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 33

tag: disease stage


title: multiple myeloma patient 29

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 29


title: F4_K27ac_rep2

value: Human induced pluripotent stem cells (hiPSCs)


title: P300KO_TET2KO_H3K27ac_ChIPseq_Rep1


title: WT_H3_ChIPseq_Rep1

value: WT


title: multiple myeloma patient 28

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 28


title: F4_K9me3_rep2

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: TET2KO_H3K27ac_ChIPseq_Rep1


title: pool2

description:
Single nucleus from liver of 3 WT and 3 hepatocyte-specific Nampt knockout mice (pooled).
SCT_count_matrix.csv


title: M2_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: P300KO_H3K27ac_ChIPseq_Rep1

value: p300 Knockout


title: pool1


title: multiple myeloma patient 27

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 27


title: M1_CTCF_rep1

value: anti-CTCF (rabbit monoclonal, CST, D31H2)


title: F4_Input_2


title: multiple myeloma patient 26

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 26


title: Liver sample 548 - WT

data_processing:
Libraries were subjected to 51-bp paired-end sequencing on a NovaSeq 6000 system (Illumina)
Bcl2fastq software (Illumina) was used for Fastq file generation
STAR v2.7.2b was used to align sequence reads onto the GRCm38 mouse genome assembly, with the GENCODE version M22 gene model
Reads were summarized onto genes by featureCounts v1.6.4
Genome_build: m38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Female hepatocyte-specific Nampt knockout mice and WT littermates were fed an L-amino acid defined purified diet (A06071314, Research Diets) for 3-5 weeks from 10-12 weeks of age.

extract_protocol:
RNA was extraced from full liver/cell pellets using trizol, followed by Rneasy mini kits
Libraries were constructed followed using the Illumina TruSeq Stranded total RNA Gold protocol.
500 ng RNA pr sample was depleted of rRNA by RiboZero beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads

treatment_protocol: Primary mouse hepatocytes were isolated using collagenase perfusion

tag: tissue/cell type

tag: background strain

value: BomTac Nampt cKO (wildtype)


title: WT_H3K27ac_ChIPseq_Rep1

value: Lin- bone marrow cells


title: P300KO_H3_ChIPseq_Rep1


title: PFC_AAVNsun2_2_ValAAC

data_processing:
Library strategy: Bisulfite tRNA-seq
Bisulfite tRNA sequencing raw fastq files were analyzed using Bisamp publicly available web server.

source_name: Mouse prefrontal cortex

extract_protocol:
1ug of total RNA was used for bisulfite conversion with the EZ RNA Methylation kit according to manufacturer’s instructions (Zymo Research). Due to the strong secondary structure of tRNAs, the PCR step during bisulfite conversion was repeated 3 times consecutively, as previously reported to completely denature tRNAs.  Following bisulfite treatment and clean-up, we performed cDNA synthesis using the reverse primer for each tRNA isodecoder.  Targeted cDNA was then PCR-amplified with the tRNA-specific forward primer and products were size-verified on a 4% agarose gel. PCR amplicons (~120nt including tRNA amplicon and overhangs for adapter ligation) were then extracted and purified (Qiaquick Gel Extraction Kit, Qiagen).  We labelled each amplicon with a unique index (Nextera XT, Illumina) and pooled up to 20 amplicons in equimolar concentrations before next-gen sequencing. Note that only read 1 from paired end sequencing was used for analysis.
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

tag: tissue type

value: Prefrontal cortex

tag: strain

value: WT C57BL/6, AAV-Nsun2 injection

tag: developmental stage

value: Adult

tag: molecule

value: Bisulfite-treated total RNA


title: Liver sample 562 - HNKO

value: BomTac Alb-Cre Nampt cKO (knockout)


title: F4_K4me3_rep2

tag: cell line


title: PFC_AAVGFP2_ValAAC

value: WT C57BL/6, AAV-GFP injection


title: Liver sample 564 - WT


title: M1_K9me3_rep2

tag: chip antibody


title: multiple myeloma patient 24

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 24

value: multiple myeloma

value: at diagnosis


title: Cell suspension sample 546 - HNKO

description: 546 CS

source_name: Cell Suspension

value: Hepatocytes

tag: genotype


title: multiple myeloma patient 25

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 25


title: M1_K27me3_rep2

value: Human induced pluripotent stem cells (hiPSCs)

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: Primary Hepatocytes sample 554 - WT

source_name: Primary Hepatocytes


title: PFC_AAVNsun2_1_ValAAC


title: PFC_AAVGFP1_ValAAC


title: Cell suspension sample 540 - HNKO

description: 540 CS


title: M1_K4me3_rep2


title: M1_Input_2


title: multiple myeloma patient 22

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 22


title: KO2_ValAAC

source_name: Mouse cortex

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.


title: multiple myeloma patient 23

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 23


title: M1_K27ac_rep2

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: WT2_ValAAC

value: Nsun2 floxed, Camk2a-Cre neg.


title: multiple myeloma patient 20

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 20


title: multiple myeloma patient 21

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 21


title: F3_K119ub1_rep1

value: anti-H2AK119ub1 (rabbit monoclonal, CST, D27C4)


title: Liver sample 558 - WT

value: Liver

value: BomTac Nampt cKO (wildtype)


title: Primary Hepatocytes sample 558 - WT


title: KO1_ValAAC


title: multiple myeloma patient 19

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 19


title: F3_K27me3_rep1


title: WT1_ValAAC


title: Primary Hepatocytes sample 542 - HNKO


title: F3_K9me2_rep1

value: anti-H3K9me2 (mouse, MBL, MABI0307)


title: M1-like macrophage single culture

description: M1-like macrophages

source_name: human PBMC derived macrophges

tag: tissue

value: peripheral blood

tag: individual

value: Healthy donor

value: PBMC-derived macrophages

tag: phenotype

tag: culture type

value: single culture


title: multiple myeloma patient 18

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 18

value: multiple myeloma


title: PFC_AAVNsun2_2_ProTGG

value: Prefrontal cortex

value: WT C57BL/6, AAV-Nsun2 injection

value: Adult

value: Bisulfite-treated total RNA


title: Cell suspension sample 554 - WT

description: 554 CS

value: Hepatocytes


title: PFC_AAVGFP2_ProTGG

value: WT C57BL/6, AAV-GFP injection


title: Primary Hepatocytes sample 548 - WT


title: multiple myeloma patient 17

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 17

value: at diagnosis


title: F3_K27ac_rep1

tag: cell type

value: Human induced pluripotent stem cells (hiPSCs)

value: anti-H3K27Ac (mouse, gift from H. Kimura)

tag: controled by


title: Liver sample 540 - HNKO

source_name: Liver

value: Liver

value: BomTac Alb-Cre Nampt cKO (knockout)


title: multiple myeloma patient 15

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 15

tag: disease


title: F3_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: Liver sample 544 - WT

value: BomTac Nampt cKO (wildtype)


title: multiple myeloma patient 16

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 16

tag: disease stage


title: F3_Input_1


title: PFC_AAVNsun2_1_ProTGG

source_name: Mouse prefrontal cortex


title: multiple myeloma patient 14

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 14


title: F3_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: KO2_ProTGG

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.


title: Liver sample 554 - WT

tag: tissue/cell type


title: WT2_ProTGG

value: Nsun2 floxed, Camk2a-Cre neg.


title: multiple myeloma patient 12

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 12

value: multiple myeloma


title: F2_K27me3_rep1

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: KO1_ProTGG

value: Adult


title: Cell suspension sample 566 - HNKO

description: 566 CS

source_name: Cell Suspension

tag: background strain


title: F2_K9me2_rep1

value: anti-H3K9me2 (mouse, MBL, MABI0307)


title: WT1_ProTGG

tag: tissue type

value: Bisulfite-treated total RNA


title: multiple myeloma patient 11

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 11


title: F2_K9me3_rep1


title: Primary Hepatocytes sample 566 - HNKO

source_name: Primary Hepatocytes

value: Hepatocytes


title: multiple myeloma patient 10

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 10

value: at diagnosis


title: PFC_AAVGFP1_ProTGG

value: Prefrontal cortex

tag: strain

value: WT C57BL/6, AAV-GFP injection


title: multiple myeloma patient 09

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 09


title: F2_K4me3_rep1

value: Human induced pluripotent stem cells (hiPSCs)


title: multiple myeloma patient 07

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 07


title: Primary Hepatocytes sample 544 - WT


title: PFC_AAVNsun2_3_GluCTC

value: WT C57BL/6, AAV-Nsun2 injection

tag: developmental stage


title: Cell suspension sample 562 - HNKO

description: 562 CS

value: BomTac Alb-Cre Nampt cKO (knockout)


title: F2_K119ub1_rep1

value: anti-H2AK119ub1 (rabbit monoclonal, CST, D27C4)


title: PFC_AAVGFP3_GluCTC

tag: molecule


title: F2_K27ac_rep1

tag: cell line

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: F2_Input_1

tag: chip antibody


title: multiple myeloma patient 08

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 08


title: Cell suspension sample 558 - WT

description: 558 CS

tag: genotype

value: BomTac Nampt cKO (wildtype)


title: PFC_AAVNsun2_2_GluCTC


title: multiple myeloma patient 13

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 13


title: PFC_AAVGFP2_GluCTC


title: multiple myeloma patient 06

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 06


title: PFC_AAVGFP1_GluCTC


title: Liver sample 552 - HNKO

value: Liver


title: Cell suspension sample 548 - WT

description: 548 CS


title: F1_K27me3_rep1


title: PFC_AAVNsun2_1_GluCTC


title: Cell suspension sample 542 - HNKO

description: 542 CS


title: F1_K9me2_rep1


title: multiple myeloma patient 04

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 04


title: Primary Hepatocytes sample 564 - WT


title: Primary Hepatocytes sample 562 - HNKO

description: 562 PH


title: F1_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: F1_K119ub1_rep1


title: F1_K27ac_rep1


title: Primary Hepatocytes sample 546 - HNKO


title: WT4_GluCTC

source_name: Mouse cortex

value: Cortex

value: Nsun2 floxed, Camk2a-Cre neg.


title: WT3_GluCTC

value: Adult


title: KO3_GluCTC

value: Nsun2 floxed, Camk2a-Cre pos.


title: multiple myeloma patient 01

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 01

value: multiple myeloma


title: F1_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: Liver sample 542 - HNKO

source_name: Liver


title: multiple myeloma patient 02

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 02

value: at diagnosis


title: F1_Input_1


title: WT2_GluCTC

value: Bisulfite-treated total RNA


title: Cell suspension sample 544 - WT

description: 544 CS

value: Hepatocytes


title: multiple myeloma patient 05

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 05


title: KO2_GluCTC


title: Primary Hepatocytes sample 552 - HNKO


title: F4_K119ub1_rep1

value: Human induced pluripotent stem cells (hiPSCs)


title: F4_K27me3_rep1

value: anti-H3K27me3 (mouse, gift from H. Kimura)


title: KO1_GluCTC


title: Primary Hepatocytes sample 556 - WT


title: WT1_GluCTC


title: Liver sample 556 - WT


title: multiple myeloma patient 03

description: Hybridized to Affymetrix DMET array

source_name: multiple myeloma patient 03


title: KO4_GluCTC


title: F4_K9me3_rep1


title: PFC_AAVNsun2_5_AspGTC

source_name: Mouse prefrontal cortex

value: Prefrontal cortex

value: WT C57BL/6, AAV-Nsun2 injection


title: F4_K9me2_rep1

value: anti-H3K9me2 (mouse, MBL, MABI0307)


title: F4_K4me3_rep1


title: F4_K27ac_rep1

value: anti-H3K27Ac (mouse, gift from H. Kimura)


title: PFC_AAVGFP5_AspGTC

value: WT C57BL/6, AAV-GFP injection


title: infertile_61099

type: RNA

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Gene expression data from sperm.

hyb_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with PARTEK Genomics Suite 6.6 (Partek, Inc., Chesterfield, MO, USA) using GC-MRA as normalization method.

label: biotin

source_name: sperm sample from infertile men but with no morphologic abnormality

extract_protocol: RNA extraction. Fresh sperm samples were resuspended and stored in RNAlater solution. Shipping was at room temperature with subsequent storage at -80°C. Immediately after thawing at room temperature, the samples were centrifuged at 16,000 x g for 10 minutes at 4°C The cell pellet was lysed by 1 ml Trizol (Invitrogen, Carlsbad, CA, USA). After chloroform extraction, the supernatant was mixed 1:1 with 96% ethanol and applied to RNeasy spin columns (Qiagen, Germantown, MD, USA). DNase I (Qiagen) was applied to the column according to the manufacturer´s protocol. Washing the column and DNA elution was according to the manufacturer´s protocol. DNase treatment or double column purification is necessary for removal of degraded DNA, which cannot be achieved by standard protocol.

tag: subject status

value: infertile but with no morphologic abnormality

value: sperm


title: infertile_60999

description: Gene expression data from sperm.

label_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual


title: Liver sample 566 - HNKO

value: Liver

value: BomTac Alb-Cre Nampt cKO (knockout)


title: PFC_AAVNsun2_4_AspGTC

value: Adult


title: F4_Input_1


title: Cell suspension sample 564 - WT

description: 564 CS

source_name: Cell Suspension

value: BomTac Nampt cKO (wildtype)


title: PFC_AAVGFP4_AspGTC


title: infertile_60992

description: Gene expression data from sperm.


title: M1_K119ub1_rep1

value: anti-H2AK119ub1 (rabbit monoclonal, CST, D27C4)


title: infertile_58494

description: Gene expression data from sperm.


title: infertile_58788

description: Gene expression data from sperm.


title: fertile_control_62484

description: Gene expression data from sperm.

source_name: sperm sample from fertile men (i.e. conception within past year from sampling)

value: fertile (i.e. conception within past year from sampling)


title: infertile_61000

description: Gene expression data from sperm.


title: PFC_AAVNsun2_3_AspGTC

value: Bisulfite-treated total RNA


title: Primary Hepatocytes sample 540 - HNKO

source_name: Primary Hepatocytes

value: Hepatocytes


title: M1_K27me3_rep1

value: Human induced pluripotent stem cells (hiPSCs)


title: Cell suspension sample 552 - HNKO

description: 552 CS


title: PFC_AAVNsun2_2_AspGTC


title: Liver sample 546 - HNKO


title: PFC_AAVGFP3_AspGTC


title: PFC_AAVGFP2_AspGTC


title: M1_K9me3_rep1

value: anti-H3K9me3 (mouse, gift from H. Kimura)


title: fertile_control_58784

description: Gene expression data from sperm.


title: Cell suspension sample 556 - WT

description: 556 CS


title: M1_K27ac_rep1


title: hashpool 1

tag: tissue

tag: genotypes

value: C57BL6/BomTac Nampt cKO (wildtype) and C57BL6/BomTac Alb-Cre Nampt cKO (knockout)


title: PFC_AAVGFP1_AspGTC

value: Prefrontal cortex


title: neutrophil DREAM KO 120 rep3

city: Austin

first: Mijeong

last: Kim

state: Texas

address: 2500 Speedway

institute: The University of Texas at Austin

data_processing:
The reads were aligned to the mouse transcriptome (mm10) using a default setting of STAR (v.020201).
Aligned reads were counted using HTseq (v. 0.6.1p1).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include TPM values for each sample

source_name: neutrophil

extract_protocol:
Mouse bone marrow neutrophils were enriched using a mouse neutrophil isolation kit (Miltenyi Biotec). Total RNAs were isolated using the RNeasy Plus Mini Kit (Qiagen)
300 ng of total RNA was used to generate RNA-seq library using the NEBNext Ultra II RNA Library Prep kit (NEB) according to the manufacturer’s instruction.

treatment_protocol: Bone marrow neutrophils isolated from WT and KO mice were treated without or with 20 ng/ml TNF-alpha for 30 or 120 minutes.

value: DREAM KO


title: neutrophil DREAM KO 120 rep1


title: neutrophil DREAM KO 120 rep2


title: fertile_control_58872

description: Gene expression data from sperm.


title: M1_K4me3_rep1

value: anti-H3K4me3 (mouse, gift from H. Kimura)


title: neutrophil WT 120 rep3

value: wild type


title: fertile_control_58373

description: Gene expression data from sperm.


title: PFC_AAVNsun2_1_AspGTC

last: Blaze

value: WT C57BL/6, AAV-Nsun2 injection


title: neutrophil WT 120 rep2


title: M1_K9me2_rep1

value: anti-H3K9me2 (mouse, MBL, MABI0307)


title: fertile_control_57968

description: Gene expression data from sperm.

value: sperm


title: M1_Input_1


title: fertile_control_57820

description: Gene expression data from sperm.


title: neutrophil WT 120 rep1


title: Homo_NC-iPSCs

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

country: China

institute: Jinan University

data_processing:
Clean reads were obtained by removing adapter dimers,, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats in the NCBI GenBank, Repbase, and Rfam databases.
Clean reads then were gathered and mapped to miRbase database (Release 22) by BLAST.
The identified miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2 × 2 test, Chi-squared nXn test, Student’s t-test, and ANOVA based on the experiments design.
Genome_build: GRCH38
Supplementary_files_format_and_content: Excel files include normalized expression values for each Sample.

source_name: The normal control human iPSCs (NC-iPSCs)  that were induced from urine of healthy donor by the same methods were purchased from Cellapy Biotechnology (Beijing, China).

extract_protocol:
Total RNA was extracted from the ADO2-iPSCs and NC-iPSCs using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s methods.
The urine-derived iPSCs were used for small RNA sequencing  library preparation according to the manufacturer's instruction.

value: Urine cells

value: human iPSCs


title: WT4_AspGTC

first: Jennifer

address: 1470 Madison Ave 9-202

institute: Icahn School of Medicine at Mount Sinai

value: Cortex

value: Nsun2 floxed, Camk2a-Cre neg.

value: Adult


title: asthenoteratozoospermia_61291

description: Gene expression data from sperm.

source_name: sperm sample with asthenoteratozoospermia

value: infertile; asthenoteratozoospermia


title: neutrophil DREAM KO 30 rep3


title: Homo_ADO2-iPSCs

source_name: The disease-specific ADO2-iPSCs with the mutation of CLCN7 (R286W) generated from urine of the proband in our previous studies.


title: asthenoteratozoospermia_61185

description: Gene expression data from sperm.


title: KO3_AspGTC

value: Nsun2 floxed, Camk2a-Cre pos.

value: Bisulfite-treated total RNA


title: WT3_AspGTC


title: C. albicans set1-KO rep2

city: Chuncheon-si, Gangwon-do

first: Jueun

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
Genome_build: Candida albicans SC5314 (PRJNA10701)

organism: Candida albicans

growth_protocol: C. albicans strains were grown in YPD media (1% yeast extracts, 2% peptone, 2% glucose) at 30˚C. Overnigh cultured cells were diluted to OD600 of 0.1 into fresh 10ml YPD and grown at 30˚C until OD600 of 1.0.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (MN, MN740955) according to the protocol of the manufacturer. For sequencing, mRNA was captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
A strand-specific sequencing library was synthesized using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, E7420) according to the instruction manual.


title: C. albicans set1-KO rep1


title: neutrophil DREAM KO 30 rep1


title: WT2_AspGTC

city: New York


title: C. albicans WT rep2

value: clinical isolate


title: KO4_AspGTC


title: KO2_AspGTC


title: asthenoteratozoospermia_61120

description: Gene expression data from sperm.


title: C. albicans WT rep1


title: neutrophil WT 30 rep3


title: KO1_AspGTC


title: HealthyDonor_WholeBlood_Homo_rep4

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped using STAR_2.6.1d aligner.
FeatureCounts v2.0.0 was used to generate the raw counts.
Genome_build: human genome GRCh37.p13 (Genome Reference Consortium 622 Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009
Supplementary_files_format_and_content: raw read count .txt file

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
Total RNA from whole blood was extracted using the PAXgene Blood RNA Kit (PreAnalytiX).
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp
mRNA libraries were pooled and paired-end 150-bp sequencing was performed on the Illumina HiSeq4000 platform.

value: whole blood

tag: disease state

value: Healthy donor

tag: genotype_affected status

value: Homozygous non mutant


title: neutrophil DREAM KO rep3

value: DREAM KO


title: PFC_AAVNsun2_5_GlyGCC

value: Prefrontal cortex


title: asthenoteratozoospermia_58768

description: Gene expression data from sperm.


title: WT1_AspGTC


title: neutrophil DREAM KO 30 rep2


title: HealthyDonor_WholeBlood_Homo_rep3


title: HealthyDonor_WholeBlood_Homo_rep2


title: neutrophil DREAM KO rep2


title: asthenoteratozoospermia_58027

description: Gene expression data from sperm.


title: asthenoteratozoospermia_58761

description: Gene expression data from sperm.


title: asthenoteratozoospermia_61181

description: Gene expression data from sperm.


title: asthenozoospermia_61178

description: Gene expression data from sperm.

source_name: sperm sample with asthenozoospermia

value: infertile; asthenozoospermia


title: asthenozoospermia_61100

description: Gene expression data from sperm.


title: neutrophil WT 30 rep2

value: wild type


title: neutrophil DREAM KO rep1


title: PFC_AAVGFP5_GlyGCC

value: WT C57BL/6, AAV-GFP injection