title: Input_si

city: New York

first: Katerina

last: Hatzi

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

data_processing:
For ChIP-seq, raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg38) using BWA. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifacts and were excluded from the analysis. Read density tracks were visualized using the UCSC browser. Peak calling was performed using MACS[34]. Each ChIP-seq dataset was normalized to its corresponding input. Peaks were annotated based on the RefSeq database (hg38). Peaks localized +/2kb of the TSS were defined as promoter peaks, peaks localized +/2kb of the TES were defined as 30 end peaks, and peaks > 2kb away from genes were defined intergenic.
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: OCI-LY1 cells (lymphoma)

growth_protocol: IMDM 10% FBS, antibiotics

extract_protocol:
Briefly OCI-Ly1 were fixed, lysed, and sonicated to generate fragments less than 400 bp. Sonicated lysates were incubated with antibodies against LSD1 (abcam 17721), BCL6 (Santa Cruz N3, sc-858), H3K4me1 (abcam, ab8895) or IgG control (abcam, ab171870) and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA (quantified using Qubit 2.0 fluorometer, Invitrogen) was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 30 ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adaptor ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250 ± 25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30 s at 98oC, 15cycles of 10 at 98oC, 30 s at 65oC, 30 s at 72oC and 5min extension at 75oC). Q-PCR was repeated to confirm retention of relative enrichment.

treatment_protocol: For ChIP-seq experiments with cells treated with siRNAs, OCI-Ly1 cells were transfected using Nucleofector 96-well Shuttle system (Lonza) with 1uM siRNA against BCL6 (HSS100968) or non- targeted siRNA (46-2001) (Stealth RNAi, Invitrogen) for 24h.

tag: antibody

tag: sirna

value: BCL6 targeted siRNA


title: Input_NT

status: Public on Dec 12 2018

type: SRA

state: NY

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: control siRNA


title: H3K4me1_NT


title: Aneuploid population T2 from tetrad dissection rep 3

city: Baltimore

first: Hung-Ji

last: Tsai

state: Maryland

address: 855 N Wolfe Street

department: Cell Biology

institute: Johns Hopkins University

description:
Processed data file: AneuSeq_GEO_RawCounts.xlsx
Processed data file: AneuSeq_GEO_DESeq.xlsx

library_source: transcriptomic

data_processing:
Illumina RTA version 2.4.11 was used for base calling. Demultiplexing was done with Bcl2fastq 2.17.1.14.
Sequenced reads were checked for read quality using FastQC v.0.11.5, trimmed for adaptor sequence, then mapped to S288c whole genome using HISAT2 v2.0.5 with default parameters.
Read counts were extracted using HTSeq v.0.6.1p1 and significant differentially expressed genes were determined using DESeq2 v.1.14.1.
Genome_build: S288c R64-2-1
Supplementary_files_format_and_content: Excel files with gene-wise raw read counts and log2 fold change in aneuploid populations with respect to euploid populations.
Supplementary_files_format_and_content: AneuSeq_GEO_RawCounts.xlsx: Raw read counts by gene for all samples.
Supplementary_files_format_and_content: AneuSeq_GEO_DESeq.xlsx: Gene expression fold change.

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: YPD rich media overnight, followed by 4 hour refresh in YPD at 23 degree in 96 deep well plate format.

extract_protocol:
Master Pure Yeast RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: genotype

value: aneuploid


title: Aneuploid population T2 from tetrad dissection rep 2


title: H3K4me1_si


title: Aneuploid population T1 from tetrad dissection rep 1


title: Aneuploid population T1 from tetrad dissection rep 2


title: Euploid population from tetrad dissection rep 3

value: euploid


title: GFP_control_rep1

status: Public on Dec 13 2018

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Illumina NextSeq 500 / Illumina Four-Channel SBS Sequencing  for base calling
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2 (Kim et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads(counts) were computed using the Feature Counts method implemented in the Bioconductor v3.2 RSubread package (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include reads(counts) values for each sample.

source_name: SK-N-BE(2)-C neuroblastoma cell line

extract_protocol:
RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-40M reads/sample.

tag: status

value: GFP control

tag: treatment

value: vehicle


title: LSD1_NT


title: LSD1_si


title: BCL6_NT


title: BCL6_si


title: Euploid population from tetrad dissection rep 1


title: Haploid control rep 1

source_name: Haploid control


title: Haploid control rep 2


title: Aneuploid population T2 from tetrad dissection rep 1


title: 6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep2

status: Public on Dec 11 2018

city: Wageningen

first: Julien

last: Rougeot

state: Gerlderland

address: Droevendaalsesteeg 1  Building 107

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research

description: FACS-sorted

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1
Quality trimmed reads were aligned to the Ensembl zebrafish genome (Zv9) using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9_79 annotation containing few additional genes.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-separated value files include gene counts for each sample

organism: Danio rerio

source_name: zebra fish larvae

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.-Aldrich)

extract_protocol:
Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer, without RNA extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing (Clonetech) according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.

tag: tissue

value: 20 mpeg1 positive macrophages

tag: cell population

value: GFP-negative

tag: developmental stage

tag: caudal vain infection

value: M marinum M strain 125cfu


title: 6dpf mpeg1:mCherryPosMmarinumGFPPos_rep1

description: FACS-sorted

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.

value: GFP-positive


title: 6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep3

description: FACS-sorted


title: 6dpf mpeg1:mCherryPos_MmarinumGFPNeg_rep1

description: FACS-sorted


title: WT_G93a_Control_rep3

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control software version 2.0.12.0, RTA version 1.17.21.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence aligned and transcripts quantified using star2.5.3a, rsem1.3.0 and samtools 1.3
Genome_build: mm10
Supplementary_files_format_and_content: aherskov_counts.txt.gz  is parsed integer counts for samples from rsem
Supplementary_files_format_and_content: aherskov_lfpkm.txt.gz is parsed fpkm for samples from rsem transformed to log2 space by adding 1 to FPKM and calculating the log2 value

organism: Mus musculus

source_name: Spinal Cord

growth_protocol: Extruded spinal cords in cold phosphate bufffered saline

extract_protocol:
Trizol extraction and Qiagen RNA miniprep
Illumina tru-seq or Roche RNA KAPA Hyperprep

value: Wild type

tag: age

value: 5-6 months

tag: library prep

value: Illumina TruSeq


title: WT_G93a_Control_rep2


title: G93a_rep1


title: G93a_rep2


title: WT_G93a_Control_rep1


title: Old_rep4

value: 18-24 months

value: Roche RNA KAPA Hyperprep


title: Old_rep3


title: Old_rep6


title: Euploid population from tetrad dissection rep 2


title: Old_rep5


title: Old_rep2


title: Old_rep8


title: Old_rep7


title: Old_rep1


title: HIC6338

city: houston

first: Cynthia

middle: Perez

last: Estrada

state: TEXAS

address: 1 Baylor Plaza  Room 906B

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing: Fastq files were processed using Juicer, and the mega.sh script. For details see: Materials and methods; PGP1f Hi-C data processing

source_name: Fibroblast from Skin, Arm

growth_protocol: Human primary skin fibroblasts of donor PGP1 (GM23248, Coriell Institute; see Materials and methods: Cell culturing) were grown at 37°C + 5% CO2 in serum-supplemented (10% v/v) Dulbecco’s Modified Eagle Medium (DMEM) (serum Gibco 10437; media Gibco 10564). The cells were also supplemented with 1% (v/v) MEM Non-Essential Amino Acids Solution (Gibco 11140050). Penicillin and streptomycin (Gibco 15070) were also added to the cell culture media to final concentrations of 50 units/ml and 50 μg/ml, respectively.

extract_protocol: in situ Hi-C was used to probe the three-dimensional structure of the PGP1F genome

tag: passages

value: seven to nine

tag: cell type

value: Fibroblast (M23248, Coriell Institute)


title: HIC6339


title: 6dpf mpeg1:mCherryPosMmarinumGFPPos_rep3

description: FACS-sorted


title: Young_rep7

value: 3-4 months


title: Young_rep5


title: Young_rep8


title: 6dpf mpeg1:mCherryPosMmarinumGFPPos_rep2

description: FACS-sorted


title: G93a_rep3


title: HIC7862


title: HIC7863


title: Young_rep3


title: Young_rep4


title: HIC7864


title: Young_rep2


title: Young_rep1


title: HIC7145


title: HIC7147


title: HIC7146


title: EB45_REF(S3)

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

description:
processed data file: cpg.var.pulex.v2.vcf.gz
processed data file: pulex_snp_cgvIN.vcf.gz

data_processing:
Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score < 20) were removed with cutadapt (v.1.11) while processing both read pairs at the same time.
The filtered read were mapped to the reference genomes of Daphnia magna (daphmag2.4,GCA_001632505.1) and Daphnia pulex (PA42 v3.0,GCA_900092285.1) using bwa meth (v.0.10) for the bisulfite-treated samples and bwa mem (v.0.7.15-r1140) for non-bisulfite-treated samples, with default settings.
Genomic variants were called genome wide using the non-bisulfite-treated samples, with samtools mpileup (0.1.19), outputting per sample read depth, with minimum mapQ score set to 10 and without discarding anomalous read pairs. Single nucleotide polymorphism (SNP) genotypes per sample were called with bcftools (0.1.19), by excluding indels and sites were the reference was not A/C/T/G.
Single nucleotide polymorphism (SNP) at the CpG sites were called using the non-bisulfite-treated samples, with samtools mpileup (0.1.19). CpG's with observed SNP’s (with quality>50) were excluded from the methylation analysis.
Methylated CpG were called from mapped reads using MethylDackel (v0.2.1). Both singletons and discordant reads were retained, while reads with low mapping quality (<10) and nucleotides with low base calling quality (Phred<30) were excluded. Seven base pairs from the ends of reads were also excluded, as they showed an excessive amount of methylation.
Differential methylation analysis was done using methylKit (v.1.3.0).
Genome_build: GCA_001632505.1, GCA_900092285.1
Supplementary_files_format_and_content: bed (methylation counts at CpGs), vcf (SNP variation calls at CpGs), vcf (SNP variant calls genome wide)
Supplementary_files_format_and_content: txt (differential methylation analysis results: daphnia.magna.bham2.txt, daphnia.pulex.eb31.eb45.txt)

organism: Daphnia pulex

source_name: whole organism

growth_protocol: Daphnia magna Bham 2 clones were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in high hardness COMBO medium (HH COMBO). Media were prepared using a protocol adapted from Baer & Goulden (1998) and Kilham et al. (1998), and renewed once a week. Animals were fed every other day with Chlorella vulgaris at a concentration of ≈27,550 cells of algae per individual Daphnia. Daphnia pulex EB45 and 31 clones were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in standard COMBO medium (COMBO). Media were prepared using a protocol adapted from Kilham et al. (1998), and renewed every other day. Animals were fed every other day with Chlorella vulgaris at a concentration of ≈27,550 cells of algae per individual Daphnia.

extract_protocol:
Daphnia samples were flash frozen in liquid nitrogen and stored in -80C until further use. DNA was extracted from the samples using MasterPure DNA purification kit (Epicentre, USA) according to the method described in our previous publication (Gonçalves Athanasio et al, 2016).
Libraries for both sodium bisulfite treated samples and input DNA samples were prepared following the EpiGnome Methyl-Seq kit (Epicentre, USA) protocol. Briefly, DNA samples (50 ng for sodium bisulfite converted and 20 ng for non-converted samples) were diluted in 9 μL of nuclease-free water, mixed with 2 μL of DNA synthesis primer and incubated at 95°C for 5 minutes. Samples were placed on ice and 5 μL of the mastermix (containing 4 μL of EpiGnome DNA synthesis premix, 0.5 μL of 100 mM DTT and 0.5 μL of EpiGnome polymerase) was added to each sample. The reactions were incubated as 25°C for 5 minutes, 42°C for 30 minutes and 37°C for 2 minutes. Then, 1 μL of exonuclease I was added to each sample and incubated for 10 minutes at 37°C, 3 minutes at 95°C followed by 2 minutes at 25°C. DNA samples were tagged by addition of TT master mix (7.5 μL of EpiGnome terminal tagging premix and 0.5 μL of DNA polymerase). Samples were incubated at 25°C for 30 minutes followed by 3 minutes at 95°C. Reactions were cooled to 4°C and purified using AMPure XP system (1.6x beads) (Beckman Coulter Inc., USA) as recommended. The final step of library construction comprised the amplification of the libraries and addition of barcodes. Each reaction contained 22.5 μL of the purified tagged DNA, 25 μL of FailSafe PCR premix E, 1 μL EpiGnome forward primer, 1 μL of EpiGnome index PCR primer and 0.5 μL of FailSafe PCR enzyme (1.25 U). PCR was performed according to the manufactures guidelines. Amplified samples were purified using AMPure XP beads (1x beads). Samples were re-suspended in 20 μL of nuclease-free water and quantity and quality of the sequencing libraries were assessed. Daphnia magna and Daphnia pulex libraries were sequenced using Illumina HiSeq-2500 platform at the Environmental Omics Sequencing Facility, University of Birmingham, UK and NextSeq platform at the Centre for Genomics and Bioinformatics, Indiana University, USA, respectively.

treatment_protocol:
Maintained under standard condition with normal levels of oxygen (6 mg/L) for 3, 8 and 15 days
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).

value: Eloise Butler (45)

tag: clone

value: Clone 45

tag: gender

value: female

value: Mix of ages of 3, 8 and 15 days

tag: exposure

value: control

tag: culturing media

value: Standard COMBO

tag: replicate

tag: molecule subtype

value: Genomic DNA


title: EB45_REF(S6)

tag: strain


title: HIC7865

tag: cell line


title: HIC7866


title: Young_rep6

tag: genotype


title: EB45_RNA(F4)

data_processing:
Illumina adapters (using core sequence: AGATCGGAAGAGC) and nucleotides with low quality (Phred score<20) were removed with cutadapt (v.1.11).
The filtered reads were mapped to the reference genome (GCA_900092285.1) using tophat2 (v.2.1.0).
The read counts for genes were extracted with HTSeq (v.0.9.1) using unstranded union mode for genes. The read counts were converted to FPKM values for expression analysis.
Genome_build: GCA_900092285.1
Supplementary_files_format_and_content: txt (gene expression count and FPKM values from RNA-seq mapping: GSF1035-F.expression.txt)

molecule: polyA RNA

growth_protocol: Daphnia pulex Eloise Butler strains were maintained in standard COMBO.

extract_protocol:
Control samples of Daphnia pulex EB clones of 3, 8 and 15 days old were pooled and RNA was extracted using RNeasy micro kit (Qiagen) according to the manufactures protocol.
Libraries were prepared and sequenced using Illumina NextSeq 500 platform at the Centre for Genomics and Bioinformatics, Indiana University.

treatment_protocol: Maintained under standard condition with normal levels of oxygen (6 mg/L) for 3, 8 and 15 days

tag: tissue

value: whole organism


title: EB45_RNA(F5)


title: Ox_N2(92)

organism: Daphnia magna

treatment_protocol:
14 days of exposure to high levels (8 mg/L) of oxygen
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).

value: Clone 2

value: 14 days

value: hyperoxia (8 mgL-1)

value: HH COMBO

value: Bisulphite-treated genomic DNA


title: F_EB31.1

value: Eloise Butler (31)

value: Clone 31


title: F_EB45.2


title: F_EB45.3


title: F_EB31.3


title: Bham2_REF(S1)

description:
processed data file: cpg.var.bham2.v2.vcf.gz
processed data file: magna_snp_cgvIN.vcf.gz

treatment_protocol:
Maintained under standard condition with normal levels of oxygen (6 mg/L) for 14 days
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).


title: EB31_REF(S2)


title: Bham2_REF(S4)


title: F_EB31.2


title: Ox_H6(91)

treatment_protocol:
14 days of exposure to low levels (2 mg/L) of oxygen
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).

value: hypoxia (2 mg L-1)


title: Ox_H3(90)


title: Aza_T4(70)

treatment_protocol:
5 days continuous treatment with 5-azacytidine at 3.7mgL-1
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).

value: 5 days

value: 5-azacytidine (3.7mgL-1)


title: Aza_C2(72)

treatment_protocol:
Maintained under standard condition with normal levels of oxygen (6 mg/L) for 5 days
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).


title: Aza_C3(73)


title: EB31_REF(S5)


title: Aza_T2(68)


title: Aza_C1(71)


title: As_C3(65)


title: As_C2(64)


title: Aza_T1(67)


title: F_EB45.1

value: Eloise Butler (45)

value: Clone 45


title: As_T4(62)

treatment_protocol:
14 days of exposure to arsenic at 100 µg/L
The exposure design followed the OECD guidelines for assessment of chronic toxicity with some modifications (OECD, 2012). Less than 24 hours old neonates were randomly assigned to either control or exposure groups. Control Daphnia were maintained under normal laboratory conditions (oxygen concentration: 6 mgL-1). Treatments consisted of 5 days of exposure to 5-azacytidine (3.7mgL-1) or 14 days of exposure to either arsenic (100 µg L-1), hypoxia (2 mg L-1), or hyperoxia (8 mgL-1).  Hypoxic and hyperoxic conditions were generated by continuous aeration of the media with 20% and 4% oxygen balanced with nitrogen, respectively. Oxygen concentrations were continuously monitored using an oxygen sensor (Unisense microrespiration system, Denmark).

value: female

value: arsenic (100 µg L-1)


title: As_T3(61)


title: As_C1(63)

value: control


title: As_T1(59)


title: Ox_N4(58)


title: shLSD1-1-r1

status: Public on Dec 10 2018

data_processing:
Illumina Casava-1.8.2 software used for basecalling
Sequenced reads were mapped to hg38 whole genome using STAR v2.5.2.a using default parameters
STAR aligner 2.5.2.a
Genome_build: hg38
Supplementary_files_format_and_content: Raw Read countd from FeatureCount v1.5.2 (hg38, genes with no reads were excluded)

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols


title: shSCR-r3


title: shLSD1-1-r2


title: shLSD1-2-r1


title: Bham2_REF(89)

value: Genomic DNA


title: shLSD1-2-r2


title: shLSD1-2-r3


title: Ox_H4(52)


title: shLSD1-1-r3


title: Ox_N1(55)


title: Ox_H5(53)


title: As_T2(60)


title: Ox_N3(57)


title: shSCR-r1


title: Aza_T3(69)


title: GCB_KO2

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were mapped to mm10 whole genome using STAR v2.5.2.a using default parameters
STAR aligner 2.5.2.a
Genome_build: mm10
Supplementary_files_format_and_content: Raw Read countd from FeatureCount v1.5.2 (mm10, genes with no reads were excluded)

source_name: Germinal center B cells (B220+, GL7+, FAS+)

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: sorted GC B cells

value: C57BL/6:Cgamma-cre+/-; Lsd1 f/f


title: GCB_KO3


title: GCB_WT2

value: C57BL/6:Lsd1 f/f


title: GCB_WT1


title: GCB_WT3


title: shSCR-r2


title: Dicer no DNA Damage

status: Public on Dec 08 2018

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
biwigs created with deepTools2
metagene profiles around AsiSI sites created with deepTools2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: OS

extract_protocol:
standard ChIP
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina #E6240S

value: U20S AsiSI


title: Salmonella inoculum Rep 3

status: Public on Dec 07 2018

city: London

first: Peter

last: Hill

address: Kensington

institute: Imperial College London

description: Dual RNA-Seq

data_processing:
Fastq reads were first trimmed using Trimmomatic (version 0.35) with options ILLUMINACLIP:${adapt}:2:30:10, where ${adapt} refers to the TruSeq SE adaptors. Alignment was always done using a two pass approach. For final alignment against the mouse genome, trimmed reads were first aligned to the Salmonella SL1344 assembly (ASM21085v2, including the Chromosome and pSLT_SL1344, pRSF1010_SL1344, and pCol1B9_SL1344 plasmids) using TopHat (version 2.0.2, with options -N 2 --library-type=fr-unstranded --b2-very-sensitive --b2-L 25). The gtf annotation for SL1344 (ASM21085v2) was downloaded from EnsemblBacteria and manually extended with small RNA annotations (Kröger et al., 2013) as a gene model with TopHat. Unaligned reads were then used for alignment against the mouse genome (GRCm38, Ensembl) using TopHat (version 2.0.2, with options -N 2 --library-type=fr-unstranded --b2-very-sensitive --b2-L 25). The gtf annotation for mouse (GRCm38.p5, Ensembl 87) was downloaded and used as a gene model with TopHat. Read counts per annotated mouse gene were then computed using HTSeq (version 0.6.1). For final alignment against the Salmonella genome, trimmed reads were first aligned to the mouse genome (GRCm38, Ensembl) using TopHat (version 2.0.2, with options -N 2 --library-type=fr-unstranded --b2-very-sensitive --b2-L 25). The gtf annotation for mouse (GRCm38.p5, Ensembl 87) was downloaded and used as a gene model with TopHat. Unaligned reads were then used for alignment against the Salmonella SL1344 assembly (ASM21085v2, including the Chromosome and pSLT_SL1344, pRSF1010_SL1344, and pCol1B9_SL1344 plasmids) using TopHat (version 2.0.2, with options -N 2 --library-type=fr-unstranded --b2-very-sensitive --b2-L 25). The gtf annotation for SL1344 (ASM21085v2) was downloaded from EnsemblBacteria and manually extended with small RNA annotations (Kröger et al., 2013) as a gene model with TopHat. Read counts per annotated Salmonella gene were then computed using HTSeq (version 0.6.1).
Genome_build: Salmonella SL1344 assembly: ASM21085v2. Mouse genome: GRCm38.
Supplementary_files_format_and_content: Read counts per gene

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella

growth_protocol: Bone marrow was extracted from tibia and femur of C57BL/6 mice (Charles River) (Racoosin and Swanson, 1989). Red blood cells were lysed in 0.83% NH4Cl for 3 min and the remaining progenitor cells were cultured in Dulbecco’s modified eagle medium with high glucose (DMEM; Sigma), containing 20% (vol/vol) L929 culture supernatant (ATCC #CCL-1), 10% (vol/vol) fetal calf serum (FCS; Gibco, Life Technologies), 10 mM HEPES (Sigma), 1 mM sodium pyruvate (Sigma), 0.05 mM beta-mercaptoethanol (Sigma), 100 U/ml penicillin (Sigma), and 100 µg/ml streptomycin (Sigma). Fresh medium was supplemented at day 3 and the differentiated bone-marrow derived macrophages (M) were harvested at day 7. M were seeded in DMEM without LCM or antibiotics in 24-wells plates (Cellstar, Greiner Bio-one, 2E5 M/well), 6-well plates (Thermo Scientific; 1E6 M per well), in tissue-culture treated petri dishes (Sarstedt; 7E6 M per petri dish) to be infected the next day. Salmonella enterica serovar Typhimurium strain SL1344 was used for the dual RNA-seq, and strains carried the fluorescence dilution plasmid pFCcGi (Figueira et al., 2013). Bacteria were grown in minimal medium (MgMES: 170 mM 2-(N-morpholino)ethanesulfonic acid (MES) at pH 5.0, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 1 mM KH2PO4, 10 mM MgCl2, 38 mM glycerol, and 0.1% casamino acids) (with 0.2% w/vol arabinose if induction of GFP was required in the inoculum) for 18 h.

extract_protocol:
For all mentioned sub-populations 100,000 events were sorted and total RNA was isolated using the mirVana kit (Thermo Fisher Scientific) following the manufacturer’s recommendations and DNase I-treated (NEB) for 45 min at 37°C.
Generation of cDNA libraries and sequencing was as previously described (Westermann et al., 2016). Briefly, bacterial and murine rRNA was depleted using the RiboZero Gold (epidemiology) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared by Vertis Biotech. AG (Freising, Germany) and sequenced on the NextSeq500 platform (Illumina)

treatment_protocol: Bacteria were opsonized with 8% mouse serum (Sigma) for 20 min, and added to the MF in an MOI of 5. Infection was synchronized by 5 min centrifugation at 110 xg. Phagocytosis was allowed to occur for another 25 min at 37oC with 5% CO2. To analyze all intracellular (G and NG) bacteria, M were washed 3x with PBS and incubated in medium with 30 µg/ml gentamicin (Sigma) for 1h. Then, cells were washed 3x with PBS again and incubated in 10 µg/ml gentamicin-containing infection medium for the remainder of the infection. To specifically analyze intracellular NG bacteria, M were treated with 200 µg/ml cefotaxime after the first wash. At indicated time points, M were washed with PBS once and detached from the surface with cold PBS and scraping.

tag: strain mouse

tag: strain salmonella

tag: macrophage subtype

value: Salmonella


title: Salmonella inoculum Rep 2

description: Dual RNA-Seq


title: Salmonella inoculum Rep 1

description: Dual RNA-Seq


title: sDC_61

city: Cantanhede

first: Andreia

last: Gomes

address: Parque Tecnológico de Cantanhede, Núcleo 4, lote 8

department: CNC

country: Portugal

institute: Universidade de Coimbra

description:
CD11c+ MHC-II + CD8a+
SC_iDC_census.counts.txt

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Aligment to GRCm38.p5 was done using Salmon version (0.8.2) and to import transcript abundances tximport was used.
Convert relative RNA-seq expression levels into relative transcript counts using Census algorithm.
Scater R package was used for QC and droping "Gm" annotated genes.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: SC_iDC_census.counts.txt

source_name: splenic Dendritic Cell

growth_protocol: MEFs were cultured in gelatin-coated plates in DMEM+10%FBS. After co-transduction with lentiviral particles encoding FUW-TetO-Pu.1, FUW-TetO-Irf8, FUW-TetO-Batf3 and FUW-M2rtTA, MEFs were cultured in the presence of Doxycycline (1 µg/mL) – day 0.

extract_protocol:
Single cells were isolated using C1 Single-Cell Auto Prep System by Fluidigm.
Illumina Nextera XT Kit was used with 0.1-0.3 ng of cDNA for the construction of sequencing libraries Illumina protocols.

treatment_protocol: Cells were sorted by FACS.

value: splenic Dendritic Cell

value: wildtype

tag: days after transduction


title: sDC_64


title: sDC_59


title: sDC_66


title: sDC_60


title: sDC_57


title: sDC_65


title: sDC_56


title: sDC_62


title: sDC_58


title: sDC_51


title: sDC_52


title: sDC_53


title: sDC_50


title: sDC_54


title: sDC_47


title: sDC_49


title: GCB_KO1


title: sDC_46


title: sDC_48


title: sDC_45


title: sDC_44


title: sDC_43


title: Dicer DNA Damage


title: sDC_55


title: sDC_38


title: sDC_40


title: sDC_39


title: sDC_30


title: sDC_42


title: sDC_63


title: sDC_32


title: sDC_35


title: sDC_34


title: sDC_37


title: sDC_33


title: sDC_31


title: sDC_41


title: sDC_36


title: sDC_26


title: sDC_14


title: sDC_28


title: sDC_25


title: sDC_15


title: sDC_27


title: sDC_17


title: sDC_12


title: sDC_29


title: sDC_23


title: sDC_16


title: sDC_18


title: sDC_19


title: sDC_22


title: sDC_21


title: sDC_13


title: sDC_20


title: sDC_11


title: sDC_24


title: sDC_10


title: sDC_9


title: sDC_4


title: sDC_6


title: sDC_5


title: sDC_7


title: iDC_d9_36

description:
Clec9a-tdTomato+ MHC-II +
SC_iDC_census.counts.txt

source_name: mouse embryonic fibroblast

value: MEF

value: mouse embryonic fibroblast derived iDC

value: Clec9aCre/WT Rosa26stopflox-tdTomato/WT


title: sDC_1


title: sDC_3


title: sDC_2


title: iDC_d9_35


title: iDC_d9_30


title: iDC_d9_28


title: iDC_d9_31


title: iDC_d9_21


title: iDC_d9_27


title: iDC_d9_23


title: iDC_d9_34


title: iDC_d9_25


title: iDC_d9_32


title: iDC_d9_24


title: iDC_d9_26


title: iDC_d9_19


title: iDC_d9_29


title: iDC_d9_22


title: iDC_d9_18


title: iDC_d9_17


title: sDC_8


title: iDC_d9_10


title: iDC_d9_12


title: iDC_d9_14


title: iDC_d9_16


title: iDC_d9_11


title: iDC_d9_15


title: iDC_d9_9


title: iDC_d9_20


title: iDC_d9_33


title: iDC_d9_1


title: iDC_d9_3


title: iDC_d9_2


title: iDC_d9_5


title: iDC_d7_35

description:
Clec9a-tdTomato+
SC_iDC_census.counts.txt


title: iDC_d7_39


title: iDC_d7_40


title: iDC_d7_37


title: iDC_d7_33


title: iDC_d7_31


title: iDC_d7_30


title: iDC_d7_38


title: iDC_d7_29


title: iDC_d9_13


title: iDC_d7_34


title: iDC_d9_8


title: iDC_d7_32


title: iDC_d9_7


title: iDC_d7_25


title: iDC_d7_27


title: iDC_d7_28


title: iDC_d7_24


title: iDC_d7_26


title: iDC_d9_6


title: iDC_d7_22


title: iDC_d7_20


title: iDC_d7_21


title: iDC_d9_4


title: iDC_d7_23


title: iDC_d7_36


title: iDC_d7_19


title: iDC_d7_13


title: iDC_d7_18


title: iDC_d7_17


title: iDC_d7_14


title: iDC_d7_12


title: iDC_d7_10


title: iDC_d7_9


title: iDC_d7_16


title: iDC_d7_8


title: iDC_d7_6


title: iDC_d7_7


title: iDC_d7_4


title: iDC_d7_11


title: iDC_d7_5


title: iDC_d7_3


title: iDC_d7_2


title: iDC_d3_20


title: iDC_d3_16


title: iDC_d3_17


title: iDC_d3_13


title: iDC_d3_15


title: iDC_d3_19


title: iDC_d3_18


title: iDC_d3_12


title: iDC_d3_14


title: iDC_d7_15


title: iDC_d3_10


title: iDC_d3_11


title: iDC_d3_6


title: iDC_d3_9


title: iDC_d3_7


title: iDC_d3_4


title: iDC_d3_2


title: iDC_d3_8


title: MEF_29

description:
unsorted cells
SC_iDC_census.counts.txt

value: mouse embryonic fibroblast


title: iDC_d3_3


title: MEF_30

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_25

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_27

description:
unsorted cells
SC_iDC_census.counts.txt


title: iDC_d3_5


title: MEF_28

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_26

description:
unsorted cells
SC_iDC_census.counts.txt


title: iDC_d3_1


title: iDC_d7_1


title: MEF_24

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_23

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_17

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_21

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_20

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_18

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_15

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_13

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_12

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_19

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_14

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_11

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_16

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_10

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_9

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_7

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_8

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_6

description:
unsorted cells
SC_iDC_census.counts.txt


title: WCE CKp25 6wk rep3

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

data_processing:
Base calling, demultiplexing and fastq file generation was performed by the Broad Institute's Genomics Platform.
ChIP-seq reads were aligned to the mm9 reference genome using the BWA algortihm (version 0.7.10) with default settings. Picard tools (version 1.1175) were used to generate bam files, sort bam files and mark duplicates.
A common set of peaks (“H3K9Ac domains”) was defined based on the 23 ChIP-seq samples from both mouse models as follows. Non-uniquely mapped reads were removed from the bam files. Then, MACS2 was applied to each sample separately with the options “gsize=mm”, “keep-dup=auto” and “broad”. All input DNA samples were pooled into one bam file and passed to MACS2 as control file. Only peaks with a q-value of <= 0.001 were considered. Genomic regions covered by a peak in at least 4 out of the 23 samples were defined as H3K9Ac domains. Domains less than 50 bp away from each other were merged. Small domains of less than 50 bp were removed. In total, we obtained 44165 H3K9Ac domains.
For each H3K9Ac domain and sample the number of overlapping DNA fragments (defined as the reads extended by the fragment size estimated by MACS2) were counted using the R package GenomicRanges. Non-uniquely mapped reads were removed. We recommend to adjust for varying ChIP efficiency by using the variable “cross correlation” when analyzing the data.
Genome_build: mm9
Supplementary_files_format_and_content: domains.bed contains the chromosomal position and an identifier for each H3K9Ac domain identified by our peak calling across samples as described in the data processing section.
Supplementary_files_format_and_content: readCounts.csv contains for each sample (columns) the number of reads overlapping a domain (rows) defined in domains.bed.

source_name: WCE CKp25 6wk_hippocampus

extract_protocol:
Mouse hippocampus was harvested immediately after euthanasia. Upon dissection tissue was flash-frozen in liquid nitrogen. The tissue was minced and crosslinked with 1% formaldehyde at room temperature for 15mins and quenched with 0.125M Glycine. The tissue was then homogenized in cell lysis buffer using the Tissue Lyser and a 5mm stainless steel bead. Then the nuclei were lysed in cell lysis buffer and chromatin was sheared by sonication. Chromatin was incubated overnight at 4C with the H3K9Ac antibody. Immune complexes were captured with Protein A-sepharose beads, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65C, phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA. Gel electrophoresis was used to retain library fragments between 300 and 600 bp. Prior to sequencing, libraries were quantified using Qubit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer. Single end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures.

treatment_protocol: Adult (3-months-old) female double-transgenic CK-p25 mice and their respective control littermates were used for the experiments. Brain tissue was collected at either 2 or 6 weeks following p25 induction.

tag: genotype/variation

tag: age

value: 4.5 months

tag: time since treatment

value: 6 weeks

value: Hippocampus

tag: cross correlation

tag: chip antibody


title: MEF_1

description:
unsorted cells
SC_iDC_census.counts.txt

tag: cell type


title: MEF_3

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_2

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_4

description:
unsorted cells
SC_iDC_census.counts.txt


title: MEF_22

description:
unsorted cells
SC_iDC_census.counts.txt


title: Bystander BMM Rep 1

description: Dual RNA-Seq

source_name: Salmonella challenged bone-marrow derived macrophages

value: Bone-marrow derived macrophages

value: Bystander


title: Bystander BMM Rep 3

description: Dual RNA-Seq


title: WCE CKp25 6wk rep2


title: WCE CK 6wk rep3

source_name: WCE CK 6wk_hippocampus

value: CK (control)


title: WCE CKp25 6wk rep1


title: WCE CK 6wk rep2


title: WCE CK 6wk rep1


title: Uninfected BMM Rep 3

description: Dual RNA-Seq

source_name: Bone-marrow derived macrophages

value: Uninfected


title: Uninfected BMM Rep 2

description: Dual RNA-Seq


title: Uninfected BMM Rep 1

description: Dual RNA-Seq


title: MEF_5

description:
unsorted cells
SC_iDC_census.counts.txt


title: WCE CK 2wk rep3

source_name: WCE CK 2wk_hippocampus

value: 3.5 months

value: 2 weeks


title: WCE CKp25 2wk rep2

source_name: WCE CKp25 2wk_hippocampus


title: WCE CK 2wk rep2


title: WCE CKp25 2wk rep1


title: WCE CK 2wk rep1


title: H3K9Ac CKp25 6wk rep1

source_name: H3K9Ac CKp25 6wk_hippocampus

value: H3K9Ac (Abcam, catalog# ab4441, lot# GR207546-1)


title: Bystander BMM Rep 2

description: Dual RNA-Seq


title: H3K9Ac CK 6wk rep3

source_name: H3K9Ac CK 6wk_hippocampus


title: Control DMSO rep1 b3

data_processing:
Base calling, demultiplexing and fastq file generation was performed by the Broad Institute's Genomics Platform.
ATAC-seq reads were aligned to the GRCh37 reference genome using the BWA algortihm (version 0.7.10) with the paired-end option and default settings. Picard tools (version 1.1175) were used to generate bam files, sort bam files and mark duplicates.
A common set of peaks (“ATAC domains”) was defined based on the 18 untreated samples as follows. Non-uniquely mapped reads were removed from the bam files. Then, MACS2 was applied to each sample separately with the options “format=BAMPE”, “gsize=hs” and “keep-dup=auto”. Only peaks with a q-value of <= 0.001 were considered. Genomic regions covered by a peak in at least 4 out of the 18 samples were defined as ATAC domains. Domains less than 50 bp away from each other were merged. Small domains of less than 50 bp were removed. In total, we obtained 40637 ATAC domains.
For each ATAC domain and sample the number of overlapping DNA fragments (defined by the paired-end reads) were counted using the R package GenomicRanges. Non-uniquely mapped reads and fragments larger than 2kb were removed. We recommend to adjust for batch and total number of read pairs when analyzing the data.
Genome_build: GRCh37
Supplementary_files_format_and_content: File domains.bed contains the chromosomal position and an identifier for each domain identified by our peak calling across samples as described in the data processing section.
Supplementary_files_format_and_content: File fragmentCounts.csv contains for each sample (columns) the number of fragments (read pairs) overlapping a domain (rows) described in domains.bed

source_name: forebrain neurons_Control DMSO

growth_protocol: Neurons were generated from the direct conversion of induced pluripotent stem cells by transduction with Neurogenin 2 as described by Zhang et al. (PMID: 23764284). Neurons were plated on Matrigel coated 96-well plates on DIV4 and maintained in media consisting of 485mL neurobasal medium (Gibco), 5mL Glutamax, 7.5mL 20% Dextrose, 2.5mL MEM NEAA with 1:50 B27, BDNF, CNTF, GDNF and doxcylcine. On DIV17, cells were transfected with a GFP expressing construct (pRosetta). Following 18-hour incubation, virus-containing media was removed and replaced with fresh media to incubate until DIV31 when harvested for ATAC-seq.

extract_protocol:
ATAC-seq was performed as previously described by Buenrostro et al. (PMID: 24097267) with three modifications: (i) To reduce mitochondrial DNA contamination, we substituted 0.1% Ipegal with 0.01% Tween in the nuclear lysis buffer. (ii) Additional tagmentation buffer (TD; 2x) was prepared as follows: 20 mM Tris(hydroxymethyl)aminomethane and 10 mM MgCl2; adjusted to pH 7.6 with 100% acetic acid before addition of 20% (vol/vol) dimethylformamide (Wang et al., 2013). (iii) We performed the PCR amplification in a 25ul total volume rather than 50ul to save half of our tagmented DNA for backup. After 31 days in vitro, iPSC neurons were trypsinised and counted to provide 50,000 live cells for ATAC-seq. iPSC-derived neurons were lysed with 0.01% Tween, 10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and nuclei pelleted, washed and transposed upon addition of 2.5 uL Nextera Tn5 Transposase in 1x TD buffer (Nextera Kit, Illumina) and incubation at 37°C for 30 mins.
Immediately following transposition, DNA fragments were purified using a Qiagen MinElute PCR Purification Kit (Qiagen) following the manufacturer’s instructions. Transposed DNA was amplified with dual indexed Nextera PCR primers for 5 cycles prior to removing a 5ul aliquot from each sample to test further amplification requirements by qPCR. Rounding up the cycle threshold from each sample decides how many additional cycles each sample needs to be amplified. For these samples, we needed to re-array and continue amplifying the remaining 20ul for 5-8 cycles. Final libraries were cleaned twice with 1.5X Ampure XP SPRI beads and eluted in 12ul of water.

treatment_protocol: Neurons were treated with DMSO for 24 hours prior to collection.

tag: tissue/cell type

value: Forebrain neurons

tag: overexpression

tag: treatment

value: DMSO

tag: batch

value: Batch 3

tag: number of read pairs


title: Control DMSO rep3 b3


title: Tau 17-DMAG 10nM rep3 b3

source_name: forebrain neurons_Tau 17-DMAG 10nM

growth_protocol: Neurons were generated from the direct conversion of induced pluripotent stem cells by transduction with Neurogenin 2 as described by Zhang et al. (PMID: 23764284). Neurons were plated on Matrigel coated 96-well plates on DIV4 and maintained in media consisting of 485mL neurobasal medium (Gibco), 5mL Glutamax, 7.5mL 20% Dextrose, 2.5mL MEM NEAA with 1:50 B27, BDNF, CNTF, GDNF and doxcylcine. On DIV17, cells were transfected with a 1:1 dilution of lentivirus-packaged open reading frames (ORF) expressing human MAPT (titer 6.2x106), resulting in overexpression of tau protein. Following 18-hour incubation, virus-containing media was removed and replaced with fresh media to incubate until DIV31 when harvested for ATAC-seq.

treatment_protocol: Neurons were treated with 10 nM 17- DMAG (alvespimycin) for 24 hours prior to collection. 17-DMAG was dissolved in DMSO.

value: MAPT

value: 17-DMAG 10nM + DMSO


title: Tau DMSO rep2 b3

source_name: forebrain neurons_Tau DMSO


title: Control DMSO rep2 b3


title: Tau DMSO rep1 b3


title: Tau 17-DMAG 10nM rep2 b3


title: Tau DMSO rep3 b3


title: H3K9Ac CK 6wk rep2


title: H3K9Ac CK 6wk rep1


title: H3K9Ac CKp25 2wk rep3

source_name: H3K9Ac CKp25 2wk_hippocampus


title: H3K9Ac CK 2wk rep3

source_name: H3K9Ac CK 2wk_hippocampus


title: H3K9Ac CK 2wk rep2


title: H3K9Ac CKp25 2wk rep1


title: Tau 17-DMAG 1nM rep3 b3

source_name: forebrain neurons_Tau 17-DMAG 1nM

treatment_protocol: Neurons were treated with 1 nM 17- DMAG (alvespimycin) for 24 hours prior to collection. 17-DMAG was dissolved in DMSO.

value: 17-DMAG 1nM + DMSO


title: WCE WT 6m rep3

source_name: WCE WT 6m_hippocampus

treatment_protocol: Adult female 6 months old and male 11 months old transgenic MAPT P301S mice with age- and gender-matched wild-type mice as controls were used.

value: wt (control)

value: 6 months


title: Tau 17-DMAG 3nM rep1 b3

source_name: forebrain neurons_Tau 17-DMAG 3nM

treatment_protocol: Neurons were treated with 3 nM 17- DMAG (alvespimycin) for 24 hours prior to collection. 17-DMAG was dissolved in DMSO.

value: 17-DMAG 3nM + DMSO


title: Tau 17-DMAG 3nM rep2 b3


title: H3K9Ac CK 2wk rep1

value: Hippocampus


title: Tau 17-DMAG 1nM rep2 b3


title: WCE WT 6m rep2


title: Tau 17-DMAG 1nM rep1 b3


title: Tau 17-DMAG 10nM rep1 b3


title: WCE CKp25 2wk rep3


title: Tau 17-DMAG 3nM rep3 b2

value: Batch 2


title: Tau 17-DMAG 3nM rep3 b3


title: WCE Tau 6m rep2

source_name: WCE Tau 6m_hippocampus

value: Tau (MAPT P301S)


title: WCE Tau 6m rep1


title: Control rep3 b3

source_name: forebrain neurons_Control

treatment_protocol: Neurons were untreated.

value: Untreated


title: Tau 17-DMAG 3nM rep2 b2


title: Control rep1 b3


title: WCE Tau 11m rep2

source_name: WCE Tau 11m_hippocampus

value: 11 months


title: Control rep2 b3


title: H3K9Ac WT 6m rep3

source_name: H3K9Ac WT 6m_hippocampus

value: H3K9Ac (Abcam, catalog# ab4441, lot# GR196840-1)


title: H3K9Ac WT 6m rep2


title: WCE Tau 11m rep1


title: Control rep3 b2


title: Tau rep1 b3

source_name: forebrain neurons_Tau


title: H3K9Ac WT 6m rep1


title: Tau rep3 b3


title: H3K9Ac CKp25 6wk rep2

value: 4.5 months

value: 6 weeks


title: H3K9Ac CKp25 6wk rep3

value: H3K9Ac (Abcam, catalog# ab4441, lot# GR207546-1)


title: H3K9Ac Tau 6m rep2

source_name: H3K9Ac Tau 6m_hippocampus


title: H3K9Ac Tau 6m rep1


title: Tau rep2 b3

value: Forebrain neurons


title: Control rep2 b2


title: Control rep1 b2


title: H3K9Ac WT 11m rep3

source_name: H3K9Ac WT 11m_hippocampus


title: Tau rep3 b2


title: Tau 17-DMAG 3nM rep1 b2


title: H3K9Ac CKp25 2wk rep2

value: 3.5 months

value: 2 weeks


title: WCE WT 11m rep3

source_name: WCE WT 11m_hippocampus


title: Tau rep1 b2

value: MAPT


title: Tau rep2 b2


title: WCE Tau 11m rep3


title: H3K9Ac WT 11m rep2


title: WCE WT 6m rep1


title: H3K9Ac Tau 11m rep3

source_name: H3K9Ac Tau 11m_hippocampus


title: H3K9Ac Tau 11m rep2


title: Control rep2 b1

value: Batch 1


title: H3K9Ac WT 11m rep1

value: wt (control)


title: Control rep1 b1


title: H3K9Ac Tau 11m rep1


title: Tau rep2 b1


title: Tau rep1 b1


title: BMM with host-killed Salmonella Rep 3

description: Dual RNA-Seq

organism:
Mus musculus
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella infected bone-marrow derived macrophages

value: Bone-marrow derived macrophages

value: Infected, with non-viable Salmonella


title: BMM with host-killed Salmonella Rep 2

description: Dual RNA-Seq


title: BMM with non-growing Salmonella Rep 3

description: Dual RNA-Seq

value: Infected, with non-growing Salmonella


title: BMM with host-killed Salmonella Rep 1

description: Dual RNA-Seq


title: WCE WT 11m rep1

value: Hippocampus


title: BMM with non-growing Salmonella Rep 2

description: Dual RNA-Seq


title: BMM with growing Salmonella Rep 1

description: Dual RNA-Seq

value: Infected, with growing Salmonella


title: BMM with growing Salmonella Rep 2

description: Dual RNA-Seq


title: Fezf2- IT-PN (3)

status: Public on Dec 06 2018

city: Dunedin

first: Alison

middle: Jane

last: Clare

state: Otago

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: fragmented mRNA

data_processing:
Real-time analysis (v1.18.54) was used for base-calling and bcl2fastq (v1.8.4) for file conversion. Sabre (https://github.com/najoshi/sabre) was used to demultiplex the samples based on their inline barcode.
Reads were trimmed to removed poor quality ends and any remaining polyA tail usingFASTX-Toolkit and any read < 50 nt discarded. Reads were then mapped to ERCC sequences or mm10 whole genome using TopHat2 (v2.1.1)
Raw counts were generated using RefFlat reference genes downloaded from table browser (Jan 2016) and multiBamCov function in bedtools2 (v2.26.0)
Raw counts were loaded into R studio (R version 3.2.5) and converted to cpm before filtering out low expressed genes (cpm > 10 in at least 2 samples). Differential expression analysis was performed using DESeq2 (version 1.10.1) and consideration of paired samples applied.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include raw counts for all samples and DESeq2 output for differential expression analysis
Supplementary_files_format_and_content: DESeq2 analysis.txt DESeq2 output
Supplementary_files_format_and_content: Raw counts.txt Raw counts for all samples
Supplementary_files_format_and_content: Raw Counts ERCC.txt Raw ERCC counts for all samples

source_name: Right hemisphere layer 5 M1

extract_protocol:
Animals were perfused with 0.9% Saline and the brain dissected out. Coronal sections (1 mm) were made using a TedPella matrix and layer 5 M1 of the right hemisphere dissected according to GFP(Fezf2) expression. Tissue was immediately dissociated into single cell suspension before FACS-purification of cells, separating cells from one animal into the Fezf2(GFP)+ CTB+ and CTB+ only cells, resulting in an average yields of 11,280 (n = 5) and 2,688 (n = 5) respectively. Cells were sorted directly into lysis solution from the RNAqueous micro kit (Thermo Fisher) and RNA extracted according to the manufacturers instructions.
An ERCC spike-in was added to each RNA sample before the incorporation of a unique inline barcode in the initial cDNA preparation of each RNA sample step before PCR amplification. All samples were then pooled for in vitro transcription to further amplify RNA. Amplified RNA was then fragmented before reverse transcription and PCR amplification to generate the final cDNA library.

treatment_protocol: Male Fezf2-Gfp mice (P23 - 25) were injected into the left hemisphere primary motor cortex with a cholera toxin subunit b conjugated Alexa 647 retrograde tracer.

tag: strain

value: Right hemisphere layer 5 primary motor cortex (M1)


title: Fezf2- IT-PN (5)

description: fragmented mRNA

tag: tissue


title: Control rep3 b1

value: Untreated


title: Fezf2- IT-PN (4)

description: fragmented mRNA


title: Fezf2- IT-PN (2)

description: fragmented mRNA


title: Fezf2+ IT-PN (2)

description: fragmented mRNA


title: Fezf2+ IT-PN (3)

description: fragmented mRNA


title: Fezf2+ IT-PN (5)

description: fragmented mRNA


title: Fezf2+ IT-PN (4)

description: fragmented mRNA


title: Fezf2- IT-PN (1)

description: fragmented mRNA


title: Tau rep3 b1


title: Fezf2+ IT-PN (1)

description: fragmented mRNA


title: BMM with non-growing Salmonella Rep 1

description: Dual RNA-Seq

tag: strain mouse


title: G4_EpiLC_48h

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description: 48h EpiLC

data_processing:
Quality control of reads (removal of reads scoring less than Q20)
Quality control of reads (removal of adaptors with cutadapt)
Mapping of reads with TopHat2
Genome_build: mm9
Supplementary_files_format_and_content: csv read counts per transcript

growth_protocol: Cells were grown in human plasma fibronectin-coated Nunc cell culture dishes. For EpiLC differentiation, ESCs cultured in N2B27/2i/LIF/1%KSR were induced as detailed in [Ref: Hayashi et al.] (also see SAMPLES section 'characteristics: culture condition')

extract_protocol:
C1 Single-Cell Autoprep System (Fluidigm)
Modified Illumina® Nextera XT DNA sample preparation protocol, according to Fluidigm's guidelines: 'Using the C1™ Single-Cell Auto Prep System to Generate  mRNA from Single Cells and Libraries for Sequencing'.

treatment_protocol: For collection, cells were rinsed once in 1xPBS, dissociated in TrypLE Express (Gibco, 12604-021) for 3 minutes at 37°C in 5% CO2 atmosphere, resuspended in N2B27/1%KSR, collected by 5 minutes centrifugation at 1.000rpm (Grant bio LMC-3000, Grant Instruments), and suspended in fresh N2B27/1%KSR. For parallel processing of single cells of three differentiation timepoints (ESCs, t=0h; EpiLCs, t=24h, t=48h), cells were differentially labelled with fluorescent dyes (see SAMPLES section 'characteristics: fluorescent labelling)' for 20 minutes at 37°C in 5% CO2 in 1ml N2B27/1%KSR each. Cells were collected by 5 minutes centrifugation at 1.000rpm (Grant bio LMC-3000, Grant Instruments), washed twice with 500ul N2B27/1% KSR and diluted at 100.000 cells 500ul-1 in N2B27/1% KSR. 20ul cell suspension of each differentiation time point were combined with 40ul C1Cell Suspension Reagent (Fluidigm, 100-5315) for a total volume of 100ul. Following gentle mixing, 20ul cell suspension composed of equal numbers of cells of all three differentiation time points were loaded on the C1 Integrated Fluidic Circuits (IFC) for mRNA seq (10-17 micron; Fluidigm, 100-5760) for 96 single-cell capture using the C1 Single-Cell Autoprep System (Fluidigm). Cell identities of individual cells were decovoluted by fluorescence microscopy using an inverted Olympus microscope, before performing on-chip (IFC) cell lysis, reverse transcription, and cDNA amplification using the C1 Single-Cell Autoprep System (Fluidigm).

tag: genotype

value: wild type

value: ESC-derived Epilblast-like cell (EpiLC)

tag: culture condition

value: 48h N2B27/KSR/bFgf/ActivinA

tag: fluorescent labelling

value: 4uM Ethidium homodimer-1 and 2uM Calcein (LIVE/DEAD® Viability/Cytotoxicity Kit for mammalian cells, Molecular Probes, Life Technologies, L3224)

tag: passage number


title: GcvB

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

country: Canada

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Reads were aligned to the Escherichia coli K12 genome assembly using Bowtie for Illumina (Galaxy Project)
Read counts were normalized by coverage according to Oshlack et al., 2010
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-GcvB/GcvB ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: Cells were harvested in exponential (OD600nm=0.5; 100 mL LB medium) and in stationary phase (OD600nm=1; 100 mL LB medium).

extract_protocol:
Cells were resuspended in 3 mL of buffer A and lysed using a French Press (430 psi, four times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 100 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 200 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 8 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ RNA-Seq Library Preparation Kit (Illumina)

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-GcvB/GcvB during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 rne131 delta_gcvB

tag: growth phase

value: exponential and stationary phases


title: G5_EpiLC_48h

description: 48h EpiLC


title: H10_EpiLC_48h

description: 48h EpiLC


title: BMM with growing Salmonella Rep 3

description: Dual RNA-Seq

tag: strain salmonella

tag: macrophage subtype


title: F5_EpiLC_48h

description: 48h EpiLC


title: G3_EpiLC_48h

description: 48h EpiLC


title: G12_EpiLC_48h

description: 48h EpiLC


title: MS2-GcvB


title: F12_EpiLC_48h

description: 48h EpiLC


title: E6_EpiLC_48h

description: 48h EpiLC


title: E4_EpiLC_48h

description: 48h EpiLC


title: B3_EpiLC_48h

description: 48h EpiLC


title: D8_EpiLC_48h

description: 48h EpiLC


title: B4_EpiLC_48h

description: 48h EpiLC


title: D2_EpiLC_48h

description: 48h EpiLC


title: E3_EpiLC_48h

description: 48h EpiLC


title: C7_EpiLC_48h

description: 48h EpiLC


title: D10_EpiLC_48h

description: 48h EpiLC


title: C11_EpiLC_48h

description: 48h EpiLC


title: B9_EpiLC_48h

description: 48h EpiLC


title: B6_EpiLC_48h

description: 48h EpiLC


title: B11_EpiLC_48h

description: 48h EpiLC


title: B12_EpiLC_48h

description: 48h EpiLC


title: A7_EpiLC_48h

description: 48h EpiLC


title: A11_EpiLC_48h

description: 48h EpiLC


title: A10_EpiLC_48h

description: 48h EpiLC


title: F2_EpiLC_24h

description: 24h EpiLC

value: 24h N2B27/KSR/bFgf/ActivinA

value: 2.5ug ml-1 CellMaskTM Deep Red plasma membrane stain (Molecular Probes, Life Technologies, C10046)


title: H8_EpiLC_24h

description: 24h EpiLC


title: G6_EpiLC_24h

description: 24h EpiLC


title: G11_EpiLC_24h

description: 24h EpiLC


title: G8_EpiLC_24h

description: 24h EpiLC


title: F11_EpiLC_24h

description: 24h EpiLC


title: E2_EpiLC_24h

description: 24h EpiLC


title: C8_EpiLC_24h

description: 24h EpiLC


title: D7_EpiLC_24h

description: 24h EpiLC


title: E11_EpiLC_24h

description: 24h EpiLC


title: A9_EpiLC_24h

description: 24h EpiLC


title: C12_EpiLC_24h

description: 24h EpiLC


title: A3_EpiLC_24h

description: 24h EpiLC


title: A8_EpiLC_24h

description: 24h EpiLC


title: H3_ESC_2iLIF

description: ESC

value: Embryonic stem cell (ESC)

value: 2ug ml-1 Hoechst 33342 (Invitrogen, 917368)


title: H11_ESC_2iLIF

description: ESC


title: B1_EpiLC_48h

description: 48h EpiLC


title: F8_ESC_2iLIF

description: ESC


title: F3_ESC_2iLIF

description: ESC


title: G7_ESC_2iLIF

description: ESC


title: E8_ESC_2iLIF

description: ESC


title: F6_ESC_2iLIF

description: ESC


title: D5_ESC_2iLIF

description: ESC


title: D9_ESC_2iLIF

description: ESC


title: E12_ESC_2iLIF

description: ESC


title: D6_ESC_2iLIF

description: ESC


title: F4_EpiLC_24h

description: 24h EpiLC


title: FACS - bottom 95% Sample 31

city: IRVINE

first: James

last: Yu

state: ca

address: Med Sci D262

department: Biological Chemistry

institute: University of California Irvine

data_processing:
For Samples 1-12, basecalling  was performed with bcl2fastq_2.16.0. For samples 13-33, basecalling was performed with bcl2fastq2_2.17.1.14.
For all samples, reads were first filtered for legiimate Hermes TIR-gDNA borders using the last 26 bases immediately downstream of  KP5113 primer binding site as a tag to filter out misprimed  reads.
Next DNA sequence was trimmed to remove TIR ends and mapped to the CLIB89 YALI1 genome using Bowtie2. Each unique read mapped was considered a Hermes insertion site; reads with multiple mapped positions were randomly assigned (less than 1.5% of reads). Hermes insertion coordinates were mapped to gene annotations using BEDTools.
Genome_build: Yali1

organism: Yarrowia lipolytica

source_name: Cell pellet

extract_protocol:
DNA was isolated by standard phenol:chloroform
After extraction, gDNA was treated with DNase-free RNaseA (100 µg/mL) (Sigma- Aldrich) at 37° C for 4 hrs, followed by Pronase (250 µg/mL) (Sigma-Aldrich) at 37°C for 2 hrs. After both RNase and Pronase treatment, another phenol:chloroform extraction was performed. Approximately 30 µg of this treated DNA was sheared to less than 1 kb in a 100 µl volume using the Biorupter Standard (Diagenode). DNA size was confirmed by gel electrophoresis. Sheared DNA was concentrated using the Clean and Concentrator with 5X ChIP DNA Binding Buffer (Zymo Research). DNA ends were made blunt using the Fast DNA End Repair kit (Thermo Scientific); 3’ adenylated using the Klenow Exo-enzyme with 0.2 mM dATP (Fisher Scientific). Custom sequencing adapters (0.5 µM) with Illumina multiplex barcodes (Additional file 1: Table S1) were ligated to DNAs in each sample using T4 ligase (Thermo Scientific) by incubating at 22°C for 12 hrs followed by 65°C for 10 min. Between enzyme reactions, samples were purified using the Agencourt AMPure XP purification beads (Beckman Coulter, Inc.). Hermes TIR –gDNA borders were enriched in PCR using the high-fidelity KOD polymerase (EMD Millipore) as follows: 95°C 5 min, 5 cycles of 95°C 30 s, 65°C 30 s, and 70°C 30 s, followed by 20 cycles of 95°C 30 s, 61°C 30 s, and 70°C 30 s, and a final 70°C incubation for 2 min. Forward primer KP5113 anneals 26 bp from the downstream 3’-end of the TIR, and reverse primer KP5112 anneals to the adapter upstream of the Illumina multiplex barcode. After sizing/purification of PCR products samples were submitted to the UCI Genomics High-throughput Facility for Bioanalyzer 2100 (Agilent) analysis, KAPA quantification and single-end 100 cycle sequencing on the Illumina HiSeq 2500.

tag: generations

tag: growth condition

value: liquid nitrogen limited minimal


title: FACS - bottom 95% Sample 32


title: D12_ESC_2iLIF

description: ESC

tag: cell type


title: B8_ESC_2iLIF

description: ESC


title: C9_ESC_2iLIF

description: ESC


title: FACS - top 5%  Sample 30


title: C10_ESC_2iLIF

description: ESC


title: FACS - bottom 95% Sample 33


title: G10_ESC_2iLIF

description: ESC


title: A4_EpiLC_24h

description: 24h EpiLC


title: F7_ESC_2iLIF

description: ESC


title: FACS - top 5%  Sample 28


title: FACS - top 5%  Sample 29


title: H1_ESC_2iLIF

description: ESC


title: B2_ESC_2iLIF

description: ESC


title: Gen80-Glycerol - trial 2 Sample 25

value: liquid YP Glycerol


title: B5_ESC_2iLIF

description: ESC


title: Gen80-Glucose - trial 2 Sample 24

value: liquid YP Dextrose


title: Gen80-Glucose - trial 2 Sample 23


title: A6_ESC_2iLIF

description: ESC


title: Gen80-Glycerol - trial 2 Sample 26


title: A5_ESC_2iLIF

description: ESC


title: A2_ESC_2iLIF

description: ESC


title: A1_ESC_2iLIF

description: ESC


title: Gen80-Glucose - trial 2 Sample 22


title: Gen20-Glycerol - trial 2 Sample 21


title: A12_ESC_2iLIF

description: ESC


title: Gen20-Glycerol - trial 2 Sample 20


title: B7_ESC_2iLIF

description: ESC


title: Gen20-Glucose - trial 2 Sample 18


title: Gen20-Glycerol - trial 2 Sample 19


title: Gen0 - trial 2 Sample 15

value: solid defined synthetic medium


title: Gen0 - trial 2 Sample 14


title: Gen20-Glucose - trial 2 Sample 16


title: Gen80-Glycerol - trial 2 Sample 27


title: Gen20-Glucose - trial 2 Sample 17


title: Gen80-Glycerol - trial 1 Sample 12


title: Gen80-Glycerol - trial 1 Sample 11


title: Gen20-Glucose - trial 1 Sample 4


title: Gen20-Glycerol - trial 1 Sample 7


title: Gen0 - trial 1 Sample 2


title: Gen80-Glucose - trial 1 Sample 9


title: Gen0 - trial 1 Sample 1


title: Gen20-Glucose - trial 1 Sample 5


title: Gen20-Glycerol - trial 1 Sample 6


title: Gen0 - trial 1 Sample 3


title: Non-stim Phen

status: Public on Dec 05 2018

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: ATAC-seq

data_processing:
Sequences were adapter stripped (Trimmomatic-0.33)
and mapped to the Mm10 genome with Bowtie2 (2.2.5).
Duplicate reads were removed (Picard) and reads were shifted 4-5bp.
After discarding fragments over 120bp enriched regions were called with MACS2 2 (broad peaks, p<0.05)
and annotated, read counted and normalized for library size in HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files are peaks for ATAC-seq

source_name: CD8 lymphocyte

extract_protocol:
DNA were transposed by using transposase Tn5 followed by purification using Qiagen MinElute PCR purification kit.
Transposed DNA fragments were amplified by PCR with custom Nextera PCR primers contains barcode, followed by  purification using Qiagen MinElute PCR purification kit.

treatment_protocol: Stimulated samples were treated with PMA (1mg/mL) and Ionomycin (10mM) for 2h.

value: Balb/c

value: unstimulated and phenelzine


title: Non-stim untreated

description: ATAC-seq

value: unstimulated and untreated


title: Health_475

status: Public on Dec 04 2018

city: Shenyang

first: shuang

last: pang

state: China

address: No.79 Chong Shan Dong Lu Street

country: China

institute: Liaoning University of Traditional Chinese Medicine

data_processing:
10 pM libraries were denatured as single-stranded DNA molecules,captured on Illumina flow cells,amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer's instructions.
After 3' adaptor-trimming by cutadapt software (version 1.9) ,the high quality trimmed reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl GFF gene annotation file with TopHat2 software.
Then,cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA,and fold change and p-value were calculated based on FPKM,differentially expressed LncRNA and mRNA were identified.
LncRNA target genes were predicted by the locations to nearby genes.
And GO and Pathway analysis were performed on these target genes.GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: excel format includes FPKM values for each sample

source_name: the whole blood

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina,USA) following the manufacturer's instrustions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA) according to the manufacturer's instructions.Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies,USA).

tag: diagnosis

value: Healthy

value: whole blood

tag: age

value: 15 years

tag: gender

value: male

tag: course of hspn

tag: type of hspn


title: Stim Phen

description: ATAC-seq

tag: strain

tag: treatment

value: stimulated and phenelzine


title: Health_473

tag: tissue

value: 12 years

value: female


title: Stim untreated

description: ATAC-seq

value: stimulated and untreated


title: Health_472

value: 8 years


title: Sick_303

value: Henoch-Schonlein Purpura Nephritis

value: 11 years

value: 20 months

value: isolated proteinuria


title: Health_460

value: 10 years


title: Gen0 - trial 2 Sample 13

value: solid defined synthetic medium


title: Sick_173

value: 60 months

value: isolated hematuria


title: Sick_105

value: 34 months


title: Sick_87

value: whole blood

value: 13 years

value: 10 months


title: Gen80-Glucose - trial 1 Sample 10

value: liquid YP Dextrose


title: Gen80-Glucose - trial 1 Sample 8


title: HDF_d2_FOS_ChIP_Form_rep1

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

description: unsorted cells

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
For ChIP-seq, the FASTQ files were mapped to the human hg19 genome using Bowtie 2.2.2.  The mapped output files were processed through MACS1.4 analysis software to determine peaks. Homer  software package was used for peak annotation and motif discovery.
Genome_build: hg19
Supplementary_files_format_and_content: HDF single cell experiment raw count table derived from R preprocessCore.

source_name: adult human dermal fibroblast

extract_protocol:
Population cells were sorted by FACS and RNA was isolated using Trizol reagent. Single cells were sorted by FACS and single cells were isolated using C1 Single-Cell Auto Prep System by Fluidigm. Chromatin immunoprecipitation followed published methods (Lee et al 2006) with the exception of FOS dual crosslink with Formaldehyde and DSG. Briefly, cells were fixed 11% formaldehyde at room temperature on a rotating platform for 10min. Formaldehyde was quenched by adding of 125nM of glicyne. Chromatin was sheared and immunoprecipitated with the antobody of interest.A control sample consisting of sonicated chromatin thta has not been immunoprecipitated was also sequenced.
For ChIP-seq, libraries were prepared using either KAPA Hyper Prep kit or NEBNext ChIP-seq Library Prep Master Mix for Illumina according to the manufacturer's guidelines. Libraries were size-selected on a 2% agarose gel for a 200-400bp fragments.

tag: cell line

value: HDFa

value: adult human dermal fibroblast

tag: genotype

value: wildtype


title: HDF_d2_GFI1B_alone_Input_rep1

description: unsorted cells


title: HDF_d2_GFI1B_alone _ChIP_rep1

description: unsorted cells


title: HDF_d2_FOS_alone_ChIP_Form+DSG_rep1

description: unsorted cells


title: HDF_d2_FOS_Input_Form_rep1

description: unsorted cells


title: HDF_d2_GFI1B_Input_rep2

description: unsorted cells


title: HDF_d2_GATA2_alone_ChIP_rep2

description: unsorted cells


title: HDF_d2_GFI1B_Input_rep1

description: unsorted cells


title: HDF_d2_GFI1B_ChIP_rep1

description: unsorted cells


title: HDF_d2_GATA2_alone_Input_rep2

description: unsorted cells


title: HDF_d2_GATA2_alone_ChIP_rep1

description: unsorted cells


title: HDF_d2_GATA2_Input_rep2

description: unsorted cells


title: HDF_d2_GATA2_ChIP_rep2

description: unsorted cells


title: HDF_d2_GATA2_Input_rep1

description: unsorted cells


title: Sick_111

value: 15 years

value: male

value: 16 months

value: hematuria and proteinuria


title: HDF_d2_GATA2_ChIP_rep1

description: unsorted cells


title: sc_UCB_55

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
For single cell mRNA-seq, alignment to GRCh38 using Gencode v25 gene annotation Reads were aligned with STAR version 020201 and gene level read counts were calculated using featureCounts Version 1.5.1 from the Subread packag. Raw counts were log2 transformed and quantile normalized using R library preprocessCore.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF single cell experiment raw count table derived from R preprocessCore.

source_name: Human Umbilical cord blood

extract_protocol:
Single cells were sorted by FACS and single cells were isolated using C1 Single-Cell Auto Prep System by Fluidigm.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage. For single cell, Illumina Nextera XT Kit was used with 0.1-0.3ng of cDNA for the construction of sequencing libraries Illumina protocols.

value: UCB

value: Human Umbilical cord blood

tag: genotype/variation

tag: cell population

value: Lin- CD34+


title: sc_UCB_54


title: sc_UCB_56


title: sc_UCB_52


title: sc_UCB_53


title: Sick_64

value: Henoch-Schonlein Purpura Nephritis

value: female

value: 12 months


title: sc_UCB_50


title: HDF_d2_FOS_ChIP_Form+DSG_rep1

description: unsorted cells


title: sc_UCB_48


title: sc_UCB_47


title: HDF_d2_GFI1B_ChIP_rep2

description: unsorted cells


title: sc_UCB_46


title: sc_UCB_42


title: sc_UCB_43


title: HDF_d2_GATA2_alone_Input_rep1

description: unsorted cells


title: sc_UCB_45


title: sc_UCB_39


title: sc_UCB_41


title: sc_UCB_40


title: sc_UCB_38


title: sc_UCB_35


title: sc_UCB_34


title: sc_UCB_31


title: sc_UCB_51


title: sc_UCB_32


title: sc_UCB_49


title: sc_UCB_33


title: sc_UCB_30


title: sc_UCB_23


title: sc_UCB_24


title: sc_UCB_28


title: sc_UCB_27


title: sc_UCB_29


title: sc_UCB_25


title: sc_UCB_26


title: sc_UCB_21


title: sc_UCB_22


title: sc_UCB_20


title: sc_UCB_37


title: sc_UCB_18


title: sc_UCB_19


title: sc_UCB_36


title: sc_UCB_44


title: sc_UCB_9


title: sc_UCB_16


title: sc_UCB_14


title: sc_UCB_10


title: sc_UCB_12


title: sc_UCB_13


title: sc_UCB_17


title: sc_UCB_11


title: sc_UCB_15


title: sc_UCB_7


title: sc_UCB_8


title: sc_UCB_5


title: sc_UCB_6


title: sc_UCB_3


title: sc_Day25_CD34CD49f_92


title: sc_Day25_CD34CD49f_93


title: sc_UCB_4


title: sc_UCB_1


title: sc_Day25_CD34CD49f_91


title: sc_UCB_2


title: sc_Day25_CD34CD49f_90


title: sc_Day25_CD34CD49f_95


title: sc_Day25_CD34CD49f_96


title: sc_Day25_CD34CD49f_85


title: sc_Day25_CD34CD49f_88


title: sc_Day25_CD34CD49f_89


title: sc_Day25_CD34CD49f_86


title: sc_Day25_CD34CD49f_82


title: sc_Day25_CD34CD49f_83


title: sc_Day25_CD34CD49f_84


title: sc_Day25_CD34CD49f_77


title: sc_Day25_CD34CD49f_76


title: sc_Day25_CD34CD49f_73


title: sc_Day25_CD34CD49f_80


title: sc_Day25_CD34CD49f_81


title: sc_Day25_CD34CD49f_74


title: sc_Day25_CD34CD49f_75


title: sc_Day25_CD34CD49f_79


title: sc_Day25_CD34CD49f_71


title: sc_Day25_CD34CD49f_72


title: sc_Day25_CD34CD49f_70


title: sc_Day25_CD34CD49f_69


title: sc_Day25_CD34CD49f_66


title: sc_Day25_CD34CD49f_67


title: sc_Day25_CD34CD49f_65


title: sc_Day25_CD34CD49f_62


title: sc_Day25_CD34CD49f_64


title: sc_Day25_CD34CD49f_68


title: sc_Day25_CD34CD49f_87


title: sc_Day25_CD34CD49f_63


title: sc_Day25_CD34CD49f_94


title: sc_Day25_CD34CD49f_60


title: sc_Day25_CD34CD49f_58


title: sc_Day25_CD34CD49f_57


title: sc_Day25_CD34CD49f_54


title: sc_Day25_CD34CD49f_78


title: sc_Day25_CD34CD49f_61


title: sc_Day25_CD34CD49f_59


title: sc_Day25_CD34CD49f_56


title: sc_Day25_CD34CD49f_51


title: sc_Day25_CD34CD49f_53


title: sc_Day25_CD34CD49f_52


title: sc_Day25_CD34CD49f_47


title: sc_Day25_CD34CD49f_49


title: sc_Day25_CD34CD49f_48


title: sc_Day25_CD34CD49f_45


title: sc_Day25_CD34CD49f_50


title: sc_Day25_CD34CD49f_46


title: sc_Day25_CD34CD49f_44


title: sc_Day25_CD34CD49f_43


title: sc_Day25_CD34CD49f_36


title: sc_Day25_CD34CD49f_34


title: sc_Day25_CD34CD49f_41


title: sc_Day25_CD34CD49f_32


title: sc_Day25_CD34CD49f_40


title: sc_Day25_CD34CD49f_35


title: sc_Day25_CD34CD49f_37


title: sc_Day25_CD34CD49f_38


title: sc_Day25_CD34CD49f_39


title: sc_Day25_CD34CD49f_33


title: sc_Day25_CD34CD49f_30


title: sc_Day25_CD34CD49f_31


title: sc_Day25_CD34CD49f_55


title: sc_Day25_CD34CD49f_28


title: sc_Day25_CD34CD49f_29


title: sc_Day25_CD34CD49f_25


title: sc_Day25_CD34CD49f_23


title: sc_Day25_CD34CD49f_27


title: sc_Day25_CD34CD49f_22


title: sc_Day25_CD34CD49f_20


title: sc_Day25_CD34CD49f_15


title: sc_Day25_CD34CD49f_26


title: sc_Day25_CD34CD49f_18


title: sc_Day25_CD34CD49f_16


title: sc_Day25_CD34CD49f_42


title: sc_Day25_CD34CD49f_19


title: sc_Day25_CD34CD49f_14


title: sc_Day25_CD34CD49f_11


title: sc_Day25_CD34CD49f_12


title: sc_Day25_CD34CD49f_7


title: sc_Day25_CD34CD49f_8


title: sc_Day25_CD34CD49f_10


title: sc_Day25_CD34CD49f_13


title: sc_Day25_CD34CD49f_5


title: sc_Day25_CD34CD49f_6


title: sc_Day25_CD34CD49f_4


title: sc_Day25_CD34CD49f_1


title: sc_Day25_CD34CD49f_9


title: sc_Day25_CD34CD49f_2


title: sc_Day25_CD34CD49f_3


title: sc_Day25_CD34CD49f_24


title: sc_Day15_CD49f_58


title: sc_Day15_CD49f_57


title: sc_Day15_CD49f_56


title: sc_Day25_CD34CD49f_21


title: sc_Day15_CD49f_52


title: sc_Day25_CD34CD49f_17


title: sc_Day15_CD49f_48


title: sc_Day15_CD49f_49


title: sc_Day15_CD49f_50


title: sc_Day15_CD49f_51


title: sc_Day15_CD49f_46


title: sc_Day15_CD49f_47


title: sc_Day15_CD49f_42


title: sc_Day15_CD49f_43


title: sc_Day15_CD49f_41


title: sc_Day15_CD49f_40


title: sc_Day15_CD49f_36


title: sc_Day15_CD49f_37


title: sc_Day15_CD49f_35


title: sc_Day15_CD49f_34


title: sc_Day15_CD49f_39


title: sc_Day15_CD49f_29


title: sc_Day15_CD49f_31


title: sc_Day15_CD49f_33


title: sc_Day15_CD49f_53


title: sc_Day15_CD49f_54


title: sc_Day15_CD49f_28


title: sc_Day15_CD49f_27


title: sc_Day15_CD49f_26


title: sc_Day15_CD49f_45


title: sc_Day15_CD49f_21


title: sc_Day15_CD49f_25


title: sc_Day15_CD49f_23


title: sc_Day15_CD49f_24


title: sc_Day15_CD49f_22


title: sc_Day15_CD49f_20


title: sc_Day15_CD49f_44


title: sc_Day15_CD49f_19


title: sc_Day15_CD49f_17


title: sc_Day15_CD49f_18


title: sc_Day15_CD49f_32


title: sc_Day15_CD49f_16


title: sc_Day15_CD49f_15


title: sc_Day15_CD49f_13


title: sc_Day15_CD49f_14


title: sc_Day15_CD49f_11


title: sc_Day15_CD49f_9


title: sc_Day15_CD49f_7


title: sc_Day15_CD49f_8


title: sc_Day15_CD49f_10


title: sc_Day15_CD49f_12


title: sc_Day15_CD49f_5


title: sc_Day15_CD49f_4


title: sc_Day15_CD49f_6


title: sc_Day15_CD49f_3


title: sc_Day15_CD49f_2


title: sc_Day15_CD49f_1


title: sc_Day2_35

value: unsorted cells


title: sc_Day2_33


title: sc_Day2_37


title: sc_Day2_34


title: sc_Day2_36


title: sc_Day2_31


title: sc_Day2_38


title: sc_Day2_32


title: sc_Day2_29


title: sc_Day2_28


title: sc_Day2_27


title: sc_Day2_25


title: sc_Day2_30


title: sc_Day2_24


title: sc_Day2_26


title: sc_Day2_21


title: sc_Day2_22


title: sc_Day2_20


title: sc_Day2_19


title: sc_Day2_17


title: sc_Day2_18


title: sc_Day2_16


title: sc_Day2_15


title: sc_Day2_14


title: sc_Day2_12


title: sc_Day2_8


title: sc_Day2_10


title: sc_Day2_9


title: sc_Day2_7


title: sc_Day2_6


title: sc_Day2_5


title: sc_Day15_CD49f_55


title: sc_Day2_4


title: sc_Day2_3


title: sc_Day2_23


title: sc_Day2_2


title: sc_Day2_1


title: sc_HDF_38


title: sc_HDF_35


title: sc_HDF_34


title: sc_HDF_32


title: sc_Day2_13


title: sc_Day2_11


title: sc_HDF_30


title: sc_HDF_28


title: sc_HDF_26


title: sc_HDF_27


title: sc_HDF_29


title: sc_HDF_31


title: sc_HDF_25


title: sc_HDF_24


title: sc_HDF_23


title: sc_HDF_22


title: sc_HDF_21


title: sc_HDF_20


title: sc_HDF_19


title: sc_HDF_17


title: sc_HDF_13


title: sc_HDF_14


title: sc_HDF_16


title: sc_HDF_15


title: sc_HDF_36


title: sc_HDF_18


title: sc_HDF_33


title: sc_HDF_37


title: sc_HDF_9


title: sc_HDF_11


title: sc_HDF_10


title: sc_HDF_8


title: sc_HDF_4


title: sc_HDF_3


title: sc_HDF_6


title: sc_HDF_1


title: sc_HDF_2


title: sc_HDF_5


title: sc_HDF_7


title: sc_HDF_12


title: high-MNase mono rep2

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

data_processing:
MNase-seq reads were aligned to hg19 assembly using bowtie2 version 2.2.2 with the following configurations: --very-sensitive-local  --no-discordant
Aligned reads exhibiting a mapping quality MAPQ < 20 were discarded using samtools version 1.1
For analysis of mono-nucleosomes fragments with a size of 140 - 200 bp and respectively 250 - 500 bp for di-nucleosomes were selected.
Nucleosome occupancy maps were generated using DANPOS2 toolkit version 2.2.2 with following configurations: dpos -u 1e-2  -m 1 -c 200000000 --extend 70 (--extend 150 bp for di-nucleosomes)
Nucleosome occupancy maps were normalized by copy number variations identified in the sonicated chromatin sample using Control-FREEC with following configurations: ploidity=3 window=500,000 step=50,000, minMappabilityPerWindow=0.8 breakPointThreshold=3
Genome_build: hg19
Supplementary_files_format_and_content: biwig files were generated using DANPOS2 toolkit and show normalized nucleosome occupancy

source_name: HeLa cells, 1000 U MNase

extract_protocol:
RNAs were degraded using RNase A and proteins were degreded by Proteinase K. DNA was precipitated from the supernatant. DNA fragments were seperated by size on an agarose gel and DNA from mono-/di-nucleosme bands were eluted.
Libraries were prepared according to NEBNext ChIP-Seq Kit for Illumina sequencing. Adapter were removed by size selection using AMPure XP magnetic beads.

treatment_protocol: Confluent grown HeLa cells were permebalized and different concentrations of MNase was added (100U for low digest and 1000U for high digest ). After 3 min chromatin digeston was stopped by adding SDS and EDTA.

value: HeLa


title: low-MNase mono rep2

source_name: HeLa cells, 100 U MNase


title: low-MNase di rep1


title: high-MNase di rep1


title: sonicated

source_name: HeLa cells, sonication


title: high-MNase mono rep1


title: HDF_d15_CD49f+_3_FPKM

description:
mRNA-Seq
Processed data file: HDF_FPKM.txt

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite.
Alignment to hg19 (GRCh37) using Tophat release 2.0.9 and Bowtie2 release2.1.0.
Differential expression performed with Cufflinks release 2.1.1 and Homo sapiens hg19 reference annotation.
Genome_build: GRCh37
Supplementary_files_format_and_content: BJ and HDF experiment FPKM tables derived from Cufflinks cuffdiff output. BJ_FPKM.txt and HDF_FPKM.txt are tab-delimited text files, zero-values removed. See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

extract_protocol:
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries using Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.

tag: time


title: HDF_d25_CD49f+CD34+_3_FPKM

source_name: HDFa, d25, CD49f+CD34+


title: HDF_d25_CD49f+_1_FPKM


title: HDF_d25_CD49f+CD34+_1_FPKM


title: HDF_d25_CD49f+_2_FPKM


title: HDF_d25_CD49f+CD34+_2_FPKM


title: HDF_d15_CD49f+_2_FPKM


title: HDF_3_FPKM

source_name: HDFa, unsorted

value: unsorted


title: HDF_d15_CD49f+_1_FPKM


title: HDF_2_FPKM


title: low-MNase mono rep1


title: BJ_d25_CD49f+CD34+_3_FPKM

description:
mRNA-Seq
Processed data file: BJ_FPKM.txt

value: BJ

value: neonatal foreskin fibroblast


title: BJ_d25_CD49f+CD34+_1_FPKM


title: BJ_d25_CD49f+_1_FPKM


title: BJ_d25_CD49f+_3_FPKM


title: BJ_d15_CD49f+_2_FPKM


title: BJ_d25_CD49f+CD34+_2_FPKM


title: HDF_d25_CD49f+_3_FPKM

value: HDFa

value: adult human dermal fibroblast


title: BJ_3_FPKM

source_name: BJ, unsorted

value: wildtype


title: HDF_1_FPKM


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 7 days post-MI surgery, replicate 2_bulk RNA

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

description:
Ki67_7dpMI_1910-M04
Murine hearts 7 days after myocardial infarction

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

tag: time point

value: 7 days post-MI surgery

value: Heart

value: proliferative cardiac cells


title: BJ_1_FPKM


title: BJ_2_FPKM


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 14 days post-SHAM surgery, replicate 1_bulk RNA

description:
Ki67_14dpSHAM_1105-M03
Murine hearts 14 days after sham surgery

value: 14 days post-SHAM surgery


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 2_bulk RNA

description:
Ki67_14dpMI_1105-M02
Murine hearts 14 days after myocardial infarction

value: 14 days post-MI surgery


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 14 days post-MI surgery, replicate 1_bulk RNA

description:
Ki67_14dpMI_1105-M01
Murine hearts 14 days after myocardial infarction


title: MB_sh1_1

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

institute: Yunnan university of Chinese Medicine

data_processing:
Reads were aligned to the h19 genome assembly using STAR_2.5.2a_modified
expression value were calculated using Version 1.4.6-p5 with the following configurations: -T 5 -a $gtf2 -t exon
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file reporting raw counts

source_name: breast cancer cell

extract_protocol:
Total RNA was isolated from cell lines using TRIzol reagent (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: triple negative breast cancer cells

value: Knockdown MIR100HG


title: MB_sh1_2


title: MB_TRC_2

value: Knockdown TRC


title: MB_sh2_1


title: MB_sh2_2


title: MB_TRC_1


title: BJ_d25_CD49f+_2_FPKM

city: New York


title: BJ_d15_CD49f+_3_FPKM


title: GM12878 HiChIP HC3C CTCF biological replicate 1

city: Stanford

first: Howard

middle: Y

state: CA

address: 269 Campus Drive

institute: Stanford University

description:
Protein-enriched long-range DNA contact
GM_HiChIP_HC3C_CTCF.hic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: bigwig: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

source_name: GM12878 cell line

growth_protocol: Grown in RPMI-1640 with 15% FBS

extract_protocol:
Protein enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% formaldehyde

value: Lymphoblastoid

value: female


title: GM12878 HiChIP CTCF biological replicate 2

description:
Protein-enriched long-range DNA contact
GM_HiChIP_CTCF.hic


title: GM12878 HiChIP CTCF biological replicate 1


title: GM12878 HiChIRP RNase TERC biological replicate 1

description:
Negative control long-range DNA contact
GM_HiChIRP_RNase_TERC.hic

data_processing:
Library strategy: HiChIRP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: bigwig: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

extract_protocol:
Rnase negative control of RNA enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% glutaraldehyde


title: GM12878 HiChIRP TERC biological replicate 2

description:
RNA-enriched long-range contact
GM_HiChIRP_TERC.hic

data_processing:
Library strategy: HiChIRP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

extract_protocol:
RNA enrichment of 3C library
Nextera

value: Lymphoblastoid cells


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 3 days post-MI surgery, replicate 1_bulk RNA

description:
Ki67_3dpMI_1910-M01
Murine hearts 3 days after myocardial infarction

value: 3 days post-MI surgery


title: GM12878 HiChIRP TERC biological replicate 1


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 3 days post-MI surgery, replicate 2_bulk RNA

description:
Ki67_3dpMI_1910-M02
Murine hearts 3 days after myocardial infarction


title: Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 7 days post-MI surgery, replicate 1_bulk RNA

description:
Ki67_7dpMI_1910-M03
Murine hearts 7 days after myocardial infarction


title: mES HiChIP HC3C Oct4 biological replicate 1

description:
Protein-enriched long-range DNA contact
mES_HiChIP_HC3C_Oct4.hic

source_name: v6.5 embryonic stem cell line

growth_protocol: Grown on gelatin-coated plates with KO DMEM supplemented with LIF

value: ES cell

value: male


title: mES HiChIP HC3C Oct4 biological replicate 2


title: BMDM HiChIRP RNase lincRNA-EPS biological replicate 2

description:
Negative control long-range DNA contact
BMDM_HiChIRP_RNase_EPS.hic

source_name: Bone-marrow derived macrophages

growth_protocol: Grown in DMEM with 15% FBS and supplemented with L929

value: Primary macrophage cells


title: GM12878 HiChIRP RNase TERC biological replicate 2


title: mES HiChIP Oct4 biological replicate 2

description:
Protein-enriched long-range DNA contact
mES_HiChIP_Oct4.hic


title: GM12878 HiChIP HC3C CTCF biological replicate 2


title: BMDM HiChIRP RNase lincRNA-EPS biological replicate 1


title: mES HiChIRP RNase 7SK biological replicate 1

description:
Negative control long-range DNA contact
mES_HiChIRP_RNase_7SK.hic


title: sc_Day15_CD49f_38

value: HDFa

value: adult human dermal fibroblast


title: BMDM EPSKO HiChIP SMC1a biological replicate 2

description:
Protein-enriched long-range contact
BMDM_EPSKO_HiChIP_SMC1a.hic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.