title: 7wk_scATAC

status: Public on Mar 08 2021

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
Chromium single-cell ATAC-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat and Signac
Trajectory analysis was carried out using Monocle 2.8
Barcodes were extracted from processed cell clusters in Seurat and Signac and used with Sinto to partition the cellranger output bam file into smaller cell type bams
Bams were filtered using Picard and Samtools with the commands MarkDuplicates and –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
Peaks were then called using Macs on the -braod setting whereupon peaks were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and h5 objects along with cloupe file can be used to visulize scATAC-seq clusters

source_name: Lung epithelial, immune, endothelial, and mesenchymal cells

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina Novaseq6000 with a 50 paired-end format with index 1 for 8cycles and index 2 for 16 cycles.

tag: age


title: COV6: COVID sample 6

status: Public on Mar 09 2021

type: SRA

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

library_source: transcriptomic

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19

molecule: total RNA

organism: Homo sapiens

source_name: Frontal cortex

growth_protocol: Autoptic human brain samples were collected. Slices of anterior frontal lobe were fresh cut into about 10 mm thickness and frozen at -80°C.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Lexogen CORALL Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

tag: disease

tag: dementia status

value: No Dementia

tag: tissue

value: Frontal cortex


title: 120hpf_uhrf1 hi272 mutant livers_clutch 5_14 livers

status: Public on Feb 12 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava  software used for basecalling.
Sequencing quality was assessed by using MultiQC v1.7
Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters
Alignment by HISTA2 with default parameters, only paired reads are aligned and multiple alignments are kept
Gene expression is counted in the exon of  ensemble gene annotation, TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq, in union mode
Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12
Genome_build: GRCz10
Supplementary_files_format_and_content: csv files for raw reads count of genes and TEs

organism: Danio rerio

source_name: embryo livers

extract_protocol: 14- 25 livers from 5 dpf (120 hpf) zebrafish embryos were dissected, pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol (https://www.thermofisher.com/ae/en/home/references/protocols/nucleic-acid-purification-and-analysis/mrna-protocols/trizol-plus-rna-purification-kit.html#prot2).

tag: background

value: ABNYU

value: 14 livers

tag: developmental stage

tag: genotype

value: uhrf1 hi272 mutant

value: fabp10:CAAX-EGFP transgenic liver


title: 120hpf_uhrf1 hi272 sibling control livers_clutch 5_15 livers

value: 15 livers

value: uhrf1 hi272 sibling control


title: 120hpf_uhrf1 hi272 mutant livers_clutch 3_20 livers

value: 20 livers


title: 120hpf_uhrf1 hi272 mutant livers_clutch 4_17 livers

value: 17 livers


title: 120hpf_uhrf1 hi272 sibling control livers_clutch 4_15 livers


title: Zta_CHIPSeq_2

status: Public on Feb 20 2021

city: Brighton

first: Alison

middle: Jane

last: Sinclair

state: E. Sussex

address: University of Sussex

department: School of Life Sciences

country: United Kingdom

institute: University of Sussex

library_source: genomic

data_processing:
Basecalls performed using RTA 1.18.61
Mapping of reads to the reference sequences was performed using BWA-BACKTRACK version 0.6.2-r126
Peaks were called using deepTools Galaxy MACS-1.4.2 with the following setting: Tag size 30bp, Bandwidth 200bp, p-value 10-^9, Do not built shifting model, arbitrary shift size 100bp, Format .wig, MFOLD range 10,30, Dynamic lambda 1000 -10000
Peaks common to CHIP1 and ChIP2 were determined using deepTools Galaxy's "Operate on Genomic Intervals" tool (Overlapping Intervals for at least 1bp ). Overlapping pieces of intervals were selected as return format.
Zta peaks common to NPC and BL cells were determined using BL data from Ramasubramanyan et al. (J.Virol. 2012) [GSE58245]  and deepTools Galaxy's "Operate on Genomic Intervals" tool (Overlapping Intervals for at least 1bp ). Overlapping pieces of intervals were selected as return format.
Genome_build: hg19
Supplementary_files_format_and_content: The .bed file was generated using deepTools Galaxy. It contains the Zta peaks that are present in both, NPC and BL cells

molecule: genomic DNA

source_name: HONE1-EBV, Zta ChIP

growth_protocol: HONE1-EBV cells were maintained in RPMI medium supplemented with 10% (vol/vol) fetal bovine serum, 100U of penicillin/ml, 100g of streptomycin/ml, and 2mM L-glutamine (Invitrogen) at 37°C with 5% CO2. EBV-positive HONE1 cells were selected with 600μg/ml G418.

extract_protocol:
Chromatin was fixed by application of 1% (v/v) formaldehyde to cells for 10min, at 20oC and was extracted as described in Bark-Jones et al. (2006). A Vibra-Cell (SONICS) was used to shear the chromatin. HONE1-EBV cell lysates were subjected to sonication in a volume of 100μl on ice for ten rounds, with 10s pulses and a 21% amplitude output. Samples were mixed after every minute. The efficacy of sonication was assessed by analysing the sample on a 1% (w/v) agarose gel. Chromatin from 3.5x10^7 cells was used to immunoprecipitate Zta-associated-DNA using 10ug EBV ZEBRA antibody (sc-17503) (Santa Cruz). Immune complexes were collected with 50% pre-blocked protein A/G-sepharose beads. Following wash steps and protein digestion of immune complexes, eluted DNA was purified using a PCR purification kit (Qiagen) and eluted in 45μl.
The DNA libraries were prepared according to the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina kit (New England Bioscience), switching the PCR and the size selection steps. Index 4 was used for the Input, Index 6 for ChIP1 and Index 12 for ChIP2. Size selection was performed on a 2% (w/v) agarose gel with SYBR Gold dye to exclude the adaptor from the sequencing process and to purify DNA fragments in the 175-225bp size range. Quality control was performed using the Agilent 2100 Bioanalyzer.

treatment_protocol: For EBV lytic induction, HONE1-EBV cells were induced with 10μM suberoylanilide hydroxamic acid (SAHA) for 48hrs at 70% confluence. Only the adherent cell population was used in experiments.

tag: cell line

tag: cell type

value: stable EBV-infected nasopharyngeal carcinoma (NPC) cell line

tag: cell origin

value: nasopharyngeal carcinoma

tag: carcinoma type

value: poorly differentiated

tag: viral strain

value: Akata EBV

tag: chip antibody

value: EBV ZEBRA (Santa Cruz, sc-17503)


title: 120hpf_uhrf1 hi272 mutant livers_clutch 2_25 livers

value: 25 livers


title: Zta_CHIPSeq_1


title: 120hpf_uhrf1 hi272 sibling control livers_clutch 1_15 livers


title: 120hpf_uhrf1 hi272 sibling control livers_clutch 3_15 livers


title: 120hpf_uhrf1 hi272 mutant livers_clutch 1_22 livers

value: 22 livers


title: 120hpf_uhrf1 hi272 sibling control livers_clutch 2_15 livers


title: KO bulk (Green)

status: Public on Feb 04 2021

city: Melbourne

first: Katharina

last: Hochheiser

state: Victoria

address: 792 Elizabeth Street

department: Department of Microbiology & Immunology

country: Australia

institute: The University of Melbourne

description:
s_16
replicate 3
mRNA

data_processing:
Illumina standard pipeline to generate FASTQ files.
Align to mm10 mouse genome using TopHat version 2.1.1. TopHat options: --no-discordant --no-mixed --library-type fr-secondstrand –b2-very-sensitive
Only keep fragments where both reads are aligned with MAPQ >= 5.
Remove duplicates using picard tools.
Map reads to genes using featureCounts function from Rsubread R (Bioconductor) package.
Perform DE analysis using edgeR R Bioconductor package. Only keep genes with at least 5 counts in every replicate in at least one condition.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_samples_counts.csv: Counts.
Supplementary_files_format_and_content: All_genes.xls: DE genes.

organism: Mus musculus

source_name: spleen

growth_protocol: 5x10^4 naïve OT-I.Lck-Cre.Ptpn2fl/fl or OT-I.Ptpn2fl/fl T cells were adoptively transferred into congenic mice (Ly5.1) infected with HSV-Ova on their flank skin 2 days prior. Spleens of recipient mice were harvested 8 days after infection.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo).
Paired-end libraries were prepared for mRNA-seq using an Illumina TruSeq RNA v2 kit and sequenced using an Illumina HiSeq2500.

treatment_protocol: Cells in single cell suspensions from spleens of recipient mice were FACS sorted: CD45.2+CD8+Va2+ (bulk - total effector cells), or CD45.2+CD8+Va2+KLRG1+ and CD45.2+CD8+Va2+KLRG1-.

tag: strain

value: adoptively transferred transgenic OT-I cells (Ovalbumin specific CD8+ T cells)

tag: timepoint after infection

value: day 8

tag: phenotype

value: not sorted for KLRG1 expression


title: WT bulk (green)

description:
s_17
replicate 3
mRNA


title: KO - (Green)

description:
s_13
replicate 3
mRNA


title: WT - (white )

description:
s_10
replicate 2
mRNA


title: KO Bulk (white)

description:
s_11
replicate 2
mRNA


title: KO + (white)

description:
s_12
replicate 2
mRNA


title: Input DNA

data_processing:
Basecalls performed using RTA 1.18.61
Mapping of reads to the reference sequences was performed using BWA-BACKTRACK version 0.6.2-r126
Peaks were called using deepTools Galaxy MACS-1.4.2 with the following setting: Tag size 30bp, Bandwidth 200bp, p-value 10-^9, Do not built shifting model, arbitrary shift size 100bp, Format .wig, MFOLD range 10,30, Dynamic lambda 1000 -10000
Peaks common to CHIP1 and ChIP2 were determined using deepTools Galaxy's "Operate on Genomic Intervals" tool (Overlapping Intervals for at least 1bp ). Overlapping pieces of intervals were selected as return format.
Zta peaks common to NPC and BL cells were determined using BL data from Ramasubramanyan et al. (J.Virol. 2012) [GSE58245]  and deepTools Galaxy's "Operate on Genomic Intervals" tool (Overlapping Intervals for at least 1bp ). Overlapping pieces of intervals were selected as return format.
Genome_build: hg1958245
Supplementary_files_format_and_content: The .bed file was generated using deepTools Galaxy. It contains the Zta peaks that are present in both, NPC and BL cells

source_name: HONE1-EBV, input


title: WT - (red )

description:
s_7
replicate 1
mRNA


title: KO + (red )

description:
s_5
replicate 1
mRNA


title: WT + (red )

description:
s_6
replicate 1
mRNA


title: KO bulk (red)

description:
s_4
replicate 1
mRNA


title: KO - (red )

description:
s_8
replicate 1
mRNA


title: endothelial cells, S/G2/M phase, rep 3

status: Public on Jan 01 2021

city: Uppsala

first: Sofia

last: Nordling

address: Dag Hammarskölds väg 20

country: Sweden

institute: Uppsala University

data_processing:
Fastq files were generated with bcl2fastq2 v2.19.0
Quality controlling and trimming was done using the Galaxy ToolShed v 1.0.2; FASTQ/A short-reads pre-processing tools
Aligned to the hg38 genome was done using HISAT2 (v 2.1.0+galaxy4)
Raw counts were generated using featureCounts (v 1.6.3+galaxy2)
Genome_build: hg38
Supplementary_files_format_and_content: Csv files containing raw counts for each replicate

source_name: endothelial cells

growth_protocol: Differentiation of cells were performed based on Qiu et al. Cell Reports. 2020.

extract_protocol:
All mRNA samples were isolated using RNeasy Plus Micro Kit (Qiagen, cat# 74034).
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: All cell were untreated

value: hESC-derived endothelial cells

tag: treatment

value: untreated


title: WT Klrg1 + (white)

description:
s_2
replicate 2
mRNA


title: WT OT-1 bulk (red)

description:
s_1
replicate 1
mRNA


title: WT + (Green)

description:
s_15
replicate 3
mRNA


title: KO + (green)

description:
s_14
replicate 3
mRNA


title: endothelial cells, S/G2/M phase, rep 5


title: endothelial cells, S/G2/M phase, rep 4


title: WT - (green)

description:
s_18
replicate 3
mRNA


title: endothelial cells, G1/S phase, rep 4


title: WT bulk (white )

description:
s_9
replicate 2
mRNA


title: endothelial cells, G1/S phase, rep 3


title: endothelial cells, late G1 phase, rep 4


title: endothelial cells, G1/S phase, rep 2


title: endothelial cells, G1/S phase, rep 5


title: endothelial cells, late G1 phase, rep 5


title: endothelial cells, late G1 phase, rep 2


title: endothelial cells, early G1 phase, rep 5


title: endothelial cells, G1/S phase, rep 1


title: endothelial cells, late G1 phase, rep 3


title: endothelial cells, early G1 phase, rep 3


title: endothelial cells, late G1 phase, rep 1


title: endothelial cells, early G1 phase, rep 2


title: PTPN2ko KLRG1- (white)

description:
s_3
replicate 2
mRNA


title: endothelial cells, early G1 phase, rep 1


title: endothelial cells, S/G2/M phase, rep 2


title: endothelial cells, early G1 phase, rep 4


title: Treatment naïve MS patients, 87817a-CD8

status: Public on Dec 31 2020

city: San Francisco

first: Sergio

middle: E

last: Baranzini

state: CA

address: 675 Nelson Rising LN, STE 240

department: Neurology

country: USA

institute: UCSF

data_processing:
We assessed quality control of raw fastq files using FastQC v0.11.7.
Adapter sequence and low-quality bases were trimmed using BBDuk of BBTools v38.05 (https://jgi.doe.gov/data-and-tools/bbtools/).
Trimmed sequence reads were mapped into the primary assembly of human genome reference (GRCh38.p12) with Gencode annotation (release 28) using STAR v2.6.0c with 2-pass mode.
QualiMap was used to assess the quality of mapped reads.
We quantified gene and transcript-isoform expression abundance using RSEM v1.3.1.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Processed data files are gene level expression estimates from RSEM. The first line contains column names (gene id, transcript id, length, effective_length, expected_count, TPM, FPKM). 'length' is average of its transcripts' lengths except poly(a) tail. 'effective_length' counts only the positions that can generate a valid fragment. 'expected_count' is the sum of the posterior probability of each read comes from its transcripts' over all reads. 'TPM' stands for Transcripts Per Million and 'FPKM' stands for Fragments Per Kilobase of transcript per Million mapped reads, are a relative measure of transcript abundance.

source_name: CD8+ T cells

extract_protocol:
PBMCs were sorted into three different cell subsets (CD4+, CD8+, and CD14+ cells) using a MoFlo Astrios cell sorter (Beckman Coulter, Pasadena, CA). CD4+ (helper) T cells were defined as CD3+CD19-CD4+, CD8+ (cytotoxic) T cells as CD3+CD19-CD8+, and CD14+ monocytes as CD14+. Total RNA was isolated using RNeasy Mini or Micro kit (Qiagen, Hilden, Germany). The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA was stored at -80 °C until used for sequencing library preparation.
We prepared strand-specific whole transcriptome RNA-seq libraries for each cell subset using 5 - 900 ng of total RNA as a template using NEBNext Ultra II directional RNA library prep kit (NEB, Ipswich, MA) and 96 index primers according to the manufacturer’s instructions. We performed cytoplasmic and mitochondrial ribosomal RNA depletion using the NEBNext rRNA depletion kit (NEB, Ipswich, MA) followed by library construction. RNA-seq libraries were pooled with 36 or 37 samples of equal amount and sequenced by 150nt paired-end on the NovaSeq instrument (Illumina, San Diego, CA).

tag: disease state

value: Multiple sclerosis (MS)

tag: gender

value: F

tag: age at exam

value: CD8+ T cells

tag: disease subtypes

value: RR

tag: disease duration

tag: edss


title: Treatment naïve MS patients, 87817a-CD4

source_name: CD4+ T cells

value: CD4+ T cells


title: Treatment naïve MS patients, 87817a-CD14

source_name: CD14+ monocytes

value: CD14+ monocytes


title: Treatment naïve MS patients, 87617a-CD8

value: M


title: Treatment naïve MS patients, 87717a-CD14

value: CIS


title: Treatment naïve MS patients, 87617a-CD4


title: Treatment naïve MS patients, 87717a-CD4


title: Healthy controls, 87417a-CD4

value: Healthy control


title: Healthy controls, 87417a-CD14


title: Treatment naïve MS patients, 87117a-CD8


title: Treatment naïve MS patients, 87017a-CD4


title: Healthy controls, 87317a-CD14


title: Healthy controls, 87317a-CD4


title: Healthy controls, 86717a-CD8


title: Treatment naïve MS patients, 87117a-CD14


title: Treatment naïve MS patients, 87117a-CD4


title: Healthy controls, 86717a-CD4


title: Treatment naïve MS patients, 87017a-CD14


title: Healthy controls, 86617a-CD8


title: Healthy controls, 86717a-CD14


title: Healthy controls, 86617a-CD14


title: Healthy controls, 86617a-CD4


title: Treatment naïve MS patients, 87717a-CD8


title: Treatment naïve MS patients, 86517a-CD8


title: Healthy controls, 86417a-CD4


title: Healthy controls, 86417a-CD8


title: Treatment naïve MS patients, 86517a-CD4


title: Treatment naïve MS patients, 87617a-CD14


title: Treatment naïve MS patients, 86517a-CD14


title: Healthy controls, 87417a-CD8


title: Healthy controls, 86217a-CD8


title: Healthy controls, 86417a-CD14


title: Treatment naïve MS patients, 87017a-CD8


title: Healthy controls, 86217a-CD4


title: Healthy controls, 86117a-CD4


title: Healthy controls, 86117a-CD8


title: Healthy controls, 86217a-CD14


title: Healthy controls, 86117a-CD14


title: Treatment naïve MS patients, 85617a-CD4


title: Treatment naïve MS patients, 85617a-CD8


title: Treatment naïve MS patients, 85917a-CD4


title: Treatment naïve MS patients, 85517a-CD8


title: Treatment naïve MS patients, 85517a-CD14


title: Healthy controls, 85317a-CD8


title: Healthy controls, 85317a-CD4


title: Treatment naïve MS patients, 85517a-CD4


title: Treatment naïve MS patients, 85217a-CD8


title: Healthy controls, 85117a-CD8


title: Healthy controls, 84917a-CD8


title: Healthy controls, 85317a-CD14


title: Healthy controls, 85117a-CD14


title: Healthy controls, 84917a-CD4


title: Healthy controls, 85117a-CD4


title: Treatment naïve MS patients, 85917a-CD8


title: Treatment naïve MS patients, 85217a-CD4


title: Healthy controls, 84917a-CD14


title: Healthy controls, 84717a-CD8


title: Healthy controls, 84817a-CD14


title: Healthy controls, 84717a-CD14


title: Treatment naïve MS patients, 85917a-CD14


title: Healthy controls, 84817a-CD8


title: Healthy controls, 84817a-CD4


title: Healthy controls, 84617a-CD4


title: Healthy controls, 84717a-CD4


title: Treatment naïve MS patients, 85617a-CD14


title: Healthy controls, 84617a-CD14


title: Treatment naïve MS patients, 85217a-CD14


title: Treatment naïve MS patients, 84517a-CD4


title: Treatment naïve MS patients, 84517a-CD8


title: Healthy controls, 84217a-CD8


title: Treatment naïve MS patients, 84317a-CD8


title: Treatment naïve MS patients, 84517a-CD14


title: Healthy controls, 84117a-CD4


title: Treatment naïve MS patients, 84017a-CD8

value: PP


title: Healthy controls, 84217a-CD14


title: Healthy controls, 84217a-CD4


title: Healthy controls, 84117a-CD14


title: endothelial cells, S/G2/M phase, rep 1


title: Treatment naïve MS patients, 83517a-CD8


title: Treatment naïve MS patients, 83517a-CD14


title: Healthy controls, 84617a-CD8


title: Healthy controls, 83417a-CD8


title: Treatment naïve MS patients, 83517a-CD4


title: Healthy controls, 83417a-CD4


title: Healthy controls, 83417a-CD14


title: Healthy controls, 83317a-CD14


title: Treatment naïve MS patients, 84017a-CD14


title: Healthy controls, 83317a-CD8


title: Healthy controls, 83217a-CD8


title: Treatment naïve MS patients, 84317a-CD14


title: Healthy controls, 87317a-CD8


title: Healthy controls, 83317a-CD4


title: Treatment naïve MS patients, 84017a-CD4


title: Healthy controls, 83217a-CD4


title: Healthy controls, 83117a-CD8


title: Healthy controls, 83117a-CD14


title: Treatment naïve MS patients, 82917a-CD8


title: Healthy controls, 83217a-CD14


title: Healthy controls, 84117a-CD8


title: Healthy controls, 83117a-CD4


title: Treatment naïve MS patients, 82917a-CD14


title: Treatment naïve MS patients, 82917a-CD4


title: Treatment naïve MS patients, 84317a-CD4


title: Treatment naïve MS patients, 82417a-CD8


title: Treatment naïve MS patients, 82417a-CD14


title: Treatment naïve MS patients, 82417a-CD4


title: Healthy controls, 82817a-CD14


title: Healthy controls, 82817a-CD8


title: Treatment naïve MS patients, 82317a-CD8


title: Treatment naïve MS patients, 82317a-CD4


title: Treatment naïve MS patients, 82317a-CD14


title: Treatment naïve MS patients, 80917a-CD8

value: Unknown


title: Treatment naïve MS patients, 81917a-CD8


title: Treatment naïve MS patients, 81917a-CD14


title: Treatment naïve MS patients, 81917a-CD4


title: Treatment naïve MS patients, 80917a-CD4


title: Treatment naïve MS patients, 81017a-CD4


title: Treatment naïve MS patients, 80417a-CD8


title: Treatment naïve MS patients, 80417a-CD4


title: Treatment naïve MS patients, 80917a-CD14


title: Healthy controls, 82817a-CD4


title: Treatment naïve MS patients, 81017a-CD14


title: Treatment naïve MS patients, 80617a-CD14


title: Treatment naïve MS patients, 80317a-CD4


title: Treatment naïve MS patients, 80317a-CD14


title: Treatment naïve MS patients, 80617a-CD8


title: Treatment naïve MS patients, 80417a-CD14


title: Treatment naïve MS patients, 80617a-CD4


title: Treatment naïve MS patients, 80217a-CD8


title: Treatment naïve MS patients, 79717a-CD8


title: Treatment naïve MS patients, 80017a-CD14


title: Treatment naïve MS patients, 80217a-CD14


title: Treatment naïve MS patients, 79717a-CD4


title: Treatment naïve MS patients, 79617a-CD14


title: Treatment naïve MS patients, 80217a-CD4


title: Treatment naïve MS patients, 80017a-CD8


title: Treatment naïve MS patients, 79317a-CD8


title: Treatment naïve MS patients, 79317a-CD14


title: Treatment naïve MS patients, 79617a-CD8


title: Treatment naïve MS patients, 80317a-CD8


title: Treatment naïve MS patients, 78917a-CD8


title: Treatment naïve MS patients, 79017a-CD8


title: Treatment naïve MS patients, 79617a-CD4


title: Treatment naïve MS patients, 78917a-CD4


title: Treatment naïve MS patients, 79017a-CD4


title: Treatment naïve MS patients, 78917a-CD14


title: Treatment naïve MS patients, 79017a-CD14


title: Treatment naïve MS patients, 78817a-CD8


title: Treatment naïve MS patients, 78817a-CD4


title: Treatment naïve MS patients, 78817a-CD14


title: Treatment naïve MS patients, 78617a-CD8


title: Treatment naïve MS patients, 78617a-CD14


title: Treatment naïve MS patients, 78417a-CD8


title: Treatment naïve MS patients, 78417a-CD4


title: Treatment naïve MS patients, 77616a-CD4


title: Treatment naïve MS patients, 78417a-CD14


title: Treatment naïve MS patients, 80017a-CD4


title: Treatment naïve MS patients, 79317a-CD4


title: Treatment naïve MS patients, 76016a-CD8


title: Treatment naïve MS patients, 75616a-CD8


title: Treatment naïve MS patients, 76016a-CD14


title: Treatment naïve MS patients, 76016a-CD4


title: Treatment naïve MS patients, 76116a-CD14


title: Treatment naïve MS patients, 75616a-CD4


title: Treatment naïve MS patients, 75216a-CD4


title: Treatment naïve MS patients, 77616a-CD8


title: Treatment naïve MS patients, 78617a-CD4


title: Treatment naïve MS patients, 75816a-CD14


title: Treatment naïve MS patients, 75616a-CD14


title: Treatment naïve MS patients, 76116a-CD4


title: Treatment naïve MS patients, 75216a-CD14


title: Treatment naïve MS patients, 75016a-CD8

value: RIS


title: Treatment naïve MS patients, 75416a-CD4


title: Treatment naïve MS patients, 79717a-CD14


title: Treatment naïve MS patients, 75416a-CD8


title: Treatment naïve MS patients, 75816a-CD4


title: Treatment naïve MS patients, 75216a-CD8


title: Treatment naïve MS patients, 74116a-CD8


title: Treatment naïve MS patients, 75816a-CD8


title: Treatment naïve MS patients, 74116a-CD14


title: Treatment naïve MS patients, 76116a-CD8


title: Treatment naïve MS patients, 75416a-CD14


title: Treatment naïve MS patients, 77616a-CD14


title: Treatment naïve MS patients, 73916a-CD8


title: Treatment naïve MS patients, 75016a-CD4


title: Treatment naïve MS patients, 73416a-CD8


title: Treatment naïve MS patients, 74116a-CD4


title: Treatment naïve MS patients, 75016a-CD14


title: Treatment naïve MS patients, 74216a-CD14


title: Treatment naïve MS patients, 72516a-CD14


title: Treatment naïve MS patients, 73416a-CD14


title: Treatment naïve MS patients, 72116a-CD8


title: Treatment naïve MS patients, 73416a-CD4


title: Treatment naïve MS patients, 72116a-CD4


title: Treatment naïve MS patients, 73916a-CD14


title: Treatment naïve MS patients, 74216a-CD4


title: Treatment naïve MS patients, 71916a-CD4


title: Treatment naïve MS patients, 72516a-CD4


title: Treatment naïve MS patients, 74216a-CD8


title: Treatment naïve MS patients, 71916a-CD14


title: Treatment naïve MS patients, 72116a-CD14


title: Treatment naïve MS patients, 71916a-CD8


title: Treatment naïve MS patients, 72516a-CD8


title: Treatment naïve MS patients, 71616a-CD4


title: Treatment naïve MS patients, 71616a-CD8


title: Treatment naïve MS patients, 71416a-CD8


title: Treatment naïve MS patients, 71616a-CD14


title: Treatment naïve MS patients, 71416a-CD14


title: Treatment naïve MS patients, 71016a-CD8


title: Treatment naïve MS patients, 73216a-CD14


title: Treatment naïve MS patients, 71416a-CD4


title: Treatment naïve MS patients, 71016a-CD4


title: Treatment naïve MS patients, 71016a-CD14


title: Treatment naïve MS patients, 73216a-CD4


title: Treatment naïve MS patients, 73916a-CD4


title: Treatment naïve MS patients, 70916a-CD8


title: Treatment naïve MS patients, 70916a-CD14


title: Treatment naïve MS patients, 70616a-CD8


title: Treatment naïve MS patients, 70916a-CD4


title: Treatment naïve MS patients, 70616a-CD14


title: Treatment naïve MS patients, 70616a-CD4


title: Treatment naïve MS patients, 70216a-CD14


title: Treatment naïve MS patients, 69716a-CD14


title: Treatment naïve MS patients, 70216a-CD4


title: Treatment naïve MS patients, 69516a-CD8


title: Treatment naïve MS patients, 69716a-CD8


title: Treatment naïve MS patients, 69716a-CD4


title: Treatment naïve MS patients, 70216a-CD8


title: Treatment naïve MS patients, 69516a-CD4


title: Treatment naïve MS patients, 69316a-CD4


title: Treatment naïve MS patients, 69316a-CD8


title: Treatment naïve MS patients, 69316a-CD14


title: Treatment naïve MS patients, 69016a-CD8plus


title: Treatment naïve MS patients, 69516a-CD14


title: Treatment naïve MS patients, 68116a-CD4


title: Treatment naïve MS patients, 68116a-CD8


title: Treatment naïve MS patients, 69016a-CD14


title: Treatment naïve MS patients, 67815a-CD8


title: Treatment naïve MS patients, 68116a-CD14


title: Treatment naïve MS patients, 67515a-CD8


title: Treatment naïve MS patients, 69016a-CD8-


title: Treatment naïve MS patients, 67815a-CD14


title: Treatment naïve MS patients, 67815a-CD4


title: Treatment naïve MS patients, 67515a-CD4


title: Treatment naïve MS patients, 67415a-CD4


title: Treatment naïve MS patients, 67515a-CD14


title: Treatment naïve MS patients, 66915a-CD14


title: Treatment naïve MS patients, 65815a-CD8


title: Treatment naïve MS patients, 66415a-CD4


title: Treatment naïve MS patients, 67415a-CD14


title: Treatment naïve MS patients, 66915a-CD8


title: Treatment naïve MS patients, 66915a-CD4


title: Treatment naïve MS patients, 66215a-CD4


title: Treatment naïve MS patients, 66215a-CD8


title: Treatment naïve MS patients, 66415a-CD14


title: Treatment naïve MS patients, 65815a-CD14


title: Treatment naïve MS patients, 65715a-CD8


title: Treatment naïve MS patients, 66215a-CD14


title: Treatment naïve MS patients, 65615a-CD4


title: Treatment naïve MS patients, 65615a-CD8


title: Treatment naïve MS patients, 65715a-CD14


title: Treatment naïve MS patients, 67415a-CD8


title: Treatment naïve MS patients, 65415a-CD4


title: Treatment naïve MS patients, 65615a-CD14


title: Treatment naïve MS patients, 65715a-CD4


title: Treatment naïve MS patients, 65415a-CD8


title: Treatment naïve MS patients, 65415a-CD14


title: Treatment naïve MS patients, 66415a-CD8


title: Treatment naïve MS patients, 65015a-CD14


title: Treatment naïve MS patients, 64215a-CD4


title: Treatment naïve MS patients, 64215a-CD8


title: Treatment naïve MS patients, 65015a-CD4


title: Treatment naïve MS patients, 65815a-CD4


title: Treatment naïve MS patients, 64215a-CD14


title: Treatment naïve MS patients, 63815a-CD8


title: Treatment naïve MS patients, 63815a-CD4


title: Treatment naïve MS patients, 63315a-CD8


title: Treatment naïve MS patients, 63315a-CD4


title: Treatment naïve MS patients, 63815a-CD14


title: Treatment naïve MS patients, 62315a-CD14


title: Treatment naïve MS patients, 62315a-CD4


title: Treatment naïve MS patients, 65015a-CD8


title: Treatment naïve MS patients, 63315a-CD14


title: Treatment naïve MS patients, 62315a-CD8


title: Treatment naïve MS patients, 62115a-CD8


title: Treatment naïve MS patients, 62115a-CD14


title: Treatment naïve MS patients, 61515a-CD14


title: Treatment naïve MS patients, 61415a-CD4


title: Treatment naïve MS patients, 61415a-CD14


title: Treatment naïve MS patients, 61515a-CD8


title: Treatment naïve MS patients, 61215a-CD14


title: Treatment naïve MS patients, 61215a-CD8


title: Treatment naïve MS patients, 60815a-CD8


title: Treatment naïve MS patients, 61515a-CD4


title: Treatment naïve MS patients, 61415a-CD8


title: Treatment naïve MS patients, 60815a-CD14


title: Treatment naïve MS patients, 60615a-CD4


title: Treatment naïve MS patients, 60815a-CD4


title: Treatment naïve MS patients, 59915a-CD8


title: Treatment naïve MS patients, 59915a-CD4


title: Treatment naïve MS patients, 62115a-CD4


title: Treatment naïve MS patients, 59215a-CD4


title: Treatment naïve MS patients, 60615a-CD14


title: Treatment naïve MS patients, 59215a-CD14


title: Treatment naïve MS patients, 59915a-CD14


title: Treatment naïve MS patients, 59015a-CD8


title: Treatment naïve MS patients, 58915a-CD4


title: Treatment naïve MS patients, 59015a-CD4


title: Treatment naïve MS patients, 59015a-CD14


title: Treatment naïve MS patients, 61215a-CD4


title: Treatment naïve MS patients, 60615a-CD8


title: Treatment naïve MS patients, 58515a-CD4


title: Treatment naïve MS patients, 58015a-CD4


title: Treatment naïve MS patients, 58515a-CD8


title: Treatment naïve MS patients, 58415a-CD4


title: Treatment naïve MS patients, 58415a-CD14


title: Treatment naïve MS patients, 58415a-CD8


title: Treatment naïve MS patients, 58515a-CD14


title: Treatment naïve MS patients, 58915a-CD14


title: Treatment naïve MS patients, 58015a-CD8


title: Treatment naïve MS patients, 59215a-CD8


title: Treatment naïve MS patients, 58015a-CD14


title: Treatment naïve MS patients, 57915a-CD8


title: Treatment naïve MS patients, 57915a-CD4


title: Treatment naïve MS patients, 57814a-CD8


title: Treatment naïve MS patients, 57814a-CD4


title: Treatment naïve MS patients, 58915a-CD8


title: Treatment naïve MS patients, 57714a-CD4


title: Treatment naïve MS patients, 57414a-CD8


title: Treatment naïve MS patients, 57714a-CD8


title: Treatment naïve MS patients, 57714a-CD14


title: Treatment naïve MS patients, 57414a-CD4


title: Treatment naïve MS patients, 57314a-CD8


title: Treatment naïve MS patients, 57314a-CD4


title: Treatment naïve MS patients, 57414a-CD14


title: Treatment naïve MS patients, 57314a-CD14


title: Treatment naïve MS patients, 57915a-CD14


title: Treatment naïve MS patients, 73216a-CD8


title: Treatment naïve MS patients, 57114a-CD4


title: Treatment naïve MS patients, 56514a-CD4


title: Treatment naïve MS patients, 57114a-CD14


title: Treatment naïve MS patients, 57114a-CD8


title: Treatment naïve MS patients, 56914a-CD4


title: Treatment naïve MS patients, 57814a-CD14


title: Treatment naïve MS patients, 56914a-CD14


title: Treatment naïve MS patients, 56914a-CD8


title: Treatment naïve MS patients, 56014a-CD8


title: Treatment naïve MS patients, 56314a-CD4


title: Treatment naïve MS patients, 56414a-CD8


title: Treatment naïve MS patients, 56514a-CD8


title: Treatment naïve MS patients, 56414a-CD14


title: Treatment naïve MS patients, 56514a-CD14


title: Treatment naïve MS patients, 56014a-CD4


title: Treatment naïve MS patients, 53114b-CD4


title: Treatment naïve MS patients, 56014a-CD14


title: Treatment naïve MS patients, 55914a-CD14rep


title: Treatment naïve MS patients, 55914a-CD4


title: Treatment naïve MS patients, 53114b-CD8


title: Treatment naïve MS patients, 52814a-CD8


title: Treatment naïve MS patients, 52814a-CD4


title: Treatment naïve MS patients, 56414a-CD4


title: Treatment naïve MS patients, 53114b-CD14


title: Treatment naïve MS patients, 52814a-CD14


title: Treatment naïve MS patients, 56314a-CD8


title: Treatment naïve MS patients, 56314a-CD14


title: Treatment naïve MS patients, 51914a-CD14


title: Treatment naïve MS patients, 52214a-CD8


title: Treatment naïve MS patients, 52314a-CD8


title: Treatment naïve MS patients, 52214a-CD14rep


title: Treatment naïve MS patients, 52214a-CD4rep


title: Treatment naïve MS patients, 52314a-CD14


title: Treatment naïve MS patients, 51914a-CD8


title: Treatment naïve MS patients, 51914a-CD4


title: Treatment naïve MS patients, 51814a-CD8


title: Treatment naïve MS patients, 52314a-CD4


title: Treatment naïve MS patients, 55914a-CD8


title: Treatment naïve MS patients, 51113a-CD4


title: Treatment naïve MS patients, 51314a-CD4


title: Treatment naïve MS patients, 51814a-CD14


title: Treatment naïve MS patients, 51013a-CD8


title: Treatment naïve MS patients, 51314a-CD8


title: Treatment naïve MS patients, 51113a-CD14


title: Treatment naïve MS patients, 51113a-CD8


title: Treatment naïve MS patients, 51314a-CD14


title: Treatment naïve MS patients, 51013a-CD4


title: Treatment naïve MS patients, 51814a-CD4


title: Treatment naïve MS patients, 50913b-CD8


title: Treatment naïve MS patients, 49713a-CD8


title: Treatment naïve MS patients, 48913b-CD8


title: Treatment naïve MS patients, 48913b-CD4


title: Treatment naïve MS patients, 50913b-CD4


title: Treatment naïve MS patients, 48813b-CD14


title: Treatment naïve MS patients, 48913b-CD14


title: Treatment naïve MS patients, 48413b-CD4


title: Treatment naïve MS patients, 47713b-CD8


title: Treatment naïve MS patients, 50913b-CD14


title: Treatment naïve MS patients, 49013a-CD14


title: Treatment naïve MS patients, 49713a-CD4


title: Treatment naïve MS patients, 51013a-CD14


title: Treatment naïve MS patients, 49013a-CD4


title: Treatment naïve MS patients, 49313a-CD14


title: Treatment naïve MS patients, 49713a-CD14


title: Treatment naïve MS patients, 49013a-CD8


title: Treatment naïve MS patients, 48413b-CD14


title: Treatment naïve MS patients, 48413b-CD8


title: Treatment naïve MS patients, 48813b-CD8


title: Treatment naïve MS patients, 47713b-CD14


title: Treatment naïve MS patients, 47713b-CD4


title: Treatment naïve MS patients, 47313a-CD4


title: Treatment naïve MS patients, 47513a-CD8


title: Treatment naïve MS patients, 47313a-CD14


title: Treatment naïve MS patients, 47413a-CD8


title: Treatment naïve MS patients, 46913b-CD4

value: SP


title: Treatment naïve MS patients, 47513a-CD14


title: Treatment naïve MS patients, 43213b-CD4


title: Treatment naïve MS patients, 43213b-CD8


title: Treatment naïve MS patients, 47513a-CD4


title: Treatment naïve MS patients, 48813b-CD4


title: Healthy controls, 13311d-CD4


title: Treatment naïve MS patients, 47413a-CD14


title: Treatment naïve MS patients, 47313a-CD8


title: MCF7 siRNA non targeting Rep 1

status: Public on Dec 30 2020

city: Dublin

first: Leonie

middle: S

last: Young

state: Dublin

address: York House, York Street,, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

description:
siRNA control MCF7 cells
MCF7siNT_rep_1

data_processing:
fastq reads QC: read adapter removal, low quality read filtering using SOAPnuke:  version：v1.5.2  parameters: -l 15 -q 0.2 -n 0.05  website: https://github.com/BGI-flexlab/SOAPnuke
read mapping and alignment to GRCH37p.13 reference genome: Bowtie2  Bowtie2 is an ultrafast, memory-efficient short read aligner,indexing the reference with a Burrows-Wheeler index to keep its memory footprint small.  :Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200  Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml
Gene expression quantification from aligned reads: RSEM :  Version: v1.2.12  Parameters: default  Website: http://deweylab.biostat.wisc.edu/RSEM
Genome_build: GRCh37 p.13
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected counts and FPKM values for each sample

growth_protocol: MCF7 cells were grown in MEM (10% FCS, 1% L-Glutamine); LetR cells were grown in Phenol-red Free MEM with 10% Charcoal-dextran-stripped FCS, 1% L-glutamine, maintained in G418, Androstenedione and letrozole)

extract_protocol:
RNA was extracted using Qiagen RNeasy Kit
Total RNA Sample QC: Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). Purification:  mRNA polyA molecules using poly-T oligo-attached magnetic beads. Fragmentation: mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. PCR yield quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.  100bp PE sequencing: BGISEQ 500 platform

treatment_protocol: Experiments were carried out under steroid depleted conditions as cells were washed with PBS and kept in PRF-MEM with 10% CDS-FBS, 1% l-glutamine for 96 hours and media changed every day.

tag: knockdown

value: siNT


title: MCF7 siRNA AIB1 Rep 3

description:
knockdown of AIB1 in MCF7 cells
MCF7siAIB1_rep_3

tag: cell line

value: siRNA AIB1


title: MCF7 siRNA non targeting Rep 2

description:
siRNA control MCF7 cells
MCF7siNT_rep_2


title: Treatment naïve MS patients, 46913b-CD8

tag: cell type


title: Treatment naïve MS patients, 46913b-CD14


title: LetR siRNA non targeting Rep 2

description:
siRNA control LetR cells
LetRsiNT_rep_2

source_name: LetR

value: LetR


title: LetR siRNA AIB1 Rep 1

description:
knockdown of AIB1 in LetR cells
LetRsiAIB1_rep_1


title: Treatment naïve MS patients, 47413a-CD4


title: 5dpf_lvr_dnmt1mut_3

status: Public on Dec 01 2020

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters
Accepted bam files were used for counting read numbers of each gene with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes and repeats

source_name: 5 dpf dissected livers

growth_protocol: Zebrafish larvae were kept in 10 cm petri dish at a density of 60 larvae/plate (30ml) in a 10:14 light/dark cycle.

extract_protocol:
Livers from between 20-30 larvae were dissected and put in 500 ul of Trizol. RNA was extracted the same day of the liver dissection. Total RNA was treated by DNAseI (Thermo Scientific) for 30 minutes at 37C.
RNA quantitiy and quality was assesed by Qbit. 80-120ng of RNA was used for library prep. RiboZero was performed to deplete ribosomal RNA, and then used for TrueSeq Illumina library prep.

treatment_protocol: Zebrafish larvae were anethetized in tricane and the liver was dissected out between 120 and 122 hpf.

tag: background

value: ABNYU

tag: tissue

value: liver

tag: developmental stage

value: 5 dpf

tag: genotype

value: dnmt1 s904 mutants

tag: pool

value: 27 livers


title: 5dpf_lvr_dnmt1sib_3

value: dnmt1 s904 siblings

value: 20 livers


title: 5dpf_lvr_dnmt1sib_2


title: Treatment naïve MS patients, 43213b-CD14

value: Multiple sclerosis (MS)

value: F

value: CD14+ monocytes

value: RR


title: Healthy controls, 22012b-CD14

value: Healthy control

value: M


title: LetR siRNA non targeting Rep 1

description:
siRNA control LetR cells
LetRsiNT_rep_1


title: 5dpf_uhrf1_sib_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters
Accepted bam files were transformed to .sam format for counting repeats read numbers with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes and repeats

source_name: 5 dpf whole larvae

extract_protocol:
10 larvae were collected and  put in 500 ul of Trizol. RNA was extracted the same day . Total RNA was treated by DNAseI (Thermo Scientific) for 30 minutes at 37C.
RNA quantitiy and quality was assesed by Qbit. 1000ng of RNA was used for library prep. RiboZero was performed to deplete ribosomal RNA, and then used for TrueSeq Illumina library prep.

treatment_protocol: Zebrafish larvae were anethetized and collected at 120 hpf.

value: sibling

value: larva


title: CD4-specific T cell KO_3

status: Public on Nov 06 2020

city: Boston

first: Stefan

last: Haemmig

state: MA

address: 77 Avenue Louis Pasteur, NRB-742

department: Medicine

institute: Brigham and Women Hospital / Harvard Medical School

description:
B30Tregpos-pos
processed data file: ExpressionBrowser.xlsx

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Differential expression analysis was performed using CLC Genomics Workbench.
Genome_build: GRCm38
Supplementary_files_format_and_content: ExpressionBrowser.xlsx: Excel file includes counts, RPKM, TPM, and CPM for each Sample.

source_name: CD4+CD25+ T reg

extract_protocol:
RNeasy mini kit plus from Qiagen.
Ribosomal RNA depletion.

tag: strain/background

tag: genotype/variation

tag: diet

value: High fat

value: Splenic CD4+CD25+ T reg cells

tag: passages

value: Freshly isolated

tag: culture conditions

value: Not treated


title: WT_1

description:
A92Tregpos-pos
processed data file: ExpressionBrowser.xlsx

value: WT


title: CD4-specific T cell KO_1

description:
B27Tregpos-pos
processed data file: ExpressionBrowser.xlsx


title: Healthy controls, 13311d-CD8

tag: disease state

tag: gender

tag: age at exam

value: CD8+ T cells


title: Liver, CL 5 CAAX 0

status: Public on Aug 22 2020

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using hisat2 with default parameters
Accepted bam files were used for counting read numbers of each gene with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes and repeats

molecule: polyA RNA

source_name: Liver

growth_protocol: Zebrafish larvae were kept in 6-well plate in embryo medium at a density of 20 larvae/wellin a 10:14 light/dark cycle.

extract_protocol:
No Treatment
12  embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions.
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol
PolyA RNA-seq library

tag: age

value: 5 dpf

tag: treatment

value: control (embryo medium)

value: Liver

tag: rna qbit concentration(ng/ul)


title: Liver, CL 6 CAAX 0


title: Healthy controls, 13311d-CD14

tag: cell type

tag: disease subtypes

tag: disease duration

tag: edss


title: MCF7 siRNA non targeting Rep 31

description:
siRNA control MCF7 cells
MCF7siNT_rep_3

tag: cell line

tag: knockdown

value: siNT


title: Liver, CL 4 CAAX 0

tag: genotype

tag: pool

tag: tissue


title: MCF7 siRNA AIB1 Rep 1

description:
knockdown of AIB1 in MCF7 cells
MCF7siAIB1_rep_1

value: siRNA AIB1


title: LetR siRNA non targeting Rep 31

description:
siRNA control LetR cells
LetRsiNT_rep_3

value: LetR


title: MCF7 siRNA AIB1 Rep 2

description:
knockdown of AIB1 in MCF7 cells
MCF7siAIB1_rep_2


title: Uhrf1hepKO male mouse liver; H2az

status: Public on Jul 17 2020

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5, then quality trimmed using Trimmomatic. were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
Reads that passed quality control were aligned to reference genome GRCm38.p4 using bwa-mem
The resulting BAM alignments were then processed through PICARD tools to clean, sort and deduplicate (PCR and Optical duplicates)
Peaks calling was generated by MAC2, naroow peak mode was used for H2A.z; -f BAMPE was set for calling peaks in ATAC-seq
Genome_build: mm10/GRCm38.p4
Supplementary_files_format_and_content: .bed called peaks

source_name: mouse liver

growth_protocol: mice were feed with normal diet

extract_protocol: ChIP-seq libraries were prepared according to Bernstein lab protocol with individual enzymes purchased from NEB. ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.

treatment_protocol: 8-12 week old mice, liver harvested between 9am-noon

tag: strain


title: LetR siRNA AIB1 Rep 3

description:
knockdown of AIB1 in LetR cells
LetRsiAIB1_rep_3


title: LetR siRNA AIB1 Rep 2

description:
knockdown of AIB1 in LetR cells
LetRsiAIB1_rep_2


title: Uhrf1hepKO male mouse liver; ATACseq


title: WT male mouse liver; H2az


title: 5dpf_lvr_dnmt1sib_1

tag: background

value: ABNYU

value: liver

tag: developmental stage

value: dnmt1 s904 siblings

value: 20 livers


title: WT male mouse liver; ATACseq


title: 5dpf_uhrf1_sib_1

value: sibling

value: larva


title: 5dpf_lvr_dnmt1mut_2

value: dnmt1 s904 mutants

value: 30 livers


title: 5dpf_lvr_dnmt1mut_1


title: 5dpf_uhrf1_mut_2


title: WT_2

description:
A96Tregpos-pos
processed data file: ExpressionBrowser.xlsx

tag: strain/background

tag: genotype/variation

tag: diet

value: High fat

value: Splenic CD4+CD25+ T reg cells

tag: passages

value: Freshly isolated

tag: culture conditions

value: Not treated


title: 5dpf_uhrf1_mut_1


title: WT at reprogramming day 10

status: Public on Sep 11 2020

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm10 assembly) using BWA-MEM version 0.7.17 (Li and Durbin, 2010) .
To identify regions of ChIP-seq of TF enrichment over background, peak callings were performed by MACS2 version 2.2.7 (Zhang et al., 2008). Peak regions were filtered for false discovery rate values < 0.05.
To visualize ChIP-seq tag counts in the IGV (Robinson et al., 2011) , mapped reads were extended and converted into the bigWig format using bedGraphToBigWig.
To link site accessibility to regulation of gene expression, we associated each peak to its nearest gene in the mm10 genome using ChIPpeakAnno version 3.22.2 (Zhu et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: reprogramming MEF transduced with SeVdp carrying KLF4 WT

growth_protocol: NANOG-GFP reporter MEFs were seeded one-day before SeVdp infection and cultured in the conditioned knockout serum replacement (KSR) mESC medium supplemented with Shield1 (25 mcM) each medium change and Blasticidin S (5 µg/ml) added from day 3 to day 5; medium change performed once in two days.

extract_protocol:
All ChIP experiments were performed with ChIP-IT Express Chromatin Immunoprecipitation kit (Active Motif), following the kit protocol with minor modifications. Briefly, day 10 reprogramming cells (6.0X105 seeding density) in a 60-mm dish were crosslinked with 0.09 mL of 37% formaldehyde to 3.3 mL of growth medium. 1.5 mL of glycine (20X) was added to quench the unreacted formaldehyde. Cells in each 60-mm plate were collected and resuspended in 0.2 ml of lysis buffer. Genomic DNA was sheared to a targeted length of 150-200 bp on Covaris S220 Focused-ultrasonicator with optimized conditions. Sheared chromatin was subjected to cross-link reversal, treated with Proteinase K and RNase A, then phenol/chloroform extracted and analysed for the shearing efficiency on 1% agarose gel electrophoresis. For KLF4 ChIP ~3.2X106 reprogramming cells and 5 mg of antibody were used for each experiment. Finally, DNA fragments were purified using Chromatin IP DNA Purification kit (Active Motif) following the manufacturer’s protocol and used for real time qPCR and ChIP-seq library preparation. The primary antibodies used as follows: Anti-Human KLF4 (R&D, AF3640).
ChIP-seq library was generated using KAPA Hyper Plus kit (Roche) by Lab Droid “Maholo” (Robotic Biology Institute) automatically.
Paired-end sequencing of the libraries was performed using Novaseq 6000 Sequencing system using SP 100 cycle kit (Illumina).

tag: strain background

tag: cell type

value: Nanog-GFP MEF-derived cells

tag: time point

value: at reprogramming day 10

tag: chip antibody

value: Anti-human KLF4 (R&D systems)


title: HK2,transcriptome 02

status: Public on Oct 14 2020

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a
Transcript abundances in TPM were caculated by  rsem 1.3.0
Genome_build: Ensembl Release 94
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: HK2,transcriptome 02

growth_protocol: Cell lines were grown on transwell (see manuscript) to confluence before RNA isolation.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney Cells


title: Mutant at reprogramming day 10

source_name: reprogramming MEF transduced with SeVdp carrying KLF4 mutant


title: 13_S13

status: Public on Jun 11 2020

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

data_processing:
Base calling software: RTA v2
Reads were quasi-mapped to the mouse genome and quantified at the transcript level using Salmon v0.11.2 ( settings: -p 20 --seqBias --validateMappings --gcBias --biasSpeedSamp 5 -i GRCm38_index -l A -1) followed by summary to the gene level using tximport v1.10.1.
Differential gene expression was performed with DESeq2 v1.22.2. Gene set enrichment analysis was performed with the MSigDB canonical pathways gene sets using FGSEA v1.8.0 run with 100,000 permutations.
Genome_build: mm10
Supplementary_files_format_and_content: The processed csv file contained raw (not normalized) gene level counts for all samples.

source_name: Striatum

growth_protocol: Female C57BL/6 mice were purchased from Charles River and maintained on a 12/12 hour light/dark cycle. Mice used in the experiments weighed between 22 and 28 g and were given food and water ad libitum. All animal experiments were approved by the Animal Care and Use Committee at the University of Virginia and conformed to the National Institutes of Health regulations for the use of animals in research.

extract_protocol:
Immediately following euthanasia, the mouse brains were harvested and the front right quadrants (FUS-treated region) were excised, placed in RNAlater (Qiagen), and stored at -80 °C. RNA extraction was performed using the RNeasy Mini Kit (Qiagen). mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, Massachusetts).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was performed using a NextSeq 500 (Illumina, San Diego, California) at a target depth of 25 million 2 x 75 bp paired end reads per sample.

treatment_protocol: Mice in groups designated “KD” received 50-70 mg/kg Ketamine and 0.25-0.5 mg/kg Dexmedetomidine via intraperitoneal injection. Mice in groups designated as “Iso” were placed in an induction chamber and received isoflurane delivered to effect in concentrations of 2.5% in medical air using a vaporizer. For isoflurane groups, anesthesia was maintained via nosecone. Once anesthetized, a tail vein catheter was inserted to permit intravenous injections of MBs and the MRI contrast agent. The heads of the mice were shaved and depilated, and the animals were then placed in a supine position over a degassed water bath coupled to an MR-compatible small animal FUS system (RK-100; FUS Instruments, Toronto, Canada). The entire system was then placed in a 3T MR scanner (Magnetom Trio; Siemens Medical Solutions, Malvern, Pennsylvania). A 2 inch cylindrical transmit-receive RF coil, designed and built in-house, was placed around the head to maximize imaging SNR. Baseline T1-weighted MR images were acquired and used to select 4 FUS target locations in and around the right or left striatum. Mice received an injection of albumin-shelled MBs , formulated as previously described. Sonication began immediately after clearance of the catheter. Sonications were performed at 0.4 MPa peak-negative pressure (PNP) using a 1.1 MHz single element focused transducer (FUS Instruments, Toronto, Canada) operating in 10 ms bursts, 0.5 Hz pulse repetition frequency and 2 minutes total duration. Immediately following the FUS treatment, mice received an intravenous injection of Gd-DPTA contrast agent (0.5 ul/g body weight; Magnevist; Bayer Health Care, Indianola, Pennsylvania), and T1-weighted contrast-enhanced images were acquired to assess BBBD.

tag: Sex

value: female

tag: treatment


title: C57BL6/J,transcriptome 03

source_name: C57BL6/J,transcriptome 03


title: Liver, CL 1 CAAX 0

tag: genotype

tag: age

value: 5 dpf

value: control (embryo medium)

value: Liver

tag: rna qbit concentration(ng/ul)


title: 21_S21

tag: strain

value: naive


title: 17_S17


title: 16_S16


title: 20_S20

value: KD


title: CD4-specific T cell KO_2

description:
B29Tregpos-pos
processed data file: ExpressionBrowser.xlsx


title: HKC8,transcriptome 03

source_name: HKC8,transcriptome 03

tag: tissue


title: 5_S5


title: Liver, CL 2 CAAX 0

tag: pool


title: 23_S23


title: 12_S12


title: 22_S22


title: 120hpf_sibling control_3

status: Public on Jun 23 2020

description: ABNYU

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

source_name: embryo

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

value: sibling control


title: 9_S9

value: iso


title: 10_S10


title: 120hpf_uhrf1 mutant_1

description: ABNYU

value: uhrf1 mutant


title: 4_S4


title: EFKD_cnt_H3K27ac_rep2

status: Public on May 12 2020

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

description:
CUT&Tag
iEF_K27ac_cutoff_peaks.bed

data_processing:
Library strategy: CUT&Tag
Illumina’s Bcl2fastq conversion software
FastQC
Quality and adapter trimming: TrimGalore!
Alignment to hg19 with bowtie2
SAM to BAM conversion with samtools
Peak calling with MACS2: first call peaks using both replicates of each condition pooled using "callpeak". Then use "bdgdiff" to call peaks up in test conditions as compared to Rb IgG. Peaks were included only if the summit in the spike-in normalized bigwig exceeded 10000.
BAM to BED and BED to spike-in normalized bedgraph with Pybedtools; spike-in normalization first normalized all samples to the same total number of reads and then to the number of spike-in reads.
Bedgraph to bigwig with bedGraphToBig UCSC util
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, genome tracks for each sample
Supplementary_files_format_and_content: bed, peak calling output from MACS2 callpeak + bdgdiff

source_name: A673 cells

growth_protocol: A673 cells were cultured in DMEM supplemented with FBS, PSQ, and NaPyruvate.

extract_protocol:
NEBNext
For KD-rescue samples cells were seeded at 50% confluency and left to adhere overnight (day 0). shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833)until days 5, and then rescue or mock-rescue was performed. Cells were then double selected in puro and hygro for 7 days before collection for CUT&Tag.

treatment_protocol: Cells were retrovirally transduced with either control shRNA (iLuc) or shRNA targeting EWS/FLI (iEF) on day 0. Cells were selected in 2 ug/mL puromycin and transduced with either empty vector or cDNA encoding 3XFLAG-wtEWS/FLI on day 4. Cells were then double selected in puro and 100 ug/mL hygromycin B for 7 days before collection for CUT&Tag

tag: transduced shrna

value: iEF + empty cDNA

tag: replicate


title: wtEF_cnt_H3K27ac_rep2

description:
CUT&Tag
714_K27ac_cutoff_peaks.bed

value: iEF + 3XFLAG-EWS/FLI


title: EFKD_cnt_Rb_rep1

description:
CUT&Tag
iEF_K27ac_cutoff_peaks.bed
iEF_LSD1_cutoff_peaks.bed
iEF_REST_cutoff_peaks.bed


title: 11_S11


title: 18_S18


title: A673_cnt_Rb_rep2

description:
CUT&Tag
iLuc_K27ac_cutoff_peaks.bed
iLuc_LSD1_cutoff_peaks.bed
iLuc_REST_cutoff_peaks.bed

value: iLuc + empty cDNA


title: 120hpf_uhrf1 mutant_3

description: ABNYU


title: A673_cnt_H3K27ac_rep1

description:
CUT&Tag
iLuc_K27ac_cutoff_peaks.bed


title: A673_cnt_H3K27ac_rep2

description:
CUT&Tag
iLuc_K27ac_cutoff_peaks.bed


title: 120hpf_sibling control_2

description: ABNYU


title: 19_S19


title: ORR_OvarianFollicleCell_MS_Replicate2

status: Public on Apr 13 2020

city: Nashville

first: Jared

last: Nordman

address: 465 21st Ave South MRB III 4268

institute: Vanderbilt University

description:
S phase DNA
processed data file: all_raw_avgRT_values.txt

data_processing:
Reads from G1 and S samples were aligned to the dm6 reference genome (Release 6.04) using Bowtie 2 (v2.3.2) default parameters (Langmead et al. 2009).
Reads with a MAPQ score greater than 10 were retained using SAMtools (v1.9) (Li et al. 2009).
txtTools coverage (v2.26.0) was used to quantify the number of reads mapping to each 100kb window, with results normalized to read depth (Quinlan and Hall 2010).
Replication timing (RT) values were obtained by averaging the S/G1 ratio of reads per million (RPM) value from each S phase replicate for a particular window size. Profiles were generated by plotting the RT value at each window versus genomic location.
Quantile normalization was performed for comparisons between samples through the preprocess Core R package to equalize the dynamic range of RT values (Bolstad 2016).
The limma statistical package was used to identify 100kb windows with significantly altered RT values (lmFit, p value adjusted for multiple testing (p<0.01); absolute log2 fold change > 0.1) (Newville et al. 2014).
BEDTools intersect (v2.26.0) was used to determine overlap of 100kb windows with -f 0.5 and -u parameters (Quinlan and Hall 2010).
TopHat default parameters (v2.1.1) (Trapnell et al. 2012) were used to align single-end reads to the dm6 version of the Drosophila genome.
Transcriptomes were generated using Cufflinks (v2.2.1, see supplementary materials for parameters). We combined the Cufflinks generated transcriptome with transposons annotated by RepeatMasker (Smit et al. 2013-2015).
Differentially expressed transcripts were determined via edgeR statistical analysis (p value <0.01) (Robinson et al. 2010; McCarthy et al. 2012).
We assigned the RT log2 fold-change and associated limma-generated adjusted p-value determined at 10kb windows to individual transcripts; if a transcript overlapped multiple 10kb windows, we assigned the average RT log2 fold change and average adjusted p-value of all from all overlapping windows to that transcript.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: all_raw_avgRT_values.txt, bigWig files

organism: Drosophila melanogaster

source_name: Adult ovarian follicle cell

extract_protocol:
Adult female flies were fattened for 2 days on wet yeast and ~200 pairs of ovaries were dissected out by hand dissection. Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

tag: genotype/variation

value: Oregon-R

value: Ovarian follicle cell

value: Female

tag: developmental stage

value: Adult

tag: phase

value: S phase


title: A1

status: Public on Apr 20 2020

city: London

first: Adam

last: Pennycuick

address: 5 University Street

department: UCL Respiratory

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Raw fastq files were trimmed using fastp version 0.20.1 with default options.
Fastq files were tagged with UMI information using UMItools version 1.0.1
Reads were aligned to human genome UCSC hg38 using RNA-STAR version 2.5.2b
Duplicate reads were removed using JE-suite version 1.2.1 (using the UMI-aware markdupes method)
Reads per transcript were counted using FeatureCounts version 1.6.4
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Tab delimited text file containing non-normalised count data; columns represent samples, rows represent genes.

source_name: Adult_Airway epithelial cells

growth_protocol: Not applicable

extract_protocol:
Samples were thawed, disrupted by lysis (incubation at 42°C for 30 mins followed by incubation at room temperature for 5 mins), vortexed and filtered using RNAeasy MinElute columns (Qiagen). RNA extraction was performed using the Arcturus PicoPure RNA Isolation Kit (Life Technologies Ltd; KIT0204) as per the manufacturer’s instructions. RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific).
Libraries were created by UCL Genomics Core Facility using the SMARTer Stranded Total RNAseq Kit (Clontech), cleaned using JetSeq (Bioline) and quality control analysis of RNA integrity was performed using High Sensitivity RNA ScreenTape and the TapeStation Analysis software (Agilent Technologies). RNA sequencing was performed using 0.5x NextSeq for 75 cycles (Illumina; 43PE, ~33M reads per sample).

treatment_protocol: Bronchoscopic biopsies from the tracheal lumen were frozen in OCT and sectioned before laser-cature microdissection to isolate only the epithelium. Samples were suspended in a 2:1 mix of Arcturus PicoPure Extraction buffer and RNAlater (Life Technologies) and stored at -80°C until use.

tag: group

value: Airway epithelial cells


title: ORR_OvarianFollicleCell_MS_Replicate1


title: Yellow-white_WingDisc_MS_Replicate2

source_name: female 3rd instar larval wing disc

extract_protocol:
Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying Rubicon Thruplex DNA-seq kit (R400427).

value: Yellow-white

value: Wing disc

value: 3rd instar larvae


title: 8_S8

value: female


title: 2_S2


title: 7_S7


title: 15_S15

value: KD


title: 1_S1


title: H3K9me3 CTRL2 colon

status: Public on Feb 05 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: chromatin

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.6.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the Nextera transposase adapter sequence.
Trimmed reads were mapped to the mouse GRCm38 genome assembly using Bowtie2 (v2.3.2)
BAM files were imported to Seqmonk v1.44.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp). All read counts quantitated as log(2) with a lower limit of 1.0 transformed by matching distributions.
Supplementary_files_format_and_content: Sublist of EdgeR probes with FDR<0.05 KO vs WT, Benjamini-Hochberg correction. MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp). All read counts quantitated as log(2) with a lower limit of 1.0 transformed by matching distributions.

source_name: colon

extract_protocol:
Crypt isolation protocol: Colons were dissected as described by Kazakevych et al., Nucleic Acids Res. 2017. Whole crypt suspensions were used for further processing.
fixation protocol: The pellet containing crypt cells was resuspended in 1 ml of PBS-1% formaldehyde and fixated for 10 minutes with gentle shaking at room temperature. The reaction was quenched with glycine at a final concentration of 0.125 M for 5 minutes. Cells were pelleted at 2400 g 4 °C for 2 minutes and washed three times with 1 ml of PBS.
ChIP protocol: Sonication was performed in 180 μl of lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA,1% SDS and protein inhibitors cocktail) in a water-cooled Bioruptor (Diagenode), high power, with 14 cycles with 30 seconds on and 30 seconds off each. The sonicated chromatin was diluted in 810 ul of RIPA buffer containing 0.1% SDS and incubated overnight with protein A/G sepharose Dynabeads previously incubated with the specific antibody for ChIP (H3K9me3 - ab8898 Abcam) for 2 hours. For the inputs 3% of the volume for each sample was used. Following incubation, the material was washed 2 times with RIPA buffer low salt (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton-X-100, 0.1 % SDS ) and 2 times with RIPA buffer high salt (containing 500 mM NaCl) and once with TE buffer (10 mM Tris-HCl, 1 mM EDTA). Samples were diluted in 200 μl of elution buffer (20 mM Tris-HCl pH 7.5, 5 mM EDTA and 50 mM NaCl) and treated with 2 μl of RNase (20 mg/ml) for 30 minutes at 37 °C. After, samples was incubated with protein k for 2 hours at 65 °C at 300 rpm. The DNA was extracted with phenol-chloroform protocol.
Libraries were generated from 5 ng total chromatin according to NEBNext UltraII DNA Library Prep kit for Illumina. Libraries were sequenced on a BGI HiSeq as 50bp single-end reads.

value: wildtype

tag: antibody

value: H3K9me3 - ab8898 Abcam

tag: cell type

value: whole crypt isolate


title: H3K9me3 CTRL1 colon

description: chromatin


title: EFKD_cnt_Rb_rep2

value: iEF + empty cDNA


title: H3K9me3 KO2 colon

description: chromatin

value: Vil-Cre mediated KO of Smarcad1


title: EFKD_cnt_H3K27ac_rep1

description:
CUT&Tag
iEF_K27ac_cutoff_peaks.bed


title: wtEF_cnt_H3K27ac_rep1

description:
CUT&Tag
714_K27ac_cutoff_peaks.bed

value: iEF + 3XFLAG-EWS/FLI


title: Striatum, treated04, 24hr, S162R

status: Public on Dec 11 2019

data_processing:
Base calling software: RTA v2
Reads were quasi-mapped to the mouse genome and quantified at the transcript level using Salmon v0.11.2 ( settings: -p 20 --seqBias --validateMappings --gcBias --biasSpeedSamp 5 -i GRCm38_index -l A -1) followed by summary to the gene level using tximport v1.10.1.
Differential gene expression was performed with DESeq2 v1.22.2. Gene set enrichment analysis was performed with the MSigDB canonical pathways gene sets using FGSEA v1.8.0 run with 10,000 permutations.
Genome_build: mm10
Supplementary_files_format_and_content: The processed csv file contained raw (not normalized) gene level counts for all samples.

growth_protocol: Male C57BL/6 mice were purchased from Charles River and maintained on a 12/12 hour light/dark cycle. Mice used in the experiments weighed between 22 and 28 g and were given food and water ad libitum. All animal experiments were approved by the Animal Care and Use Committee at the University of Virginia and conformed to the National Institutes of Health regulations for the use of animals in research.

treatment_protocol: Male C57BL/6 mice were anesthetized with an intraperitoneal injection of 120 mg/kg ketamine, 12 mg/kg xylazine, and 0.08 mg/kg atropine in sterilized 0.9% saline. A tail vein catheter was inserted to permit intravenous injections of MBs, plasmid, and the MRI contrast agent. The heads of the mice were shaved and depilated, and the animals were then placed in a supine position over a degassed water bath coupled to an MR-compatible small animal FUS system (RK-100; FUS Instruments, Toronto, Canada). The entire system was then placed in a 3T MR scanner (Magnetom Trio; Siemens Medical Solutions, Malvern, Pennsylvania). A 2 inch cylindrical transmit-receive RF coil, designed and built in-house, was placed around the mouse’s head to maximize imaging SNR. Baseline T1-weighted MR images were acquired and used to select 4 FUS target locations in and around the right striatum.

value: male

tag: harvest timepoint

value: Striatum


title: Striatum, treated04, 24hr, S161R

tag: Sex


title: wtEF_cnt_Rb_rep2

description:
CUT&Tag
714_K27ac_cutoff_peaks.bed
714_LSD1_cutoff_peaks.bed
714_REST_cutoff_peaks.bed


title: A4

value: Bronchoscopic biopsies from the tracheal lumen


title: Striatum, treated02, 24hr, S164R

tag: treatment


title: H3K9me3 KO3 colon

description: chromatin

tag: genotype


title: A673_cnt_Rb_rep1

value: iLuc + empty cDNA


title: Striatum, treated02, 24hr, S165R


title: H3K9me3 KO colon input

description: chromatin


title: Striatum, treated02, 24hr, S163R


title: Striatum, treated01, 24hr, S168R


title: Striatum, treated01, 24hr, S167R


title: H3K9me3 CTRL3 colon

description: chromatin


title: Striatum, treated01, 24hr, S169R


title: H3K9me3 KO1 colon

description: chromatin


title: Striatum, treated04, 6hr, S197R


title: Striatum, treated01, 24hr, S166R


title: Striatum, treated04, 6hr, S196R


title: Striatum, treated04, 24hr, S160R


title: H3K9me3 CTRL colon input

description: chromatin


title: Yellow-white_WingDisc_MS_Replicate1

value: Female

value: S phase


title: Striatum, treated02, 6hr, S205R


title: Striatum, treated02, 6hr, S199R


title: wtEF_cnt_Rb_rep1


title: Striatum, AnMB, 24hr, 228R

value: AnMB


title: Striatum, AnMB, 24hr, 227R


title: Striatum, AnMB, 24hr, 229R


title: Striatum, treated04, 6hr, S195R


title: Striatum, treated02, 6hr, S200R


title: Fed Colon

status: Public on Nov 22 2019

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

institute: WEHI

data_processing:
Read alignment and count summarization were performed using CellRanger v3.0.2 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: gene_count.csv.gz: Gene counts with barcodes from the Fed_Colon and Fed_SI samples. Data are post-quality filtering (but pre-doublet detection) and were used as input for downstream analyses.

source_name: ILCs

extract_protocol:
Purified ILCs were resuspended at 10.000 cells per µl and loaded in a single cell A chip.
RNA libraries were prepared for sequencing using the 10x Genomics Chromium single-cell 3′ v2 kit

treatment_protocol: Small intestine and colon were digested and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted

tag: age

value: 8 weeks

value: Colon

value: Sorted IL7ra+ ILC


title: Striatum, AnMB, 6hr, 217R


title: Striatum, treated01, 6hr, S204R


title: Striatum, treated01, 6hr, S203R


title: 6_S6

value: female


title: Striatum, treated01, 6hr, S202R


title: WT repl2

status: Public on Sep 30 2019

city: Montpellier

first: Dominique

last: Helmlinger

address: 1919 route de Mende

department: CRBM

country: France

institute: CNRS

description: Illumina TruSeq Stranded mRNA Library

data_processing:
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to Schizosaccharomyces_pombe_1.1 reference genome using HISAT2 v2.1.0 with strand-specific information (--rna-strandness R) and otherwise default options
Reads were then counted for gene and exon features using htseq-count v0.9.1 in union mode (--mode union), reverse stranded (--stranded Reverse), and a minimum alignment quality of 10 (--minaqual 10)
Variance-mean dependence was estimated from count tables and tested for differential expression based on a negative binomial distribution, using DESeq2 v1.18.1. Pairwise comparison or one-way analysis of variance were run with a parametric fit and genotype as the source of variation (factor: ‘mutant’ or ‘control’)
Genome_build: Schizosaccharomyces_pombe_1.1
Supplementary_files_format_and_content: Tab-delimited txt files wee merged into one Excel spreadsheet, in which each sheet includes Gene ID, Log2 fold-change and normalized P values (P-adj) for each DESeq2 analysis. Tab-delimited text file with raw count data for all samples.

organism: Schizosaccharomyces pombe

source_name: Liquid cultures

growth_protocol: Yeast grown to mid-logarithmic phase

extract_protocol:
RNA was extracted from 50 mL of exponentially growing cells RNA using TRIzol. DNA was removed by DNase I digestion, using the TURBO DNA-free™ kit. RNA was cleaned using the RNeasy Mini kit. Total RNA quality and concentration was determined using an Agilent Bioanalyzer. Transcripts were purified by polyA-tail selection.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit

tag: strain genotype

value: WT

tag: growth conditions

value: YES

tag: strain number in table s2


title: Striatum, treated01, 6hr, S201R

tag: strain

tag: tissue


title: tra1D repl2

description: Illumina TruSeq Stranded mRNA Library


title: Striatum, AnMB, 6hr, 218R


title: Striatum, AnMB, 6hr, 219R


title: WT repl3

description: Illumina TruSeq Stranded mRNA Library


title: Border Zone mouse 40 [BZ-40]

status: Public on Jul 22 2019

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

description: PCM-1 sorted

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: BZ-PCM1-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).

source_name: Cardiomyocytes border zone

growth_protocol: Murine cardiac tissue was obtained 7 days after LAD (Ligation of the left ascecning permanent ligation of the left anterior descending coronary artery)

extract_protocol:
Nuclei were extracted from snap-frozen samples, and stained with PCM-1 rabbit polyclonal antibody (Atlas Antibodies) for flow cytoemtry analysis. RNA was isolated using the RNeasy Plus MicroKit (Quiagen)
NuGEN's Ovation RNA-seq V2 kit. Input cDNA synthesis: 500 pg

treatment_protocol: Border zone and remote myocardium were microdissected and snap-frozen

value: FVB

tag: time point

value: 7 days after LAD

value: infarcted myocardium

tag: tissue subtype

value: Cardiomyocytes border zone

tag: molecule subtype

value: nuclear RNA


title: Border Zone mouse 34 [BZ-34]

description: PCM-1 sorted


title: Fed SI

value: Small Intestine


title: tra1D repl1

description: Illumina TruSeq Stranded mRNA Library


title: Striatum, AnMB, 6hr, 216R

value: male

value: Striatum


status: Public on Jun 06 2019

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

institute: New York University Abu Dhabi

description:
WT, baseline, h3k27me3
Regenerating WT H3K27me3 - 0hr (round 3)

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5, then quality trimmed using Trimmomatic. were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
Reads that passed quality control were aligned to reference genome GRCm38.p4 using bwa-mem
The resulting BAM alignments were then processed through PICARD tools to clean, sort and deduplicate (PCR and Optical duplicates)
Peaks calling was generated by MAC2, for calling broader H3K27me3 peaks, SICER with parameter: window size, 200; gap size, 600; false discovery rate, 0.05 was adopted
Genome_build: mm10/GRCm38.p4
Supplementary_files_format_and_content: .bed called peaks

extract_protocol: ChIP-seq libraries were prepared according to Bernstein lab protocol with individual enzymes purchased from NEB

value: liver


title: WT repl1

description: Illumina TruSeq Stranded mRNA Library


title: Remote Myocardium mouse 40 [RM-40]

description: PCM-1 sorted

source_name: Cardiomyocytes remote myocardium

value: Cardiomyocytes remote myocardium


title: baseline Uhrf1hepKO H3K4me3 (round 2)

description:
Uhrf1hepKO, baseline, h3k4me3
baseline Uhrf1hepKO H3K4me3 (round 2)

source_name: mouse liver


title: Input (round 3)

description:
input_s3
Input (round 3)

value: none (input)


title: baseline WT H3K4me3 (round 2)

description:
WT, baseline, h3k4me3
baseline WT H3K4me3 (round 2)


title: tra1D repl3

description: Illumina TruSeq Stranded mRNA Library


description:
WT, 30hr, h3k27me3
Regenerating WT H3K27me3 - 30hr (round 3)


title: Uhrf1hepKO, baseline, h3k27me3

data_processing:
Illumina Casava1.8 software used for basecalling
The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
The surviving paired reads were aligned against the mouse reference genome (GRCm38.p4) using bwa-mem
The resulting BAM alignments were then processed through PICARD  tools, to clean, sort and deduplicate
narrow peaks were called with MACs2 and broad peaks of H3K27me3 were called with SICER with window size 1000bp and gap size 4000bp
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeak and csv files containing called peaks

tag: chip antibody


title: Border Zone mouse 32 [BZ-32]

description: PCM-1 sorted

value: 8 weeks


title: Remote Myocardium mouse 43 [RM-43]

description: PCM-1 sorted


description:
WT, 96hr, h3k27me3
Regenerating WT H3K27me3 - 96hr (round 3)


title: WT, PHx, 4wks rep 2

status: Public on May 31 2019

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_WT2

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignments of trimmed reads were performed using tophat2  v2.1.0, with the parameters “–no-novel-junctions” and “–G”
Cufflinks  v2.2.1 was used to derive FPKM values. Read counts were generated using HTseq count
Test of differential expression  was implemented by DESeq2 in Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing reads counts and FPKM

extract_protocol:
RNA was extracted using Zymo Duet DNA/RNA dual-extraction kit
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation with polyA
RNA-seq, Illumina Hi-Seq platform, 100bp paired-end reads

treatment_protocol: 8-12 week old mice underwent 2/3 partial hepatectomy surgery between 9am - noon

value: PHx

tag: time


title: Uhrf1hepKO, PHx, 4wks rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_KO3


title: WT, PHx, 7days rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
7days_WT3


title: WT, PHx, 7days rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
7days_WT2


title: Uhrf1hepKO, PHx, 96hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_KO3


title: baseline Uhrf1hepKO H3K9me3 (round 2)

description:
Uhrf1hepKO, baseline, h3k9me3
baseline Uhrf1hepKO H3K9me3 (round 2)

tag: antibody


title: baseline WT H3K9me3 (round 2)

description:
WT, baseline, h3k9me3
baseline WT H3K9me3 (round 2)


description:
WT, 40hr, h3k27me3
Regenerating WT H3K27me3 - 40hr (round 3)


title: Input (round 2)

description:
input_s2
Input (round 2)


title: WT, baseline, h3k4me3


title: WT, baseline, h3k27me3


title: Patient 14_lh 24

status: Public on Sep 26 2019

type: RNA

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 10 HK genes (SF3A3, PPIA, POLR2A, MRPS5, MTMR14, GUSB, G6PD, ERCC3, EIF2B4, COG7). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, ten reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Classical Hodgkin Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of classical Hodgkin Lymphoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Pretreatment diagnostic biopsies from ABVD-treated classical Hodgkin Lymphoma patients

tag: subject status

value: patient affected by Hodgkin Lymphoma

tag: gender

value: M

tag: Stage

value: IV A

value: yes

tag: interim pet response

value: negative


title: input control

description: input


title: Uhrf1hepKO, PHx, 4wks rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_KO2

tag: genotype

tag: treatment


title: Uhrf1hepKO, PHx, 4wks rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_KO1


title: WT, PHx, 4wks rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_WT1

value: WT


title: Uhrf1hepKO, PHx, 7days rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
7days_KO3


title: WT, PHx, 4wks rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
4wks_WT3


title: WT, PHx, 96hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_WT3


title: Uhrf1hepKO, PHx, 40hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_KO3


title: Uhrf1hepKO, baseline, h3k4me3


title: WT, PHx, 48hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
48hrs_WT3


title: WT, PHx, 40hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_WT1


title: Uhrf1hepKO, PHx, 96hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_KO1


title: WT, PHx, 96hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_WT2


title: Uhrf1hepKO, PHx, 48hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
48hrs_KO3


title: KO, baseline rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_KO3

value: baseline


title: Uhrf1hepKO, PHx, 48hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
48hrs_KO2


title: Uhrf1hepKO, PHx, 40hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_KO1


title: Uhrf1hepKO, PHx, 40hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_KO2


title: Uhrf1hepKO, PHx, 96hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_KO2


title: Uhrf1hepKO, PHx, 48hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
48hrs_KO1


title: WT, baseline rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_WT1


title: WT, PHx, 7days rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
7days_WT1


title: WT, baseline rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_WT2


title: KO, baseline rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_KO1


title: KO, baseline rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_KO2


title: Uhrf1hepKO, PHx, 7days rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
7days_KO1


title: WT, PHx, 48hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
48hrs_WT2


title: WT, PHx, 96hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
96hrs_WT1


title: WT, baseline rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_b_WT3


title: Uhrf1hepKO, PHx, 30hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
30hrs_KO2


title: Uhrf1hepKO, PHx, 30hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
30hrs_KO3


title: Uhrf1hepKO, PHx, 30hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
30hrs_KO1


title: WT, PHx, 30hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
30hrs_WT3


title: WT, PHx, 40hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_WT2


title: Uhrf1hepKO, PHx, 24hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_KO3


title: WT, PHx, 30hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
30hrs_WT2


title: WT, PHx, 24hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_WT3


title: WT, PHx, 40hrs rep 3

description:
Gene_counts.csv, Gene_FPKMs.csv
40hrs_WT3


title: WT, PHx, 24hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_WT2


title: WT, PHx, 24hrs rep 1

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_WT1


title: nATF63: 5 dpf Livers of ATF6 transgenic zebrafish-3

status: Public on May 08 2019

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

source_name: liver/pooled

extract_protocol:
Tg(fabp10:nAtf6-cherry; cmlc2:GFP)C+/, were outcrossed to WT TAB 14 and the embryos were sorted and segregated basing on the expression of Cmlc2:GFP. The three different clutches of embryos were collected and dissected over three different days. The embryos were collected inbetween 10- 11 AM. The Liver dissection was also performed on the 5dpf larvae before noon. 25 livers from 5dpf embryos were pooled per sample( Transgenic and WT siblings in two different tubes) and RNA extracted with Trizol as per manufacturer's instructions.The RNA was later treated with DNAse to remove any DNA. They RNA concentration was taken on the Q bit, and then analysed on the Bioanalyser for the integrety and quality of RNA. The RIN score for the samples was above 8.5
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold (Catalog #: RS-122-2501)

value: pooled liver

tag: genotype/variation

value: ATF6 transgenic


title: nATF61: 5 dpf Livers of ATF6 transgenic zebrafish-1


title: nATF62: 5 dpf Livers of ATF6 transgenic zebrafish-2


title: sibslivr3: 5 dpf Livers non transgenic siblings-3


title: sibslivr2: 5 dpf Livers non transgenic siblings-2


title: B6N_ChIP_replicate_2

status: Public on Mar 07 2019

city: Bar Harbor

first: Mary Ann

last: Handel

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Single Stranded DNA Sequencing (SSDS)

data_processing:
Fastq files for paired-end sequenced DMC1 samples were trimmed using Trimmomatic (v0.32) and subsequently parsed for detection and selection of paired reads having homology at the 5’ and 3’ ends as established by protocols for single strand DNA enrichment.
These selected paired-end reads represent the detectable single stranded DNA reads. Selected reads were aligned to mm10 genome using BWA (0.5.10-tpx) and bam files were parsed for detection and subsequent selection of single ended reads containing true genomic sequence versus fill-in sequence at the homologous region.
Fastq files were created containing only the single ended, single stranded DNA reads for subsequent alignments. Peaks were called utilizing MACS 2.0 with the read extension parameter set to 800 in order to force pileups.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome_build: mm10
Supplementary_files_format_and_content: MACS callpeak

source_name: Anti-DMC1 B6N_testis_SSDS_2

growth_protocol: Germ cells were extracted from 8 weeks old testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol:
To determine the sites and frequencies of double-stranded breaks in mouse spermatocytes ChIP was performed on 2-month old testis samples using anti-DMC1 antibody which specifically recognizes single-stranded end protruding from germ cell-specific double-stranded ends as per Brick et. al. 2012. Germ cells were isolated from the desired genotypes using Dounce Homogenizer, crosslinked, sonicated and immunoprecipitated with anti-DMC1(C-20) antibody.
The libraries were prepared using adapters from TruSeq DNA LT sample prep kit. Libraries were prepared according to the prescribed protocols and amplified for 12 cycles. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation. The amount of DNA after PCR is low to reduce background. Important comments:  The samples were run on Bioanalyzer for quality control. Libraries were sequenced on an Illumina® HiSeq 2500, with 75 bp paired-end reads.

value: Testis

value: Wildtype

value: Anti-DMC1 (C-20); vendor:Santa Cruz; sc-8973


title: B6N_ChIP_replicate_3

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 B6N_testis_SSDS_3


title: B6N_ChIP_replicate_1

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 B6N_testis_SSDS_1