title: Scn5a_RE6-9_ventricles_HET5

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
RNA-seq: reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
RNA-seq: Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: WT-vs-HET-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

source_name: RE6-9+/- ventricles

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

extract_protocol:
Total RNA was isolated from the ventricular tissue of heterozygous RE6-9 mice and wildtype littermates using Tri Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Sigma Aldrich) and further purified using Nucleospin RNA Clean-up Kit with DnaseI treatment (Macherey-Nagel)
cDNA was prepared with the Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E). Total RNA (1 µg) was purified and sheared into small fragments followed by cDNA synthesis and ligation of the adapter. The quality and size distribution of the cDNA library templates were validated with Agilent DNA 1000 on 2100 Bioanalyzer (Agilent Technologies). cDNA samples were pooled per lane of paired-end 125 bp sequencing on an Illumina HiSeq 2500 instrument.

value: FVB/NJ

value: 2 weeks after birth

tag: tissue

value: ventricles


title: Scn5a_RE6-9_ventricles_HET6

status: Public on Oct 04 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age


title: miRNA array for ID103pc

type: RNA

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

description: miRNA array for ID103pc sample plasma

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The results of microchip analysis were preprocessed by the RMA method using Affymetrix Expression Console software (version 1.4.1.46) at RMA+DABG-NO-NORM-Human-only setting.

label: biotin

organism: Homo sapiens

source_name: Blood plasma

label_protocol: biotin

extract_protocol: RNA was isolated by a modified protocol [PMID: 31028584]: 400 μl sample of plasma was added to 1.2 ml Qiazol Lysis Reagent (Qiazol), thoroughly mixed for 15 sec, and incubated for 10 min at room temperature for complete dissociation of nucleoprotein complexes. After that, 1.6 μl of Ambion GlycoBlue Coprecipitant (15 mg/ml; Life Technologies) was added to the mixture to increase the efficiency of RNA precipitation during isolation on columns. Then, 320 μl chloroform was added to the mixture, the sample was stirred for 45 sec and incubated at room temperature for 5 min; then, the mixture was centrifuged at 16 000g and 4oC for 20 min and total RNA was isolated using miRNeasy Serum reagent/Plasma Kit (Qiagen) according to manufacturer’s protocol.

tag: Sex

value: male


title: AD_Hippocampus_rep1

city: NANJING

first: XIAOLEI

last: ZHU

state: JIANGSU

address: 321 ZHONGSHAN ROAD

department: Neurology

country: China

institute: Nanjing Drum Tower Hospital

hyb_protocol: Each sample was resuspended in 17ml nuclease free water. A master hybridization master mix was made consisting of diluted Hyb Spike-In controls, Agilent 10X blocking agent and Agilent Hi-RPM hybridization buffer. Aliquots of the master mix were added to each resuspended sample to a final volume of 45ml. The hybridization mix was incubated for 5 min at 1000C and then transferred to an ice/water bath to be incubated for 5 min. The samples were then briefly centrifuged to collect any condensation from the tube caps. The entire amount for each sample was dispensed into the center of a gasket well of an Agilent Mouse miRNA Release 21.0, 8x60K microarray slide (8 samples/slide). Once all samples were applied to the gasket slide, the chamber cover was clamped in place. The assembled slide cassette was placed into the hybridization oven and hybridized for 20 hrs at 550C at 20 rpm.

scan_protocol: The array was scanned using Agilent Scan Control vA.8.5.1 with the AgilentG3_miRNA protocol at a resolution of 5mm.

data_processing: miRNAs with Absent calls across all samples were filtered out. Quantile normalization was used to normalize the remaining miRNAs.

source_name: brain

label_protocol: Total RNA (100ng) from each sample (3 samples/group) was labeled using the Agilent miRNA Complete Labeling and Hybridization kit.

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: The hippocampus were isolated and homogenized using a Tissue homogenizer, and the RNA was extracted and purified using RNeasy Mini Kit.

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then hippocampus were rapidly dissected from the fresh brains.

tag: genotype/variation


title: Scn5a_RE6-9_ventricles_HET4


title: miRNA array for ID98c

description: miRNA array for ID98c sample plasma


title: miRNA array for ID106b

description: miRNA array for ID106b sample plasma


title: miRNA array for ID56pc

description: miRNA array for ID56pc sample plasma


title: miRNA array for ID134pc

description: miRNA array for ID134pc sample plasma


title: miRNA array for ID97c

description: miRNA array for ID97c sample plasma


title: miRNA array for ID130b

description: miRNA array for ID130b sample plasma


title: miRNA array for ID66c

description: miRNA array for ID66c sample plasma


title: Scn5a_RE6-9_ventricles_WT2

source_name: RE6-9+/+ ventricles


title: Granuloma_macrophages_Balb/c_infected_ 2

city: Münster

first: Niels-Arne

last: Münck

address: Roentgenstraße 21

department: Insitute of Immunology

country: Germany

institute: University of Münster

description: Primary murine macrophages isolated from phagocyte traps

hyb_protocol: GeneChips were washed and stained in an Affymetrix Fluidics Station 450

scan_protocol: Scanning was performed on a GeneChip Scanner 3000 7G

data_processing: Data was normalised using the MAS5 algorithm in Affymetrix MicroArray Suite

label: Biotin

source_name: Macrophages isolated from poly-acryl amide phagocyte traps

label_protocol: Labeling was done using a 3'IVT kit according to the manufacturers instructions.

growth_protocol: Phagocytes where isolated from phagocyte traps according to the protocol published in Model for Generation of Large Numbers of Primary, Inflammatory Skin-Derived Neutrophils, and Macrophages by John et al., 2013 in Methods in molecular biology, DOI: 10.1007/978-1-62703-227-8_27

extract_protocol: Total RNA extraction was performed using a Quiagen RNeasy micro kit.

treatment_protocol: Macrophages where isolated from the primary phagocyte mixture by adherence overnight and either infected with 5x MOI of metacyclical Leishmania major or left untreated as uninfected controls for 4h a 37°C

value: BALB/c

tag: cell type

value: macrophages

tag: infection status

value: infected


title: ccr4D Replicate #3

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

country: USA

institute: UTHSC

data_processing:
QC trimming Q >= 30 using fastx-trim
Alignment with STAR using S288C reference
Raw read counts collected
Differential Expression using DeSeq2
Genome_build: S288C_reference
Supplementary_files_format_and_content: csv file containing raw reads for each sample

organism: Saccharomyces cerevisiae

source_name: BY4741 yeast genetic background

growth_protocol: All samples and replicates were grown in yeast nutrient rich YPD (1% yeast extract/2%peptone/2%dextrose) to mid-log phase

extract_protocol:
Total RNA was extracted using the hot acid phenol approached.  After RNA extraction, samples were treated with Dnase I to rid samples of contaminating genomic DNA.
Lexogen RNASeq Kit

treatment_protocol: No treatment.

tag: genotype


title: miRNA array for ID7b

description: miRNA array for ID7b sample plasma


title: ccr4D Replicate #1


title: miRNA array for ID47b

description: miRNA array for ID47b sample plasma


title: ccr4D Replicate #2


title: miRNA array for ID14pc

description: miRNA array for ID14pc sample plasma


title: Wild-type Replicate #3

value: Wild-type


title: Scn5a_RE6-9_ventricles_WT1


title: let-7i-3p

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping  (READemption 0.3.0)
Size filtering: discarding reads shorter than 14 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: Human Genome GRCh37
Supplementary_files_format_and_content: CSV with reads per gene

source_name: HeLa-229 cells_let-7i-3p

growth_protocol: HeLa cells grown in standard conditions  (DMEM 1 g/L glucose (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom), maintained in a 5% CO2, humidified atmosphere, at 37°C)

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: MicroRNAs were transfected into HeLa-229 cells using a standard reverse transfection protocol (Lipofectamine RNAiMAX, Life Technologies), at a final miRNA concentration of 50 nM. Cells were collected 72h pos-transfection.

tag: treatment

value: transfection with miR-744-5p (50nM, 72h)

tag: cell line


title: Wild-type Replicate #1


title: Wild-type Replicate #2


title: control-miR_cel-miR-231

source_name: HeLa-229 cells_control-miR_cel-miR-231

value: transfection with control miR (50nM, 72h)


title: miRNA array for ID67c

description: miRNA array for ID67c sample plasma


title: J906_7Rp_p3_7

city: Atlanta

first: Jack

middle: L

last: Arbiser

state: GA

address: 101 Woodruff Circle WMB 5309

department: Dermatology

institute: Emory School of Medicine

data_processing:
Image acquisition and data extraction were performed with an Illumina HiScan laser scanner and GenomeStudio software.  Data were aligned to the murine reference genome using STAR. Sequencing data was first checked by FastQC for quality control and then aligned to the mouse “indexed” reference genome (mm10) using STAR (Spliced Transcripts Alignment to a Reference). Gene quantification was done using HTSeq-count. Gene count data from HTSeq-count was filtered before analysis to remove lowly expressed genes (For example a gene is retained if it has 10 or greater counts for at least 33% samples). CPM (counts per million) data was generated after normalization using trimmed method of M-values (TMM), as implemented in the Bioconductor package EdgeR.
Genome_build: mm10

source_name: tumor tissue

extract_protocol:
Previously frozen tumor tissue was lysed and homogenized in QIAzol reagent until fully disrupted.  RNA extraction was performed using Qiagen miRNeasy kit with on-column DNase treatment according to the manufacturer’s specifications.  The concentration of RNA eluted in nuclease-free water was determined and analyzed for quality control prior to RNAseq.
RNAseq library preparation was performed at Novogene Corporation utilizing the NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (New England Biolabs, Ipswich, MA). Sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Santa Clara, CA) and quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA) as well as by quantitative PCR (Applied Biosystems, Foster City, CA). The libraries were sequenced on an Illumina sequencer using a 2x150 Paired End (PE) configuration.  Raw sequence data (.bcl files) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq software.

tag: strain background

value: Nu/Nu nude

value: R-propranolol


title: Scn5a_RE6-9_ventricles_WT3


title: J906_5Rp_p1_5


title: J906_10Rp_p5_9


title: J906_8Rp_p4_8


title: DIPG8 [gene-level]

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Gene expression data from pediatric DIPG biopsies.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HTA 2.0 Array. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Transcript Analysis Console 4.0 was used for gene- and exon-level normalization and signaling summarization by evaluating QC values for the array. This allows performing an evaluation of gene and exon expression between the samples (brain stem tumors and tumors from other locations /GSE72269) and the control tissues. At this level, the expression analysis was carried out by groups and not in individual samples.
Parameters used for the analysis were: One-Way Between-Subjects ANOVA (Unpaired); Fold Change (linear) < - 2 or Fold Change (linear) > 2; and p-value in ANOVA (Condition pair) < 0.05.
CHP files include both gene- and exon-level RMA data.

source_name: Pediatric DIPG biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Six DIPG biopsies were collected from children, from 1 through 15 years of age at Hospital de Pediatría “Silvestre Frenk Freund”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), during a four-year period from 2015 to 2019.

extract_protocol: Total RNA was extracted from all tissue samples as previously described by Ruiz Esparza-Garrido et al. Tissue (2-10mg) was resuspended in 0.8 ml TRIZOL®, mechanically homogenized, and incubated for 30 minutes at room temperature (RT; ˜25°C). Then, 0.16 ml (per 1 ml TRIZOL®) chloroform was added to each sample and the sample was vigorously stirred (˜15 sec), and incubated for 15 minutes at RT. After, samples were centrifuged at 15,000xg for 15 min at 4°C and the aqueous phase –which corresponds to RNA- was transferred to a nuclease-free tube. Furthermore, 0.5 ml isopropanol was added to each sample to precipitate the RNA, and it was incubated for 30 min at RT, and centrifuged at 15,000xg (4°C) for 30 minutes. The obtained pellet was washed three times with 75% ethanol, air-dried, and resuspended in 10-15 μl nuclease-free water. The quantification and determination of RNA quality was determined using a NanoDrop 1000 (Thermo Fisher).

treatment_protocol: All samples were collected during surgery, snap frozen in liquid nitrogen, and stored at −80 °C until use. The DIPG diagnosis was performed based on clinical and MRI features, according to the approved protocol by the Ethics Committee of the Centro Médico Nacional Siglo XXI, IMSS. All the patients provided written informed consent before study entry and the samples were used to confirm the histopathology diagnosis and molecular tests.

tag: diagnosis

value: Pediatric diffuse intrinsic pontine glioma (DIPG)

value: Tumor biopsy


title: DIPG7 [gene-level]


title: J906_4_Cont_4

value: vehicle


title: J906_1_Cont_2


title: J906_1_Cont_1


title: DIPG4 [gene-level]


title: DIPG5 [gene-level]


title: J906_3_Cont_3


title: DIPG3 [gene-level]


title: GA-CFP 262

city: Munich

first: Qihui

last: Zhou

address: Feodor-Lynen-Str. 17

institute: German Center for Neurodegenerative Diseases

data_processing:
Demultiplexed fastq files using Illumina Index file (Version 1.0) in Galaxy.
Adaptor sequence trimmed using Clip adaptor sequence (Version 1.0.0) in Galaxy.
Alignment using RNA STAR Gapped-read mapper (Version 2.5.2b-0) in Galaxy.
Count table generated using HTSeq-count (Version 1.0.0) in Galaxy.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tabular.txt: Tab-delimited count tables generated using HTSeq-count.

source_name: spinal cord

extract_protocol:
Spinal cord from thoracic segment T8 to T13 were dissected, snap frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: WT or GA-CFP transgenic mice treated with either PBS or OVA-(GA)10 at age of 32 weeks.

tag: strain/background

value: spinal cord T8-T13

value: WT

value: OVA


title: GA-CFP 274


title: GA-CFP 273


title: GA-CFP 291

value: TG

value: PBS


title: GA-CFP 269


title: GA-CFP 265


title: GA-CFP 276


title: patient J [C189_CD_M3]

city: Montreal

first: Marika

last: Sarfati

state: Quebec

address: 900 rue St Denis

country: Canada

institute: CRCHUM

data_processing:
A differential expression analysis was performed using RNA-sequencing data counts for 23686 genes. The count dataset was produced from two experimental batches so the batch removal procedure from the limma R package had to be used.
Samples having less than 6000 genes expressed as well as an outlier revealed by PCA (Principal Component Analysis) were removed. Genes with no observable expression count for more than half of the samples were also removed from the dataset.
A TMM (trimmed mean of M values) normalization (EdgeR package) was then applied to the remaining 12231 genes on all samples.
A differential expression analysis was performed on all samples with limma. Contrast matrix was applied to assess for the differential expression of FACS-sorted DC-like versus Mono/MF-like populations from MLNs of 5 UC and 7 CD patients, respectively.
Gene set enrichment analysis (GSEA) was obtained using the regression data from Limma using the camera algorithm (Camera: a competitive gene set test accounting for inter-gene correlation) to scan the publicly available MySigDB database.
Supplementary_files_format_and_content: TPM (transcripts per million) matrix txt file

source_name: Mesenteric lymph nodes

extract_protocol:
Cells were lysed in a solution of TCL (Qiagen) and 1% 2-Mercaptoethanol.  RNA samples were   isolated using the Qiagen RNeasy Mini kit following the manufacturers recommendations. RNA quality check was done using Agilent RNA Nano 6000 chip (Agilent Technologies). Whole Transcriptome amplification (WTA) was performed using a modified SMART-Seq2 protocol, with Maxima Reverse Transcriptase (Life Technologies) used in place of Superscript II. Whole transcriptome amplification (WTA) products were cleaned with Agencourt XP DNA beads and 70% ethanol (Beckman Coulter, Brea, CA).
Illumina sequencing libraries were prepared using Nextera XT (Illumina, San Diego, CA). The library of each sample was pooled together, and cleaned with two rounds of 0.8x DNA SPRIs (Beckman Coulter). Library quality was assessed with a high sensitivity DNA chip (Agilent) and quantified with a high sensitivity dsDNA Quant Kit (Life Technologies). Samples were sequenced on an Illumina NextSeq 500 instrument using the 75 cycles NextSeq 500/550 High Output Kit v2 (37base pairs paired-end reads).

tag: cell phenotype


title: GA-CFP 275


title: patient K [C163_CD_M3]


title: J906_6Rp_p2_6


title: GA-CFP 286


title: patient I [C277_CD_M3]


title: GA-CFP 288


title: GA-CFP 287


title: patient H [C254_CD_M3]


title: patient G [C153_CD_M3]


title: GA-CFP 285


title: GA-CFP 284


title: GA-CFP 271


title: NDV_37_P2-3

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

description:
NDV P2-3
replicate 3 of passage 2

data_processing:
Illumina Casava software used for basecalling
bowtie2 for alignment
Genome_build: KY295917 (with some modification for technical reason; 'TAA' at the positon of 4004-4006 is replaced by 'TAATAA')
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: avian paramyxovirus 1

source_name: baby hamster kidney cells

growth_protocol: Viruses were amplified in Bsr-T7 cells, then virus cotaining supernatant were collected when infection became confluent in the cells.

extract_protocol:
QIAamp viral RNA extraction kit were used to extract RNA from supernatant.
RNAs were reverse transcribed and amplified by superscript III one-step. Amplified amplicon were processed by TruSeq DNA LT Sample Prep Kit.

tag: host cell type

value: Bsr-T7 cells

tag: passages

tag: molecule subtype

value: RNA from the virion


title: patient E [C248_UC_M3]


title: NDV_37_P2-2

description:
NDV P2-2
replicate 2 of passage 2


title: DIPG2 [gene-level]

tag: tissue


title: NDV_37_P2-1

description:
NDV P2-1
replicate 1 of passage 2


title: NDV_37_P1-3

description:
NDV P1-3
replicate 3 of passage 1


title: patient D [C154_UC_M3]


title: patient C [C287_UC_M3]


title: patient B [C136_UC_M3]


title: GA-CFP 282


title: NDV_InputDNA_sheared_DNA

description: NDV Input

library_source: genomic

molecule: genomic DNA

source_name: plasmid DNA

value: plasmid DNA


title: NDV_Rescue_P0

description:
NDV P0
passage 0

value: passage 0


title: patient A [C283_UC_M3]


title: Ctrl MLN 3

city: Kingston

first: David

last: Lillicrap

state: ON

address: 88 Stuart Street

department: Pathology and Molecular Medicine

institute: Queen's University

hyb_protocol: As per NanoString Technologies Inc, Seattle, WA

data_processing:
Data were quantified, normalized and analyzed using the NanoString Mouse Immunology panel (NanoString Technologies Inc, Seattle, WA). All data was normalized to 14 housekeeping genes (nSolver).
Up/down regulated genes defined as transcript fold change > 1.25 with an alpha = 0.05. After checking assumptions, Welch’s T Test was used to calculate p values. Expression data was standardized by calculating Z-scores and visualized in a heat map using squared Pearson distance metric with Ward’s clustering method.

source_name: Ctrl MLN 3

extract_protocol: Spleen and mesenteric lymph nodes are immediately dissected and stored in RNAlater (Invitrogen). mRNA was isolated using RNeasy Plus Mini Kit (Qiagen) and quantified.

treatment_protocol: Mice are treated with ampicillin by gavage at 3 weeks of age or not

tag: strain

value: C57BL6 Exon 16 KO Hemophilia A

tag: strain id

value: Mouse 12

value: Control

value: Mesenteric Lymph Nodes


title: Ctrl MLN 2

scan_protocol: As per NanoString Technologies Inc, Seattle, WA

source_name: Ctrl MLN 2

value: Mouse 11


title: patient I [C277_CD_M2]


title: Ctrl MLN 1

source_name: Ctrl MLN 1

label_protocol: As per NanoString Technologies Inc, Seattle, WA

value: Mouse 10


title: patient J [C189_CD_M2]


title: NDV_37_P1-2

description:
NDV P1-2
replicate 2 of passage 1


title: patient G [C153_CD_M2]


title: Ctrl Spleen 1

source_name: Ctrl Spleen 1

value: Mouse 7

value: Spleen


title: MNase_WT_sgs1Δ_3241_G1 (M_4_IGO_09486_B_12_S32)

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

description:
MNase of sgs1Δ in G1 phase of the cell cycle
Mnase
M_4_IGO_09486_B_12_S32

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  without futher smoothing or ratio.

source_name: Mnase

growth_protocol: Cells were grown on YPD at 25°C

extract_protocol:
Standard protocol for preparation of yeast genomic DNA, chromatin immunoprecipitation and micrococcal nuclease digestion
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)

treatment_protocol: Samples were either collected from G1 synchronised cultures or from cell released from alpha-factor arrest into S phase for 60 minutes in the presence of 200 mM HU (hydroxyurea).

value: Untreated

tag: cell-cycle phase

tag: antibody


title: Ctrl Spleen 3

source_name: Ctrl Spleen 3

value: Mouse 9


title: MNase_WT_exo1Δ sgs1Δ_3239_HU 200mM 60min (M_6b_IGO_09486_B_15_S35)

description:
MNase of exo1Δ sgs1Δ in HU phase of the cell cycle
Mnase
M_6b_IGO_09486_B_15_S35

value: exo1{delta} sgs1{delta}

value: HU 200mM 60min

value: S-Phase


title: MNase_WT_exo1Δ_3240_G1 (M_3_IGO_09486_B_11_S31)

description:
MNase of exo1Δ in G1 phase of the cell cycle
Mnase
M_3_IGO_09486_B_11_S31


title: patient H [C254_CD_M2]


title: MNase_WT_872_HU 200mM 60min (M_5_IGO_09486_B_13_S33)

description:
MNase of Wild type in HU phase of the cell cycle
Mnase
M_5_IGO_09486_B_13_S33

value: WT


title: Ctrl Spleen 2

source_name: Ctrl Spleen 2

value: Mouse 8


title: Amp MLN 3

source_name: Amp MLN 3

value: Mouse 6

value: Ampicillin Treated


title: NDV_37_P1-1

description:
NDV P1-1
replicate 1 of passage 1

value: Bsr-T7 cells

value: RNA from the virion


title: patient L [C169_CD_M2]


title: MNase_WT_sgs1Δ_3241_HU 200mM 60min (M_8_IGO_09486_B_17_S37)

description:
MNase of sgs1Δ in HU phase of the cell cycle
Mnase
M_8_IGO_09486_B_17_S37


title: patient E [C248_UC_M2]


title: Amp MLN 2

source_name: Amp MLN 2

value: C57BL6 Exon 16 KO Hemophilia A

value: Mouse 5


title: patient F [C164_CD_M2]


title: patient D [C154_UC_M2]


title: Amp Spleen 3

source_name: Amp Spleen 3

value: Mouse 3


title: MNase_WT_872_G1 (M_1_IGO_09486_B_9_S46)

description:
MNase of Wild type in G1 phase of the cell cycle
Mnase
M_1_IGO_09486_B_9_S46


title: input_WT_sgs1Δ_3241_HU 200mM 60min (Inp8_IGO_09486_B_8_S45)

description:
Input of sgs1Δ in HU phase of the cell cycle
Input
Inp8_IGO_09486_B_8_S45

source_name: Input

value: input


title: patient K [C163_CD_M2]


title: MNase_WT_exo1Δ_3240_HU 200mM 60min (M_7_IGO_09486_B_16_S36)

description:
MNase of exo1Δ in HU phase of the cell cycle
Mnase
M_7_IGO_09486_B_16_S36


title: input_WT_exo1Δ_3240_HU 200mM 60min (Inp7_IGO_09486_B_7_S44)

description:
Input of exo1Δ in HU phase of the cell cycle
Input
Inp7_IGO_09486_B_7_S44


title: input_WT_exo1Δ sgs1Δ_3239_HU 200mM 60min (Inp6_IGO_09486_B_6_S43)

description:
Input of exo1Δ sgs1Δ in HU phase of the cell cycle
Input
Inp6_IGO_09486_B_6_S43


title: MNase_WT_exo1Δ sgs1Δ_3239_G1 (M_2_IGO_09486_B_10_S30)

description:
MNase of exo1Δ sgs1Δ in G1 phase of the cell cycle
Mnase
M_2_IGO_09486_B_10_S30


title: Amp Spleen 2

source_name: Amp Spleen 2

value: Mouse 2


title: patient C [C287_UC_M2]


title: input_WT_872_HU 200mM 60min (Inp5_IGO_09486_B_5_S42)

description:
Input of Wild type in HU phase of the cell cycle
Input
Inp5_IGO_09486_B_5_S42


title: DIPG8 [exon-level]

source_name: Pediatric DIPG biopsy

value: Pediatric diffuse intrinsic pontine glioma (DIPG)

value: Tumor biopsy


title: Amp Spleen 1

source_name: Amp Spleen 1

value: Mouse 1

value: Spleen


title: patient B [C136_UC_M2]

source_name: Mesenteric lymph nodes


title: DIPG7 [exon-level]


title: input_WT_sgs1Δ_3241_G1 (Inp4_IGO_09486_B_4_S41)

description:
Input of sgs1Δ in G1 phase of the cell cycle
Input
Inp4_IGO_09486_B_4_S41

value: Untreated


title: DIPG4 [exon-level]


title: DIPG5 [exon-level]


title: Amp MLN 1

source_name: Amp MLN 1

value: Mouse 4

value: Mesenteric Lymph Nodes


title: input_WT_exo1Δ_3240_G1 (Inp3_IGO_09486_B_3_S40)

description:
Input of exo1Δ in G1 phase of the cell cycle
Input
Inp3_IGO_09486_B_3_S40


title: CLB-GA-shCtrl_rep2

city: Gent

first: Dries

last: Rombaut

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

data_processing:
Reads were determined using Kallisto, a pseudo-alignment algorithm.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts per transcript for each Sample

source_name: neuroblastoma

extract_protocol:
Total RNA was extracted from fresh cells using TRIzol® Reagent (Invitrogen) and the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CLB-GA-cells were treated with doxycycline for 5 days, together with cells treated with a control

value: CLB-GA

tag: shRNA

value: control

value: no dox


title: CLB-GA-shPHOX2B_rep2

value: shRNA against PHOX2B

value: dox


title: CLB-GA-shCtrl_rep1


title: input_WT_872_G1 (Inp1_IGO_09486_B_1_S38)

description:
Input of Wild type in G1 phase of the cell cycle
Input
Inp1_IGO_09486_B_1_S38

value: WT


title: DIPG3 [exon-level]


title: DIPG2 [exon-level]


title: MNAse_rad50Δ_1591_HU 200mM 60min (9113_IGO_09486_8_S8)

description:
MNase of rad50Δ in HU phase of the cell cycle
MNAse
9113_IGO_09486_8_S8

value: HU 200mM 60min

value: S-Phase


title: risk (CC), pooled [ChIP-Seq]

city: Farmington

first: Annabelle

last: Rodriguez

state: CT

address: 263 Famington Ave, MC-3501

department: Center for Vascular Biology

institute: UCONN Health

description: risk.bdg

data_processing:
The reads were trimmed for quality with fastx-trimmer.  The trimmed reads were mapped to the reference genome (UCSC hg19) using bwa mem.
The alignments were processed for peak-detection using macs2, and the peaks were annotated using HOMER annotate-peaks.pl.
Genome_build: hg19 (37.2)
Supplementary_files_format_and_content: bedGraph file for each of the conditions

source_name: PBMCs

growth_protocol: Cells were maintained in RPMI and the media was changed every third day.

extract_protocol:
Immunoprecipitation was performed using Active Motif #61213 to produce 10ng ChIP DNA
TruSeq DNA

treatment_protocol: Basal level

value: PBMCs

tag: cell type

value: EBV (Epstein Barr Virus)-transformed B lymphocyte cells

value: (GG)

tag: gender

value: female


title: reference (GG), pooled [ChIP-Seq]

description: reference.bdg

tag: genotype

value: (CC)


title: MNAse_rad50Δ_1591_G1 (917_IGO_09486_4_S4)

description:
MNase of rad50Δ in G1 phase of the cell cycle
MNAse
917_IGO_09486_4_S4

tag: treatment


title: input_WT_exo1Δ sgs1Δ_3239_G1 (Inp2_IGO_09486_B_2_S39)

description:
Input of exo1Δ sgs1Δ in G1 phase of the cell cycle
Input
Inp2_IGO_09486_B_2_S39

value: exo1{delta} sgs1{delta}

value: input


title: risk (CC), (008, rep 3) [ChIP-Seq]

description: risk.bdg


title: patient A [C283_UC_M2]


title: MNAse_WT_872_G1 (913_IGO_09486_2_S2)

description:
MNase of Wild type in G1 phase of the cell cycle
MNAse
913_IGO_09486_2_S2

value: Untreated


title: input_WT_872_HU 200mM 60min (91C_IGO_09486_5_S5)

description:
Input of Wild type in HU phase of the cell cycle
input
91C_IGO_09486_5_S5


title: input_rad50Δ_1591_HU 200mM 60min (91D_IGO_09486_7_S7)

description:
Input of rad50Δ in HU phase of the cell cycle
input
91D_IGO_09486_7_S7


title: CLB-GA-shPHOX2B_rep1

tag: cell line


title: MNAse_WT_872_HU 200mM 60min (9110_IGO_09486_6_S6)

description:
MNase of Wild type in HU phase of the cell cycle
MNAse
9110_IGO_09486_6_S6


title: input_rad50Δ_1591_G1 (91B_IGO_09486_3_S3)

description:
Input of rad50Δ in G1 phase of the cell cycle
input
91B_IGO_09486_3_S3


title: reference (GG), (003, rep 2) [ChIP-Seq]

description: reference.bdg


title: reference (GG), (003, rep 1) [ChIP-Seq]


title: MNAse_set1Δ_2290_HU 200mM 60min (M8_S28_L005_R1_HJM3KBBXX_1)

description:
MNase of set1Δ in G1 phase of the cell cycle
MNAse
M8_S28_L005_R1_HJM3KBBXX_1


title: reference (GG), (003, rep 3) [ChIP-Seq]

description: reference.bdg


title: input_WT_872_G1 (91A_IGO_09486_1_S1)

description:
Input of Wild type in G1 phase of the cell cycle
input
91A_IGO_09486_1_S1


title: risk (CC), (008, rep 1) [ChIP-Seq]


title: risk (CC), (008, rep 2) [ChIP-Seq]

description: risk.bdg


title: MNAse_gcn5Δ_2029_HU 200mM 60min (M7_S27_L005_R1_HJM3KBBXX_1)

description:
MNase of gcn5Δ in G1 phase of the cell cycle
MNAse
M7_S27_L005_R1_HJM3KBBXX_1


title: MNAse_set1Δ_2290_G1 (M4_S24_L005_R1_HJM3KBBXX_1)

description:
MNase of set1Δ in G1 phase of the cell cycle
MNAse
M4_S24_L005_R1_HJM3KBBXX_1


title: MNAse_rad50Δ_1591_HU 200mM 60min (M6_S26_L005_R1_HJM3KBBXX_1)

description:
MNase of rad50Δ in G1 phase of the cell cycle
MNAse
M6_S26_L005_R1_HJM3KBBXX_1


title: MNAse_WT_872_HU 200mM 60min (M5_S25_L005_R1_HJM3KBBXX_1)

description:
MNase of Wild type in G1 phase of the cell cycle
MNAse
M5_S25_L005_R1_HJM3KBBXX_1


title: LAG3, risk (CC), (008, rep 2) [4C-Seq]

data_processing:
Library strategy: 4C-Seq
The analysis was done using the 4C-ker method (PLoS Computational Biology, 2016).
A reduced genome was created for the NlaIII restriction enzyme from the hg19 (UCSC) reference genome.  The reduced genome was indexed using bowtie.
The reads were trimmed for quality and aligned against the reduced genome.  The aligned files were converted to bedGraph format and counts were generated.  As the bait/anchor sequence and its position was known the reads mapping to fragments immediately upstream of the bait and downstream of the bait were removed.  The resulting files were proccessed using the R.4Cker package in R.
Genome_build: hg19 (37.2)
Supplementary_files_format_and_content: The files have the following columns chromosome, start, end, baseMean, log2Foldchange, lfcSE, stat, pvalue, padj.  The lfcSE is the calculated standard error, stat is the value of the statistic generated, pvalue is the p-value for that comparison, and adjusted p.value is the BH corrected p-value for the multiple hypothesis testing.

extract_protocol:
Chromatin was processed as stated in van de Werken et al. (2012).
DNA libraries were prepared as stated in van de Werken et al. (2012).


title: LAG3, reference (GG), (003, rep 2) [4C-Seq]


title: MNAse_rad50Δ_1591_G1 (M2_S22_L005_R1_HJM3KBBXX_1)

description:
MNase of rad50Δ in G1 phase of the cell cycle
MNAse
M2_S22_L005_R1_HJM3KBBXX_1


title: Col-0Plec_rep3: Col-0 PcBMM inoculated. Replicate 3

city: Pozuelo de Alarcón

first: Laura

last: Bacete

state: Madrid

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas. Universidad Politécnica de Madrid.

description: Biological replicate 3 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants.

hyb_protocol: 1650 ng of Cy3 probes were mixed and hybridized to an Arabidopsis 4 Oligo Microarray 4x44K (G2519F_021169, Agilent Technologies) for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in an hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Arrays were scanned at 3mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent Technologies). Local background correction and normalization of expression data were performed using normexp and loess methods, respectively. To have similar distribution across arrays and to achieve consistency among arrays, log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg . The expected false discovery rate was controlled to be less than 5%.

organism: Arabidopsis thaliana

source_name: 18 days-old Col-0 plants, Plectosphaerella cucumerina BMM-inoculated (1 dpi)

label_protocol: 200 ng of total RNA was reverse transcribed using T7 promoter primer and the cDNA was converted to aRNA using T7 RNA polimerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

growth_protocol: Arabidopsis plants were grown during 18 days in phytochambers under short-day conditions (10 hours of light/14 hours of dark) on sterile soil-vermiculite (3:1) 21-20 ªC, light intensity of 120 μE/m2s and with 65% of relative humidity.

extract_protocol: Frozen samples were ground using mortar and pestle and total RNA was extracted with a phenol/chloroform method, as described in Berrocal-Lobo et al., 2002. Total RNA was further purified using the RNeasy Kit (Qiagen) and quantified with a NanoDrop ND-100 spectrophotometer (Thermo Scientific). RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies.

treatment_protocol: For PcBMM pathogenicity assays, 18-day-old plants growing on soil were sprayed with a spore suspension (4×106 spores/ml) of the fungus. After inoculation, plants were placed in a tray and covered with plastic wrap to maintain high humidity. Trays were kept in a growing chamber under short-day conditions with a daytime temperature of 24 ºC and a night-time temperature of 22 ºC. At least 20 plants per genotype were inoculated in each experiment, and water-treated (mock) plants were included as a control.

tag: ecotype

value: Wild-type

value: Plectospharella cucumerina BMM, 4·106 spores/mL

value: 18 day-old leaves


title: MNAse_WT_872_G1 (M1_S21_L005_R1_HJM3KBBXX_1)

description:
MNase of Wild type in G1 phase of the cell cycle
MNAse
M1_S21_L005_R1_HJM3KBBXX_1


title: Col-0Plec_rep1: Col-0 PcBMM inoculated. Replicate 1

description: Biological replicate 1 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants.


title: LAG3, risk (CC), (008, rep 1) [4C-Seq]


title: LAG3, reference (GG), (003, rep 1) [4C-Seq]


title: Col-0mock_rep3: Col-0 mock-treated. Replicate 3

description: Biological replicate 3 of 3. Gene expression at 1 day post-inoculation in mock-treated wild-type plants.

source_name: 18 days-old Col-0 plants, mock treated (1 dpi)

value: mock (H2O)


title: arr6-3Plec_rep3: arr6-3 PcBMM inoculated. Replicate 3

description: Biological replicate 3 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected arr6-3 plants.

source_name: 18 days-old arr6-3 plants, Plectosphaerella cucumerina BMM-inoculated (1 dpi)


title: Col-0Plec_rep2: Col-0 PcBMM inoculated. Replicate 2

description: Biological replicate 2 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants.


title: MNAse_gcn5Δ_2029_G1 (M3_S23_L005_R1_HJM3KBBXX_1)

description:
MNase of gcn5Δ in G1 phase of the cell cycle
MNAse
M3_S23_L005_R1_HJM3KBBXX_1

source_name: Mnase


title: rs10846744, risk (CC), (008, rep 1) [4C-Seq]


title: rs10846744, reference (GG), (003, rep 2) [4C-Seq]


title: rs10846744, reference (GG), (003, rep 1) [4C-Seq]


title: rs10846744, risk (CC), (008, rep 2) [4C-Seq]


title: arr6-3Plec_rep2: arr6-3 PcBMM inoculated. Replicate 2

description: Biological replicate 2 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected arr6-3 plants.


title: shNR2F2-008-2 risk (CC), (replicate, 008 knockdown NR2F2)

data_processing:
The reads were trimmed for quality and aligned to the reference genome (UCSC hg19 from the iGenomes) with reference annotation using tophat2 (version 2.1.1).
Cuffdiff was used with the aligned reads and reference annotation to generate the transcript abundance estimates, and calculate the differential gene-expression.
The results were plotted using R and cummeRbund.
Genome_build: hg19 (37.2)
Supplementary_files_format_and_content: The gene difference data table genrated by cuffdiff/cummeRbund is given here.

extract_protocol:
RNA from EBV (Epstein Barr Virus)-transformed B lymphocyte cells, from 3 carriers of the risk (CC) allele, 3 non-carriers of the (GG) reference allele, replicates of one chosen risk (CC), reference (GG) and knockdown of risk (CC) were isolated using the Qiagen RNeasy-Midi kit (Cat#75142). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Basal levels, no treatment or shNR2F2 silencing by lentiviral particles


title: Col-0mock_rep2: Col-0 mock-treated. Replicate 2

description: Biological replicate 2 of 3. Gene expression at 1 day post-inoculation in mock-treated wild-type plants.


title: Col-0mock_rep1: Col-0 mock-treated. Replicate 1

description: Biological replicate 1 of 3. Gene expression at 1 day post-inoculation in mock-treated wild-type plants.


title: α-H3_set1Δ_2290_G1 (IP_8_S44_L007_R1_HJM3KBBXX_1)

description:
Ip-H3 of set1Δ in G1 phase of the cell cycle
ChIP-Seq, α-H3 antibody
IP_8_S44_L007_R1_HJM3KBBXX_1

value: Anti-H3 antibodies_Abcam_ Ab1791


title: shNR2F2-008-3 risk (CC), (replicate, 008 knockdown NR2F2)


title: arr6-3mock_rep2: arr6-3 mock-treated. Replicate 2

description: Biological replicate 2 of 3. Gene expression at 1 day post-inoculation in mock-treated arr6-3 plants.

source_name: 18 days-old arr6-3 plants, mock treated (1 dpi)


title: α-H3_gcn5Δ_2029_G1 (IP_6_S40_L006_R1_HJM3KBBXX_1)

description:
Ip-H3 of gcn5Δ in G1 phase of the cell cycle
ChIP-Seq, α-H3 antibody
IP_6_S40_L006_R1_HJM3KBBXX_1


title: α-H3_WT_872_G1 (IP_1_S30_L005_R1_HJM3KBBXX_1)

description:
Ip-H3 of Wild type in G1 phase of the cell cycle
ChIP-Seq, α-H3 antibody
IP_1_S30_L005_R1_HJM3KBBXX_1


title: S008 risk (CC), (replicate, 008)


title: α-H3_rad50Δ_1591_G1 (IP_5_S38_L006_R1_HJM3KBBXX_1)

description:
Ip-H3 of rad50Δ in G1 phase of the cell cycle
ChIP-Seq, α-H3 antibody
IP_5_S38_L006_R1_HJM3KBBXX_1


title: α-H3_set1Δ_2290_HU 200mM 60min (IP_16_S60_L008_R1_HJM3KBBXX_1)

description:
Ip-H3 of gcn5Δ 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-H3 antibody
IP_16_S60_L008_R1_HJM3KBBXX_1


title: arr6-3mock_rep3: arr6-3 mock-treated. Replicate 3

description: Biological replicate 3 of 3. Gene expression at 1 day post-inoculation in mock-treated arr6-3 plants.


title: S8 risk (CC), (replicate, 008)


title: S971 reference (GG), (replicate, 003)


title: α-H3_gcn5Δ_2029_HU 200mM 60min (IP_14_S56_L008_R1_HJM3KBBXX_1)

description:
Ip-H3 of set1Δ 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-H3 antibody
IP_14_S56_L008_R1_HJM3KBBXX_1


title: shNR2F2-008-1 risk (CC), (replicate, 008 knockdown NR2F2)


title: arr6-3mock_rep1: arr6-3 mock-treated. Replicate 1

description: Biological replicate 1 of 3. Gene expression at 1 day post-inoculation in mock-treated arr6-3 plants.


title: IMR90_shSMARCB1-2

city: seoul

first: SungKyung

last: Choi

address: 120, Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea

country: South Korea

institute: Konkuk university

description:
Replicate 2
SAMPLE 8

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit

treatment_protocol: shRNA were selected in the presence of 1.25 μg/mL puromycin.

value: fibroblast

value: SMARCB1 knockdown


title: α-H3_rad50Δ_1591_HU 200mM 60min (IP_13_S54_L008_R1_HJM3KBBXX_1)

description:
Ip-H3 of rad50Δ 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-H3 antibody
IP_13_S54_L008_R1_HJM3KBBXX_1

value: HU 200mM 60min


title: S003 reference (GG), (replicate, 003)


title: Basal057 risk (CC)


title: IMR90_shSMARCB1-1

description:
Replicate 1
SAMPLE 7


title: donor1_in gel (array)

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description: SAMPLE 4

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: iPSCs differentiated toward MSCs

growth_protocol: MSCs were isolated from bone marrow after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (permit number: EK128/09). MSCs from three different donors (passage 2) were infected with pCXLE-based episomal plasmids (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, LIN28 and L-MYC genes. Established iPSCs were cultured on TCP coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol: Genomic DNA was isolated using the Macherey-Nagel NucleoSpin Tissue Kit.

treatment_protocol: Three different iPSC lines (donors 1-3) were differentiated toward MSCs under the following conditions: iPSCs were either seeded on fibrin gel or within fibrin gel. Differentiation toward MSCs was initiated by medium change to Dulbecco ́s modified Eagle ́s medium-Low Glucose (DMEM-LG, Gibco/Thermo Fisher Scientific, Darmstadt, Germany) supplemented with 10% human platelet lysate (hPL-medium), 5 U/ml heparin (Rotexmedica, Trittau, Germany), 10 µM of the Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Abcam, Cambridge, UK), and 250 U/ml aprotinin (Nordic Pharma, Reading, UK). Differentiation was stopped after 21 days.

tag: individual

value: donor 1

value: iPSCs differentiated toward MSCs

tag: passage

value: passage 3

tag: growth protocol

value: in gel


title: input_WT_872_HU 200mM 60min (Inp_9_S45_L007_R1_HJM3KBBXX_1)

description:
Input of Wild type 60' after release in S-Phase in presence of HU(200mM)
input
Inp_9_S45_L007_R1_HJM3KBBXX_1

value: WT

value: S-Phase


title: Basal098 risk (CC)

value: EBV (Epstein Barr Virus)-transformed B lymphocyte cells

value: (CC)

value: female


title: IMR90_controlsh-2

description:
Replicate 2
SAMPLE 6

value: control


title: donor2_in gel (RNA-Seq)

description:
SAMPLE 8
processed_data.txt

data_processing:
Preprocessing of raw data was performed with SortMeRNA (https://www.ncbi.nlm.nih.gov/pubmed/23071270) to exclude rRNA sequences and TrimGalore for adapter trimming. Reads were aligned with the STAR aligner (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/) and count tables were created with HTSeq (https://academic.oup.com/bioinformatics/article/31/2/166/2366196). Differential gene expression analysis was performed using the R package DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: hg19
Supplementary_files_format_and_content: processed_data.txt

extract_protocol:
RNA was isolated using the Macherey-Nagel RNA Plus Kit.
QuantSeq 3´-mRNA Library Prep/Lexogen, Standard 3' Seq (SR, 50 cycles)

treatment_protocol: Three different iPSC lines (donors 1-3) were differentiated toward MSCs with the following conditions: iPSCs were either seeded onTCP, on fibrin gel or within fibrin gel. Differentiation toward MSCs was initiated by medium change to Dulbecco ́s modified Eagle ́s medium-Low Glucose (DMEM-LG, Gibco/Thermo Fisher Scientific, Darmstadt, Germany) supplemented with 10% human platelet lysate (hPL-medium), 5 U/ml heparin (Rotexmedica, Trittau, Germany), 10 µM of the Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Abcam, Cambridge, UK), and 250 U/ml aprotinin (Nordic Pharma, Reading, UK). Differentiation was stopped after 21 days.

value: donor 2


title: input_set1Δ_2290_G1 (Inp_8_S43_L007_R1_HJM3KBBXX_1)

description:
Input of set1Δ in G1 phase of the cell cycle
input
Inp_8_S43_L007_R1_HJM3KBBXX_1

value: Untreated

value: input


title: donor1_on gel (array)

description: SAMPLE 1

label_protocol: Standard Infinium HD Methylation Assay protocol

value: on gel


title: input_gcn5Δ_2029_G1 (Inp_6_S39_L006_R1_HJM3KBBXX_1)

description:
Input of gcn5Δ in G1 phase of the cell cycle
input
Inp_6_S39_L006_R1_HJM3KBBXX_1


title: donor3_in gel (RNA-Seq)

description:
SAMPLE 9
processed_data.txt

value: donor 3


title: IMR90_controlsh-1

description:
Replicate 1
SAMPLE 5

value: fibroblast


title: Basal008 risk (CC), (replicate, 008)

description:
gene-difference-data-table_2.txt
gene-difference-data-table_1.txt


title: Basal036 reference (GG)

value: (GG)


title: donor2_on gel (array)

description: SAMPLE 2


title: ARPE19_shSMARCB1-1

description:
Replicate 1
SAMPLE 3

value: retinal pigmented epithelium

value: SMARCB1 knockdown


title: donor1_in gel (RNA-Seq)

description:
SAMPLE 7
processed_data.txt

value: donor 1

value: iPSCs differentiated toward MSCs


title: Basal003 reference (GG), (replicate, 003)


title: donor2_on gel (RNA-Seq)

description:
SAMPLE 5
processed_data.txt


title: Basal022 reference (GG)


title: input_WT_872_G1 (Inp_1_S29_L005_R1_HJM3KBBXX_1)

description:
Input of Wild type in G1 phase of the cell cycle
input
Inp_1_S29_L005_R1_HJM3KBBXX_1

value: WT


title: donor3_on gel (array)

description: SAMPLE 3

value: passage 3


title: donor2_in gel (array)

description: SAMPLE 5

value: in gel


title: input_set1Δ_2290_HU 200mM 60min (Inp_16_S59_L008_R1_HJM3KBBXX_1)

description:
Input of gcn5Δ 60' after release in S-Phase in presence of HU(200mM)
input
Inp_16_S59_L008_R1_HJM3KBBXX_1

value: HU 200mM 60min

value: S-Phase


title: itch_lesions

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

description:
chronic scratching with facial lesions
data-lesions.csv

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads were processed using the Drop-seq cookbook (v 1.12) from the McCarroll lab (http://mccarrolllab.com/dropseq/) for Drop-seq libraries.  Sequence reads from 10x libraries were processed using Cell Ranger 2.1.0 from 10x Genomics (https://www.10xgenomics.com/)
Reads were aligned using STAR (v 2.5.3a) to a pre-mRNA mm10 genome.
Seurat package (v2 and v3) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: mm10
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

source_name: trigeminal nuclei

extract_protocol:
Trigeminal ganglia were harvested and incubated in RNAlater (ThermoFisher) at 4oC overnight.  Tissues were then transferred and stored at -80oC until use.  Tissues were homogenized using a glass dounce homogenizer on ice.  Neuronal nuclei were isolated using rabbit anti-NeuN antibody (Abcam) followed by anti-rabbit IgG microbeads (Miltenyi Biotec) and LS column (Miltenyi Biotec).
Libraries construction were performed either with the Drop-seq protocol from the McCarroll lab (for Drop-seq runs) or with method from 10x Genomics for 10x Chromium runs.

value: FVBN/C57BL/129 mix

tag: age

value: > 6 wks

tag: genotype/variation

value: chronic scratching with lesions


title: donor3_in gel (array)

description: SAMPLE 6


title: input_rad50Δ_1591_G1 (Inp_5_S37_L006_R1_HJM3KBBXX_1)

description:
Input of rad50Δ in G1 phase of the cell cycle
input
Inp_5_S37_L006_R1_HJM3KBBXX_1

value: Untreated

value: input


title: facial injury

description:
Three cuts on each cheek and two cuts on forehead
data-cuts.csv

value: facial injury


title: ARPE19_shSMARCB1-2

description:
Replicate 2
SAMPLE 4


title: input_rad50Δ_1591_HU 200mM 60min (Inp_13_S53_L008_R1_HJM3KBBXX_1)

description:
Input of rad50Δ 60' after release in S-Phase in presence of HU(200mM)
input
Inp_13_S53_L008_R1_HJM3KBBXX_1


title: ARPE19_controlsh_2

description:
Replicate 2
SAMPLE 2

value: control


title: ARPE19_controlsh_1

description:
Replicate 1
SAMPLE 1


title: SNI_75dpi

description:
spared nerve injury was performed on the infraorbital nerve.  Nuclei were isolated for snRNA-seq 75 days after injury
D75-10x.csv

value: spared nerve injury


title: α-PK_Scc1-PK gcn5Δ_2628_HU 200mM 60min (IP_E_S31_L007_R1_HJCMYBBXX_1)

description:
Ip-PK of set1Δ with Scc1-PK tagged 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-PK antibody
IP_E_S31_L007_R1_HJCMYBBXX_1

source_name: Ip-PK

value: Scc1-PK gcn5{delta}

value: Anti-PK (anti-V5 tag) antibodies_AbD Serotec_ MCA1360G


title: arr6-3Plec_rep1: arr6-3 PcBMM inoculated. Replicate 1

description: Biological replicate 1 of 3. Gene expression at 1 day post-inoculation in PcBMM-infected arr6-3 plants.

value: Plectospharella cucumerina BMM, 4·106 spores/mL

tag: tissue

value: 18 day-old leaves


title: donor1_TCP (RNA-Seq)

description:
SAMPLE 1
processed_data.txt

value: donor 1

value: iPSCs differentiated toward MSCs

value: tissue culture plastic


title: input_gcn5Δ_2029_HU 200mM 60min (Inp_14_S55_L008_R1_HJM3KBBXX_1)

description:
Input of set1Δ 60' after release in S-Phase in presence of HU(200mM)
input
Inp_14_S55_L008_R1_HJM3KBBXX_1

value: HU 200mM 60min

tag: strain


title: donor3_TCP (RNA-Seq)

description:
SAMPLE 3
processed_data.txt

value: donor 3


title: donor1_on gel (RNA-Seq)

description:
SAMPLE 4
processed_data.txt

value: on gel


title: donor2_TCP (RNA-Seq)

description:
SAMPLE 2
processed_data.txt

value: donor 2


title: SNI_21dpi

description:
spared nerve injury was performed on the infraorbital nerve.  Nuclei were isolated for snRNA-seq 21 days after injury
D21-10x.csv

value: > 6 wks


title: α-PK_Scc1-PK_1418_HU 200mM 60min (IP_D_S29_L006_R1_HJCMYBBXX_1)

description:
Ip-PK of Wild type with Scc1-PK tagged 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-PK antibody
IP_D_S29_L006_R1_HJCMYBBXX_1

value: S-Phase


title: SNI_7dpi

description:
spared nerve injury was performed on the infraorbital nerve.  Nuclei were isolated for snRNA-seq 7 days after injury.
D7-10x.csv


title: D11 B

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Illumina OLB 1.9.4 software used for basecalling and bcl conversion/demultiplexing/fastq creation.
Transcripts Per Million (TPM) were quantified using kallisto v0.44.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Boundary organoid

growth_protocol: colonies of hiPSCs were isolated in Accutase and 150,000 cells/mL were plated on Matrigel coated tissue culture plate. Medium was changed to RPMI 1640 medium containing 100 ng/mL Activin A and 50 ng/mL bone morphogenetic protein 4 at Day 1, 100 ng/mL Activin A and 0.2 % fetal calf serum at Day 2 and 100 ng/mL Activin A and 2% FCS at Day 3. For Day 4-7, cells were cultured in gut growth medium (Advanced DMEM/F12 with 15 mM HEPES, 2 mM L-glutamine, penicillin-streptomycin, B27 and N2) supplemented with 200 ng/mL noggin, 500 ng/ml fibroblast growth factor 4 and 2 µM CHIR99021 for anterior gut cell induction and supplemented with 500 ng/ml FGF 4 and 3 µM CHIR99021 for posterior gut cell induction. Cultures for cell differentiation were maintained at 37°C in an atmosphere of 5% CO2 / 95% air and the medium was replaced every day.   On Day 7, anterior or posterior gut cells were dissociated to single cells by incubation with TrypLE Express at 37°C. Cells were centrifuged at 1000 rpm for 3 minutes and, after removing supernatant, the pellet was re-suspended in gut growth medium containing 10 uM of Y-27632 dihydrochloride. The anterior or posterior gut cell suspensions were plated on 96 well round bottom ultra-low attachment plate at density of 10,000 cells/well and incubated at 37°C for 24 hours to form spheroid. On Day 8, generated single anterior spheroid and posterior spheroid were mixed on 96 well round bottom ultra-low attachment plate in gut growth medium for 24 hours to form fused boundary spheroids (A-P spheroids). On Day9, A-P spheroids were embedded in Matrigel drop and were cultured in gut growth medium to generate multi-organ organoids.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany).
Sample preparation for RNA sequencing was performed using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) according manufacture’s user manual.

value: iPSC derived boundary organoid

tag: region

value: Boundary part of micro-dissected organoid

tag: culture period

value: day11 from undifferentiated iPSC


title: D11 A

value: Anterior part of micro-dissected organoid


title: WT_TG_5_10x

description:
wildtype TG
D0-10x.csv

value: wildtype


title: α-HA_Rad50-HA set1Δ_1870_HU 200mM 60min (IP_B_S25_L005_R1_HJCMYBBXX_1)

description:
Ip-HA of set1Δ with Rad50-HA tagged 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-HA antibody
IP_B_S25_L005_R1_HJCMYBBXX_1

source_name: Ip-HA

value: Rad50-HA set1{delta}

tag: cell-cycle phase

tag: antibody

value: Anti-HA antibodies_Santa Cruz_ SC-7392


title: SNI_2dpi

description:
spared nerve injury was performed on the infraorbital nerve.  Nuclei were isolated for snRNA-seq 2 days after injury.
D2-10x.csv

value: spared nerve injury


title: input_Scc1-PK gcn5Δ_2628_HU 200mM 60min (Inp_E_S30_L006_R1_HJCMYBBXX_1)

description:
Input of set1Δ with Scc1-PK tagged 60' after release in S-Phase in presence of HU(200mM)
input
Inp_E_S30_L006_R1_HJCMYBBXX_1

source_name: Input

value: Scc1-PK gcn5{delta}

value: input


title: input_Scc1-PK_1418_HU 200mM 60min (Inp_D_S28_L006_R1_HJCMYBBXX_1)

description:
Input of Wild type with Scc1-PK tagged 60' after release in S-Phase in presence of HU(200mM)
input
Inp_D_S28_L006_R1_HJCMYBBXX_1


title: reference (GG), (003) [Hi-C]

data_processing:
The reads were trimmed for quality.  The analysis was setup according to the HiCPro pipeline (Servant et al. Genome Biology, 2015).
The reads were aligned to the hg19 (UCSC) genome version.  The output was further converted to "hic" format for visualization. The contact probablities were analyzed using HiCPlotter package in R.
Genome_build: hg19 (37.2)
Supplementary_files_format_and_content: hic files that can be opened on juicebox program

extract_protocol:
Chromatin was processed as stated in Lieberman-Aiden, van Berkum et al. (2009).
DNA libraries were prepared as stated in  Lieberman-Aiden, van Berkum et al. (2009).

value: PBMCs

tag: cell type

value: EBV (Epstein Barr Virus)-transformed B lymphocyte cells

value: (GG)

value: female


title: α-HA_Rad50-HA_1567_HU 200mM 60min (IP_A_S23_L005_R1_HJCMYBBXX_1)

description:
Ip-HA of Wild type with Rad50-HA tagged 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-HA antibody
IP_A_S23_L005_R1_HJCMYBBXX_1

value: HU 200mM 60min


title: WT_TG_4_DropSeq

description:
wildtype TG
D0-Drop.csv

value: > 6 wks


title: risk (CC), (008) [Hi-C]

value: (CC)

tag: gender


title: input_Rad50-HA set1Δ_1870_HU 200mM 60min (Inp_B_S24_L005_R1_HJCMYBBXX_1)

description:
Input of set1Δ with Rad50-HA tagged 60' after release in S-Phase in presence of HU(200mM)
input
Inp_B_S24_L005_R1_HJCMYBBXX_1

tag: genotype

value: S-Phase


title: Scn5a_P1_2_liver3

city: Amsterdam

first: Vincent

last: Christoffels

address: Meibergdreef 15  K2-159

institute: Amsterdam UMC

data_processing:
Library strategy: 4C-seq
Sequencing reads were demultiplexed and subsequently trimmed using FourCSeq package python tool "demultiplex.py" (Klein et al., 2015). Trimmed reads were aligned with bowtie2 (v2.2.5) using standard parameters and quality filter set to 1 (-q 1) and processed as described in {van de Werken, 2012 #11476}
Trimmed reads were aligned with bowtie2 (v2.2.5) using standard parameters and quality filter set to 1 (-q 1) and processed as described in (van de Werken et al., 2012). In short, reads are mapped to a restricted mouse reference genome (mm9) consisting of sequences directly flanking the 4C primary restriction enzyme sites (DpnII), termed 4C frag-ends. Non-unique frag-ends are discarded for posterior analysis. The frag-end with highest coverage is removed from the dataset in the normalization process and data is read-depth normalized to 1 million aligned intrachromosomal reads. 4C-Seq coverage profile is obtained using "running means", i.e. coverage averages of 21 consecutive 4C frag-ends.
Genome_build: mm9

source_name: WT

extract_protocol:
4C templates were prepared as previously described (van de Werken et al., 2012). In short, snap frozen adult mouse hearts of Scn5a RE6-9 mutant mice and wildtype littermates were crushed, dissociated and dounce homogenized to obtain single cell suspension. Chromatin was cross-linked with 2% formaldehyde in PBS with 10% FCS for 10 minutes at room temperature. Nuclei were isolated and cross-linked DNA was digested with DpnII, followed by proximity ligation. Cross-links were removed and a secondary restriction digestion with Csp6I performed, followed again by proximity ligation. Per viewpoint, 8 PCR reactions were performed on 200 ng of 4C template each, to a total of 1.6 µg.
PCR reactions were pooled and purified for next generation sequencing. The 4C-seq PCRs were essentially performed as previously described (van de Werken et al., 2012) using reading primers (Scn5a_P1+2 – GTCCCAAGGGCACACTGATC and Scn5a_enh1 – GAGACCCACACGTTAGGATC) as 4C viewpoints combined with non-reading primers (Scn5a_P1+2 – CCTCTAGAGAGCCTAGTCCC and Scn5a_enh1 – ACGGTGAGGACAACATAGAC). The primers were extended with Illumina adapter sequences and the samples were sequenced on the Nextseq.

value: FVB

value: 8-12 weeks

value: Liver

value: Wild type


title: rde-1(ne219); virEx26 replicate 1

city: La Jolla

first: Emily

last: Troemel

state: CA

department: Cell and Developmental Biology

institute: University of California, San Diego

description: processed data file header: rde1v26_rep1_S3_L007_R1_001

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Reads were trimmed with Trimmomatic v0.36 using the parameters SE -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27
Reads were mapped to the Ensembl Caenorhabditis_elegans.WBcel235.dna.toplevel.fa reference genome using STAR v2.5.3a with default parameters
Read quantification was performed using RSEM v1.3.0 with default parameters and Ensembl annotation Caenorhabditis_elegans.WBcel235.96.gtf, which is based on WormBase release WS260
Genome_build: WormBase release WS235
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

organism: Caenorhabditis elegans

source_name: L4 stage whole animal

growth_protocol: For all strains, bleached L1s were sorted on myo-2::YFP (Orsay RNA1 transgenic array marker) to obtain a population enriched for the array. After sorting, worms were incubated at 20C for 48h until L4 stage, then heat shocked at 34C for 2h to induce RNA1 expression then recovered at 20C for 6h prior to collection for RNA.

extract_protocol:
Total RNA was extracted using TriReagent (Molecular Research Center, Inc.) and cleaned using RNeasy (Qiagen) column purification with on-column Dnase I digestion. RNA quality was assesed using Tapestation analysis.
Paired-end sequencing libraries were constructed using TruSeq Stranded mRNA (Illumina) prep kit.

treatment_protocol: All strains were heat shocked at 34C for 2h at L4 stage to induce HSP::RNA1 expression

value: rde-1(ne219) V; virEx26[HSP::OrsayRNA1 D601A; myo-2p::YFP]

value: whole animals

tag: treatment

value: heat shock 34C 2h

tag: developmental stage

value: L4 stage


title: rde-1(ne219); virEx26 replicate 3

description: processed data file header: rde1v26_rep3_S11_L007_R1_001


title: SLC-F4 rep4

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
After quality control with FastQC, raw reads were trimmed using trim galore to remove Illumina adapters and bases below a sequencing quality of 30.
Reads were then aligned to Danio rario transcriptome (GRCz10, Ensembl.org) and reads per gene were quantified using STAR-2.6.1d
Differential expression was calculated using edgeR and significant genes were taken to be those below a p-value of 0.05
Genome_build: GRCz10
Supplementary_files_format_and_content: non-normalized counts of reads per gene

organism: Danio rerio

source_name: SLC-F4_whole embryos

extract_protocol:
Total RNA was isolated from 48 hpf whole larvae from four separate batches of injected embryos. The samples used for mRNA isolation were first frozen at minus 80 degrees C, then extracted altogether with Direct-Zol RNA miniprep kit (Zymo). The concentration and purity of total RNA were determined using BR-RNA Qubit assay kit (Invitrogen). Amplification grade DNAse I (Invitrogen) was used for DNA traces degradation in RNA samples.
RNA sequencing library was prepared according to KAPA mRNA Hyper prep kit Illumina platforms protocol with the following parameters: initial RNA input was 100 ng; fragmentation step (3.3) was 6 min at 94°C; amplification step (9.3) was 14 cycles. The final libraries were pooled at a loading concentration of 2.0 nM and run on the NovaSeq 6000 using an SP flow cell and run in Standard Mode, SE100 (single end, 100 cycles).

value: the fourth generation (F4) of slc25a46 knockout mutant

value: whole embryos


title: rde-1(ne219); virEx26 replicate 2

description: processed data file header: rde1v26_rep2_S7_L007_R1_001


title: input_Rad50-HA_1567_HU 200mM 60min (Inp_A_S22_L005_R1_HJCMYBBXX_1)

description:
Input of Wild type with Rad50-HA tagged 60' after release in S-Phase in presence of HU(200mM)
input
Inp_A_S22_L005_R1_HJCMYBBXX_1

value: input


title: Scn5a_P1_2_liver2


title: SLC-F4 rep3


title: SLC-F4 rep2


title: D11 P

value: iPSC derived boundary organoid

value: Posterior part of micro-dissected organoid

value: day11 from undifferentiated iPSC


title: input_gcn5Δ_2029_HU 200mM 60min (160817_SNK268_A_L003_GYC-79_R1)

description:
Input of gcn5Δ 60' after release in S-Phase in presence of HU(200mM)
input
160817_SNK268_A_L003_GYC-79_R1

value: HU 200mM 60min


title: rde-1(ne219); virEx23 replicate 3

description: processed data file header: rde1v23_rep3_S9_L007_R1_001

value: rde-1(ne219) V; virEx23[HSP::OrsayRNA1; myo-2p::YFP]


title: Scn5a_P1_2_liver1


title: rde-1(ne219); virEx23 replicate 1

description: processed data file header: rde1v23_rep1_S1_L007_R1_001


title: input_set1Δ_1871_HU 200mM 60min (160817_SNK268_A_L003_GYC-77_R1)

description:
Input of set1Δ 60' after release in S-Phase in presence of HU(200mM)
input
160817_SNK268_A_L003_GYC-77_R1

value: S-Phase


title: Scn5a_P1_2_del3

description: TALEN deletion of RE6-9

source_name: HET

value: FVB

value: Whole heart

value: Scn5a RE6-9 mutant


title: SLC-F4 rep1


title: rde-1(ne219); virEx23 replicate 2

description: processed data file header: rde1v23_rep2_S5_L007_R1_001


title: input_WT_872_HU 200mM 60min (160817_SNK268_A_L003_GYC-75_R1)

description:
Input of Wild type 60' after release in S-Phase in presence of HU(200mM)
input
160817_SNK268_A_L003_GYC-75_R1

value: WT


title: rde-1(ne219); drh-1(ok3495); virEx26 replicate 3

description: processed data file header: drh1rde1v26_rep3_S12_L007_R1_001

value: h-1(ok3495) IV; rde-1(ne219) V; virEx26[HSP::OrsayRNA1 D601A; myo-2p::YFP]


title: Scn5a_P1_2_del2

description: TALEN deletion of RE6-9

value: 8-12 weeks


title: rde-1(ne219); drh-1(ok3495); virEx26 replicate 2

description: processed data file header: drh1rde1v26_rep2_S8_L007_R1_001

value: whole animals

value: heat shock 34C 2h


title: Scn5a_P1_2_del1

description: TALEN deletion of RE6-9


title: SLC-F0 rep4

source_name: SLC-F0_whole embryos

value: the first generation (F0) slc25a46 mosaic mutant (crispant)


title: SLC-F0 rep3

value: whole embryos


title: input_set1Δ_1871_G1 (160817_SNK268_A_L003_GYC-71_R1)

description:
Input of set1Δ in G1 phase of the cell cycle
input
160817_SNK268_A_L003_GYC-71_R1

value: Untreated

value: input


title: input_gcn5Δ_2029_G1 (160817_SNK268_A_L003_GYC-73_R1)

description:
Input of gcn5Δ in G1 phase of the cell cycle
input
160817_SNK268_A_L003_GYC-73_R1


title: rde-1(ne219); drh-1(ok3495); virEx26 replicate 1

description: processed data file header: drh1rde1v26_rep1_S4_L007_R1_001

value: L4 stage


title: SLC-F0 rep2


title: Scn5a_P1_2_WT2

value: Wild type


title: Scn5a_P1_2_WT3


title: SLC-F0 rep1


title: Control rep4

source_name: Control_whole embryos

value: control


title: rde-1(ne219); drh-1(ok3495); virEx23 replicate 2

description: processed data file header: drh1rde1v23_rep2_S6_L007_R1_001

value: drh-1(ok3495) IV; rde-1(ne219) V; virEx23[HSP::OrsayRNA1; myo-2p::YFP]


title: Control rep3


title: Scn5a_enh1_liver3

value: Liver


title: Scn5a_P1_2_WT1

value: FVB


title: Control rep2


title: input_rad50Δ_1591_HU 200mM 60min (160120_SND393_A_L007_GYC-60_1)

description:
Input of rad50Δ 60' after release in S-Phase in presence of HU(200mM)
input
160120_SND393_A_L007_GYC-60_1

value: HU 200mM 60min

value: S-Phase


title: Scn5a_enh1_liver2


title: rde-1(ne219); drh-1(ok3495); virEx23 replicate 1

description: processed data file header: drh1rde1v23_rep1_S2_L007_R1_001


title: Scn5a_enh1_liver1


title: Control rep1


title: rde-1(ne219); drh-1(ok3495); virEx23 replicate 3

description: processed data file header: drh1rde1v23_rep3_S10_L007_R1_001


title: input_rad50Δ_1591_G1 (160120_SND393_A_L007_GYC-54_1)

description:
Input of rad50Δ in G1 phase of the cell cycle
input
160120_SND393_A_L007_GYC-54_1


title: HumanizedMouse_liver_fed3

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were trimmed using trimgalore
Trimmed reads were aligned to a combined human (b38) and mouse (mm10) genome using HISAT2 align with parameters --no-mixed --no-discordant
Aligned reads were transformed into .bam files and sorted by coordinate using sambamba view and sambamba sort.
Read counts were generated using the featureCounts program from the subread package with parameters -p -P
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

organism:
Homo sapiens
Mus musculus

source_name: liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: TK-NOG mice, in which a herpes simplex virus type 1 thymidine kinase (TK) transgene under a mouse albumin promoter is expressed within the liver of highly immune-deficient NOG mice, were obtained from Taconic Biosciences. The TK converts an antiviral medication ganciclovir (GCV) into a toxic product that allows selective elimination of TK positive cells in vivo. The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. The humanized TK-NOG mice were prepared as previously described (Hasegawa, M. et al.). Briefly, The TK-NOG mice at 8-9 weeks old received an i.p. injection of GCV at a dose of 25 mg/kg. One week later, 50ul volume of 1  106 human primary hepatocytes suspended in HBSS solution were transplanted via intra-splenic injection. 8-12 weeks after transplantation, the serum human albumin in the mice were measured as an index of the extent of human hepatocytes replacement. Humanized TK-NOG mice with serum human albumin levels above 0.5 mg/ml were used for experiments, in which human hepatic genes could be reliably detected by q-PCR. Reference paper PMID: 21238430.

tag: host organism

value: TKNOG Mus musculus

tag: xenograft organism

value: Homo sapiens


title: HumanizedMouse_liver_fed4


title: HumanizedMouse_liver_fed2


title: Scn5a_enh1_del3

description: TALEN deletion of RE6-9

value: 8-12 weeks

value: Whole heart

value: Scn5a RE6-9 mutant


title: input_WT_872_G1 (160817_SNK268_A_L003_GYC-69_R1)

description:
Input of Wild type in G1 phase of the cell cycle
input
160817_SNK268_A_L003_GYC-69_R1

value: WT


title: input_WT_872_G1 (160120_SND393_A_L007_GYC-52_1)

description:
Input of Wild type in G1 phase of the cell cycle
input
160120_SND393_A_L007_GYC-52_1


title: HumanizedMouse_liver_fed1


title: HCT116-Hx8-sh2-rep2_1

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on BGISEQ-500 platform.
Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the single-end 50bp sequence tags from BGISEQ-500 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
We used FPKM method to calculate expression level of genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: shRNAs targeting HOXB8 stably transduced into HCT116 and induced with dox

growth_protocol: HCT116 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from HCT116 cells using RNeasy kit from Qiagen according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: HCT116 cells stably expressing shRNAs targeting HOXB8 were treated with or without 1 ug/ml doxycycline for 72 hours. After 72h of treatment, cells were harvested and total RNA was extracted.

value: Colon cancer cell line

tag: cell line


title: input_WT_872_HU 200mM 60min (160817_SNK268_A_L003_GYC-64_R1)

description:
Input of Wild type 60' after release in S-Phase in presence of HU(200mM)
input
160817_SNK268_A_L003_GYC-64_R1

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  without futher smoothing or ratio.

extract_protocol:
Standard protocol for preparation of yeast genomic DNA, chromatin immunoprecipitation and micrococcal nuclease digestion
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)


title: Scn5a_enh1_del2

description: TALEN deletion of RE6-9


title: Scn5a_enh1_del1

description: TALEN deletion of RE6-9


title: HCT116-Hx8-sh2-rep1_1


title: input_WT_872_HU 200mM 60min (160120_SND393_A_L007_GYC-58_1)

description:
Input of Wild type 60' after release in S-Phase in presence of HU(200mM)
input
160120_SND393_A_L007_GYC-58_1


title: Scn5a_enh1_WT3


title: HumanizedMouse_liver_fasting3


title: HCT116-Hx8-sh2+dox-rep2_1

value: HOXB8 knock-down


title: HCT116-Hx8-sh2+dox-rep1_1


title: HumanizedMouse_liver_fasting2


title: Scn5a_enh1_WT2


title: α-H3_WT_872_HU 200mM 60min (IP_9_S46_L007_R1_HJM3KBBXX_1)

description:
Ip-H3 of Wild type 60' after release in S-Phase in presence of HU(200mM)
ChIP-Seq, α-H3 antibody
IP_9_S46_L007_R1_HJM3KBBXX_1

value: Anti-H3 antibodies_Abcam_ Ab1791


title: D29 HES1KO

growth_protocol: colonies of hiPSCs were isolated in Accutase and 150,000 cells/mL were plated on Matrigel coated tissue culture plate. Medium was changed to RPMI 1640 medium containing 100 ng/mL Activin A and 50 ng/mL bone morphogenetic protein 4  at Day 1, 100 ng/mL Activin A and 0.2 % fetal calf serum at Day 2 and 100 ng/mL Activin A and 2% FCS at Day 3. For Day 4-7, cells were cultured in gut growth medium (Advanced DMEM/F12 with 15 mM HEPES, 2 mM L-glutamine, penicillin-streptomycin, B27 and N2) supplemented with 200 ng/mL noggin, 500 ng/ml fibroblast growth factor 4 and 2 µM CHIR99021 for anterior gut cell induction and supplemented with 500 ng/ml FGF 4 and 3 µM CHIR99021 for posterior gut cell induction. Cultures for cell differentiation were maintained at 37°C in an atmosphere of 5% CO2 / 95% air and the medium was replaced every day.   On Day 7, anterior or posterior gut cells were dissociated to single cells by incubation with TrypLE Express at 37°C. Cells were centrifuged at 1000 rpm for 3 minutes and, after removing supernatant, the pellet was re-suspended in gut growth medium containing 10 uM of Y-27632 dihydrochloride. The anterior or posterior gut cell suspensions were plated on 96 well round bottom ultra-low attachment plate at density of 10,000 cells/well and incubated at 37°C for 24 hours to form spheroid. On Day 8, generated single anterior spheroid and posterior spheroid were mixed on 96 well round bottom ultra-low attachment plate in gut growth medium for 24 hours to form fused boundary spheroids (A-P spheroids). On Day9, A-P spheroids were embedded in Matrigel drop and were cultured in gut growth medium to generate multi-organ organoids.

value: iPSC derived boundary organoid

value: HES1 knock out orgnaoid

value: day29 from undifferentiated iPSC


title: HCT116-Hx8-sh1-rep1_1

value: control


title: HCT116-Hx8-sh1-rep2_1


title: LM_HN_intact_RNA seq

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

data_processing:
The clean data was obtained by removing the poor-quality bases and adapter sequences from the raw sequencing data.
The TopHat2 software (Kim et al., 2013) was used to map the clean data to the porcine reference genome (Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/).
Then Cufflinks (Trapnell et al., 2010) was used to perform the transcript assembly and abundance estimation. The Findcirc software was used to predict the circRNAs (Memczak et al., 2013).The lncRNA was identified by the following steps: (1) Transcripts were removed that were detected in fewer than two experiments. (2) Transcripts with single exon and with the length less than 200 bp were removed. (3) Transcripts with coverage of less than 3 were removed; (4) Transcripts similar to or the same as known porcine small RNAs were removed. (5) Transcripts that did not pass any analyses of Coding Potential Calculator (CPC), Coding-Non-Coding-Index (CNCI), and Pfam software were removed.
The expression profile of circRNAs, mRNAs and lncRNAs were reflected by the fragments per kilo base per million reads (FPKMs).
Genome_build: Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/
Supplementary_files_format_and_content: circRNAs-FPKM, lncRNAs-FPKM, mRNAs-FPKM

organism: Sus scrofa

source_name: longissimus muscle

growth_protocol: Three HN intact male pigs aged 300 days were obtained from the Henan Xing Rui Agricultural and Animal Husbandry Technology Co., LTD in the Henan province of China. All of the pigs were fed on a standard diet and watered ad libitum under normal condition.

extract_protocol:
LM were removed from HN and DLY pigs, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The ribosomal RNA (rRNA) was removed using Ribo-ZeroTM kit (Epicentre, Madison, WY, USA) from the DNA-free RNA. Then, the DNA and rRNA-free RNA was used to prepare the library using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs lnc., Beverly, MA), and then sequenced by HiSeq 2500 (Illumina, San Diego, CA, USA).

value: 300 days

value: longissimus muscle


title: D29 Ctrl

value: Control organoid


title: Scn5a_enh1_WT1

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

value: FVB

value: Wild type


title: HCT116-Hx8-sh1+dox-rep2_1


title: HumanizedMouse_liver_fasting4

value: TKNOG Mus musculus

value: Homo sapiens

value: Liver


title: K562-input_HFLFWCCXY_L3

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Genome_build: hg19
Supplementary_files_format_and_content: The bedGraph files containing signal per million reads produced from MACS2 were converted to bigwig files with ucsctool kit.

growth_protocol: K562 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with a HOXB8 antibody.
Libraries of purified ChIP DNA for Illumina sequencing were prepared using the Illumina TruSeq DNA Sample Preparation v2 kit according to manufacturer's instructions.

treatment_protocol: Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 2 μg primary antibodies as listed in Supplementary Table S4 or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.

value: myelogenous leukemia cell line

tag: passages

tag: chip antibody


title: D22 HES1KO

value: day22 from undifferentiated iPSC


title: CHIP-K562-HoxB8_HFLFWCCXY_L2

value: HOXB8 antibody (Abcam, cat# ab125727)


title: HCT116-Hx8-sh1+dox-rep1_1

value: Colon cancer cell line

tag: genotype/variation

value: HOXB8 knock-down


title: D22 Ctrl

value: iPSC derived boundary organoid


title: HumanizedMouse_liver_fasting1

tag: tissue


title: hiPSC, biological replicate-3

city: Los Angeles

first: Lu

last: Li

address: Room 706, 1985 Zonal Ave

department: School of Pharmacy

institute: University of Southern California

description: Gene expression data from hiPSCs

hyb_protocol: Following fragmentation and Labeling  samples were hybridized for at 60 RPM for 16 hrs at 45C on Clariom™ S Assay, human array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 4G.

data_processing:
The data were preprocessed and analyzing using Partek Genomic Suite.
Probe level data were summarized using the RMA. Background are adjusted using RMA background correction.  Quantile normalization was used to correct for array bias. All probe level intensities were log 2 transformed. Probesets were summarized using median polish.

source_name: human induced pluripotent stem cells

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, The standard Affymetrix WT plus protocol was used to generate cDNA from 250 ng total RNA. First and second strand cRNA synthesis was according to the manufacturer’s instructions. ss-cDNA synthesis was followed by 15ug of cRNA in vitro transcription and a second round of ss-cDNA synthesis according to the manufacturer’s instructions. Fragmentation of 5.5ug of single-stranded cDNA was performed using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol per the manufacturer's instructions   Reagent Kit   (Affymetrix).

growth_protocol: The hiPSC line GM25256*B was induced to differentiate into human Leydig cell-like cells (hLLCs) and human adrenal cell-like cells (hALCs), respectively.

extract_protocol: Total RNA samples were prepared using  Ambion® RiboPure™ Kit (Thermofisher Scientific, AM1924), according to the manufacture's instructions.

value: hiPSC line GM25256*B

value: induced pluripotent stem cells

tag: differentiation stage

value: Initial


title: cnmc710t Exome capture

status: Public on Oct 03 2019

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

description:
cnmc710t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC51 primary tumor
primary tissue WES/WGS

data_processing:
ChIP-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls. Broad peak calling was used for H3K27me3 and EED
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
ChIP-Rx reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference and then unmapped reads (--un-conc) were aligned to dm6 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates from both hg19 and dm6 alignments
Normalization to 1M dm6 reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: RRPM bigwig
RNA-seq reads were trimmed of adaptors with cutadapt
Aligned to hg19 with tophat2 v2.1.1
Reads counted in hg19 RefSeq genes using featureCounts
Transcript per million (TPM) for each gene was determined as 1,000,000 * (reads per kilobase of transcript)/(total sum of reads per kilobase of all transcripts)
Genome_build: hg19
Supplementary_files_format_and_content: TPM spreadsheet
ATAC-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Full depth technical replicate bam files were then merged with samtools merge and peak calls we performed once more on the merged replicate file using macs2 version 2.1.1.20160309
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
WES/WGS reads were trimmed of adaptors with cutadapt
Reads were aligned to the hg19 reference sequence using bwa mem v0.7.15. PCR duplicates were removed using picardtools MarkDuplicates.
Reads were then processed using GATK best practices, including indel realignment and base recalibration
Variants were called with GATK UnifiedGenotyper
Genome_build: hg19
Supplementary_files_format_and_content: VCF variant calls

source_name: primary tumor tissue

extract_protocol: Tissues are homogenized and gDNA is extracted with Qiagen Dneasy or Gentra Puregene.

value: primary human patient tumor tissue


title: cnmc741t Exome capture

description:
cnmc741t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC57 primary tumor
primary tissue WES/WGS


title: hiPSC, biological replicate-2

description: Gene expression data from hiPSCs


title: hALC, biological replicate-1

description: Gene expression data from hiPSC-derived cells toward Adrenal cells

source_name: human adrenal cell-like cells

value: adrenal cell-like cells

value: Terminal


title: hLLC, biological replicate-3

description: Gene expression data from hiPSC-derived cells toward Leydig cells

source_name: human Leydig cell-like cells

value: Leydig cell-like cells


title: hiPSC, biological replicate-1

description: Gene expression data from hiPSCs


title: hALC, biological replicate-3


title: hALC, biological replicate-2


title: hLLC, biological replicate-1


title: MA9+SETDB1_ChIPseq_H3K79me2_2

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Quality control performed on fastq files using FastQC version 0.11.7
RNA-seq fastq files were trimmed for quality using Cutadapt version 1.18, parameters = -q20,20 --minimum-length 30; ATAC-seq and ChIP-seq fastq files were trimmed for quality, adapter removal, and polyG removal using AfterQC version 0.9.6, parameters = -q20 -u 19 -p19 -s 25
RNA-seq fastq files were aligned to the mouse genome using STAR version 2.6.0c, parameters = genomeGenerate: --sjdbOverhang 49, Alignment: --outSamtype BAM SortedByCoordinate; ATAC-seq and ChIP-seq files were aligned to the mouse genome using Bowtie2 version 2.3.4.3, parameters = --very-sensitive -X 2000
RNA-seq aligned BAM files were assigned to genes and features were counted using HTSeq 0.11.0, parameters= -s reverse -r pos
RNA-seq count files were analyzed for differential expression using DESeq2 version 3.8, parameters = alpha = 0.05 lfcThreshold = log2(1.5)
ChIP-seq and ATAC-seq aligned BAM files were sorted and filterd for quality using SAMtools version 1.9, parameters = view -b -q 25 -f 0x2
ChIP-seq and ATAC-seq filtered BAM files had duplicates removed using Picard version 2.18.19
ChIP-seq and ATAC-seq filtered and deduplicated BAM files were used for peak calling using MACS version 2.1.2; 10% input was used as control for ChIP-seq experiments; parameters varied for different conditions: for H3K9ac ChIP-seq =  -f BAMPE -g mm --keep-dup all; for H3K9me3 and H3K79me2 ChIP-seq = -f BAMPE -g mm --scale-to-large --braod --keep-dup all; for ATAC-seq = -f BAM -g mm --nomodel --shift -100 --extsize 200 --keep-dup all
ChIP-seq BAM files were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000
ATAC-seq pileup files from MACS peak calling were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --extendReads
Genome_build: GRCm38 (M20 build from GENCODE)
Supplementary_files_format_and_content: RNAseq counts files contain the HTSeq assigned genes and count from the aligned BAM files; ChIP-seq and ATAC-seq BAM files contain the filtered and deduplicated aligned reads to the mouse genome.

growth_protocol:
AML cell line generated from mouse bone marrow and grown in culture for 8-12 weeks
MLL-AF9+SETDB1 or MLL-AF9+MSCVpuroEmpty Vector (EV) control cells were generated by harvesting lin- mouse BM and spininfecting with MLL-AF9 and either SETDB1 or EV. Cells were selected for ~3-6 weeks using puromycin in IMDM supplemented with IL-3, SCF, and pen/strep.

extract_protocol:
Cells were fixed with 1%paraformaldehyde, the fixation was quenched with glycine, and the fixed cells were snap-frozen and stored at -80C. Cells were slow thawed on ice for 15 minutes, then lysed in 1% SDS lysis buffer. Chromatin was sheared on a water bath sonicator, and IPs were performed using the indicated antibodies and protein G magnetic beads. DNA was decrosslinked and purified using Qiagen PCR purification kit.
Libraries were prepped using 5ng DNA and the iDeal library prep kit. Amplification cycles of the library preps were optimized using qPCR.

tag: tissue source

value: bone marrow

tag: cell line background

value: MLL-AF9 (MA9) acute myeloid leukemia cell line

tag: retroviral transduction

value: MLL-AF9 + SETDB1


title: MA9+EV_ChIPseq_H3K79me2_2

value: MLL-AF9 + EV control


title: MA9+SETDB1_ChIPseq_H3K9me3_2


title: MA9+SETDB1_ChIPseq_H3K79me2_1


title: MA9+SETDB1_ChIPseq_H3K9me3_1


title: MA9+SETDB1_ATACseq_2

extract_protocol:
Cells were slow frozen and shipped on dry ice to Active Motif. Extraction was performed as described by Buenrostro, et al Curr Protoc Mol Biol. 2015.
Library prep was performed by Active Motif as described by Buenrostro, et al Curr Protoc Mol Biol. 2015.

treatment_protocol: Cells harvested for ATAC-seq were pretreated with Dnase I at 200units/mL for 30 minutes at 37C.


title: MA9+EV_ATACseq_1


title: MA9+SETDB1_ATACseq_1


title: MA9+EV_ChIPseq_H3K79me2_1


title: MA9+EV_ATACseq_2


title: MA9+EV_ChIPseq_H3K9ac_1


title: MA9+SETDB1_ChIPseq_H3K9ac_2


title: MA9+SETDB1_ChIPseq_H3K9ac_1


title: MA9+EV_ChIPseq_H3K9ac_2


title: MA9+SETDB1_ChIPseq_input_2


title: hLLC, biological replicate-2


title: MA9+SETDB1_ChIPseq_input_1


title: MA9+EV_ChIPseq_input_2


title: MA9+EV_ChIPseq_H3K9me3_2