title: NS542_HAT2KD_48h_H2AZ_ChIP_4

description:
CpB_ws1_ss1_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS546_HAT2KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS542_HAT2KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Sox9eGFP Low Chow RNA-seq Rep #1

status: Public on Feb 24 2020

type: SRA

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

country: USA

institute: Cornell University

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC180

library_source: transcriptomic

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

molecule: total RNA

organism: Mus musculus

source_name: Intestine

extract_protocol: Clonetech SMARTer Ultra Low Input library preparation kit combined with Nextera XT DNA sample preparation kit

tag: tissue

value: small intestine

tag: strain

tag: diet

value: Chow


title: C-16

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were aligned using STAR against the mouse genome assembly (mouse NCBI build38 (mm10) UCSC transcripts)
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package with default parameters
The read counts were used for the identification of global differential gene expression between specified populations and genotypes using the DESeq2 package.
Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Bone marrow

extract_protocol:
Cells were sorted into 4μL of lysis buffer containing; 0.2% Triton X-100, 2.5 uM OligodT, 2.5 mM dTNPs, RNase Inhibitor 20 U and ERCC spike-in 1:4,000,000. cDNA synthesis and PCR amplification were performed based on the published Smart-seq 2 protocol with some modifications.
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using one forth of the standard volume recommended by Illumina

treatment_protocol: 100 CD45.2+LKFcgRII/II+CD55-, CD45.1-EGFP-CD71hiTer119-/locKit+, and CD45.2+Mac1+cKitlo were isolated by fluorescent activated cell sorting for each sample

value: Bone marrow

tag: cell type

tag: tumour stage

value: Pre-leukaemia

tag: genotype

value: KLG


title: Rh41 parental, biological rep3

type: RNA

city: Indianapolis

first: Ricardo

last: Martinez

state: IN

address: 307 E Merrill St

institute: Eli Lilly and Company

description: A pan-cancer transcriptome analysis to identify the molecular mechanism of prexasertib resistance

hyb_protocol: After fragmentation and labeling, DNA target was hybridized on Affymetrix Clariom™S Array, Human (ThermoFisher Scientific-Affymetrix) according to Covance Inc.'s standard protocol.

scan_protocol: CEL. intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc).

data_processing: Raw CEL files were imported, log2-transformed, and normalized using GC-content adjusted Signal Space Transformation-Robust Multi-array Average (GC-STT-RMA) algorithm. And final expression results were quantile-normalized for differential expression anlaysis.

label: biotin

organism: Homo sapiens

source_name: Parental, prexasertib sensitive Rh41 cell line

label_protocol: Affymetrix  GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Inc) was used to generate biotinylated sense-stranded DNA targets according to Covance Inc.'s standard protocol.

extract_protocol: Total RNA was extracted using Direct-zol RNA kit (Zymo Research)according to the manufacturer's instructions.

treatment_protocol: The prexasertib resistant lines were generated through a long-term drug concentration escalation protocol.

value: pediatric alveolar rhabdomyosarcoma

tag: cell line


title: C-14


title: Tissue venom gland [HUB-JP-043]

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Single cells from venom gland tissue were sorted.
Tissue_allPlates.csv

data_processing:
The code used for data processing is deposited on GitHub: https://github.com/BuysDB/reptillianOrganoids
In brief, data were demultiplexed, mapped using STAR, deduplicated for UMI-scaffold pairs, counted using fractional counting and scaffolds pooled by BLAST annotation
Genome_build: De novo Aspidelaps lubricus transcriptome assembly.
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts, pooled by BLAST annotation. De novo transcriptome assembly using Trinity (transcriptome-assembly_min500bp (1).fna)

organism: Aspidelaps lubricus cowlesi

source_name: Tissue venom gland

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Live cells were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

value: Wildtype

value: Venom gland


title: NS539_HAT2KD_0h_H2AZ_ChIP_3

city: Planegg-Martinsried

first: T.

middle: Nicolai

last: Siegel

address: Großhaderner Str. 9

department: Department of Physiological Chemistry

country: Germany

institute: Ludwig-Maximilians-Universität

description:
CpB_ws1_ss1_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS543_HAT2KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS539_HAT2KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

library_source: genomic

data_processing:
Reads were mapped using Bowtie 2 local
BAM files were sorted and indexed using SAMtools version 1.8
The number of reads was normalised per billion mapped reads and coverage files were generated in the wiggle format using COVERnant version 0.3.0 with the subcommand ratio
Genome_build: HGAP3_Tb427v9; from Zenodo https://doi.org/10.5281/zenodo.823671
Supplementary_files_format_and_content: wiggle format containing coverage tracks

molecule: genomic DNA

organism: Trypanosoma brucei brucei

source_name: T. brucei 2T1 bloodstream form

growth_protocol: Cells were grown in HMI-11 medium to a density of 0.9 mio cells per ml. For depletion of HAT1 or HAT2, cells were treated with 1 µg/ml Doxycylcin for 48 h.

extract_protocol:
In brief, 2 x 10e8 cells were harvested, crosslinked in 1% formaldehyde, lysed using 200 µM digitonin (final concentration) and chromatin was fragmented using 1 U/µl MNase (Sigma-Aldrich). see Wedel et al. 2017 #1 (DOI: 10.15252/embj.201695323) and Wedel et al. 2017 #2 (10.1016/j.exppara.2017.03.003 ) Immunoprecipitation was performed using Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen) coupled to 10 µg polyclonal affinity-purified H2A.Z rabbit antibody. Bound material was washed and eluted, and cross-links were reversed at 65 °C for ~11 h in the presence of 300 mM NaCl (final concentration).
ChIP-seq libraries were constructed using 35 ng of immunoprecipitated or input DNA for sequencing on an Illumina platform. Following blunt-ending and poly(A)-tailing, Y-shaped adapters (Ford et al., 2014) containing the Illumina Truseq-Adapter-sequences are ligated to each end of a DNA molecule. The library concentrations were determined in duplicates using Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. Q32854) for Qubit 2.0 Fluorometer (Invitrogen, cat. no. Q32866). ChIP-seq libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, cat. no. KK4824) according to the manufacturer’s instruction and sequenced in paired-end mode with 2 x 76 cycles using an Illumina NextSeq 500 platform.

tag: genotype/variation

tag: time

tag: chip antibody

value: polyclonal affinity-purified H2A.Z rabbit antibody (available from T. N. Siegel)


title: raw_RV-THP_D6-3

city: Dallas

first: Igor

middle: M

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 22.0
Supplementary_files_format_and_content: excel,expression profiles

organism:
Mycobacterium tuberculosis
Homo sapiens

source_name: THP-1 infected with Mtb H37Rv for 6 days

growth_protocol: Infected cell culture was used

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: Cells were either uninfected or infected for 3 days or 6 days

tag: treatment

value: infected with Mtb H37Rv for 6 days

tag: molecule subtype

value: small RNA


title: Tissue venom gland [HUB-JP-042]


title: raw_RV-THP_D6-2


title: NS538_HAT1KD_48h_H2AZ_Input_4

description:
CpB_ws1_ss1_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz


title: raw_RV-THP_D6-1


title: Sox9eGFP Low  HFD RNA-seq Rep #2

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RNAseq_normalized_counts.csv
BC182

value: HFD


title: Rh41 prexasertib resistant, biological rep2

source_name: Prexasertib-resistant Rh41 cell line


title: raw_RV-THP_D3-3

source_name: THP-1 infected with Mtb H37Rv for 3 days

value: infected with Mtb H37Rv for 3 days


title: Tissue venom gland [HUB-JP-039]


title: C-12

value: G


title: Rh41 parental, biological rep1


title: NS540_HAT2KD_0h_H2AZ_ChIP_4

description:
CpB_ws1_ss1_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS544_HAT2KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS540_HAT2KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: raw_RV-THP_D3-2


title: raw_RV-THP_D3-1


title: NS537_HAT1KD_48h_H2AZ_Input_3

description:
CpB_ws1_ss1_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz


title: NS536_HAT1KD_0h_H2AZ_Input_4

description:
CpB_ws1_ss1_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz


title: C-10


title: Venom gland organoid plate 8

description: Single cells from venom gland organoids were sorted. Cells with headers 1-192 correspond to cells in expansion medium, cells 193-384 to cells in differentiation medium

data_processing:
The code used for data processing is deposited on GitHub:  https://github.com/BuysDB/reptillianOrganoids
In brief, data were demultiplexed, mapped using STAR, deduplicated for UMI-scaffold pairs, counted using fractional counting and scaffolds pooled by BLAST annotation
Genome_build: De novo Aspidelaps lubricus transcriptome assembly.
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts, pooled by BLAST annotation. De novo transcriptome assembly using Trinity (transcriptome-assembly_min500bp (1).fna)

source_name: Venom gland organoids

treatment_protocol: Live cells  were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.


title: NS535_HAT1KD_0h_H2AZ_Input_3

description:
CpB_ws1_ss1_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz


title: C-13


title: 27163-IP

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 65)
To obtain reads mapping only to W303;
ChIP-Seq reads were first mapped with MiniMap2 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to W303
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to W303
Unmapped W303 reads were filtered using samtools
Unmapped W303 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to W303 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (W303)), calibrated W303 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig
Genome_build: Saccharomyces cerevisiae W303 & s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: Method: S cerevisiae cells expressing either mitotic cohesin, Scc1-3HA (449) or meiotic-cohesin, Rec8-3HA (27163) from the GAL1 promoter were synchronized with a-factor and arrested in mitosis by addtion of nocodazole/benomyl for 2.5 hr. Samples were harvested, fixed in fomraldehyde and snap-frozen in liquid nitrogen. All samples were spiked with S. pombe (AM76=Rad21-3HA; 1 cell pellet S. pombe/1 cell pellet S cerevisiae), anti-HA ChIP was performed and input and IP samples were sequenced for all strains. Strains are of W303 genetic background that was used as reference genome for alignment.

extract_protocol:
Libraries were prepared as described in Makrantoni et al., 2019 (doi: 10.1007/978-1-4939-9520-2_10)
ChIP-Seq was performed using Illumina HiSeq 2000 Sequencer. Paired -end run was performed and the listed NextFlex adaptors were used.

tag: tag

tag: expressing

value: meiotic-cohesin, Rec8-3HA (27163)

value: anti-HA


title: NS534_HAT1KD_48h_H2AZ_ChIP_4

description:
CpB_ws1_ss1_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS538_HAT1KD_48h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS534_HAT1KD_48h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Venom gland organoid plate 6


title: 27163-Input


title: NS533_HAT1KD_48h_H2AZ_ChIP_3

description:
CpB_ws1_ss1_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS537_HAT1KD_48h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS533_HAT1KD_48h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: JHU083 CD8TIL6

city: Baltimore

first: Jonathan

middle: D.

last: Powell

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

data_processing:
Sequencing was performed on NextSeq 500/550 V2 Systems 75 cycles (1x75bp). NextSeq 500/550 V2 Systems suite version 2.1.2, bcl2fastq2 version 2.17.1.14. Data processing Illumina NextSeq 500/550 V2 reads were trimmed and clipped for quality control based on sliding windows considering quality and length thresholds to determine the quality at which it is sufficiently low to trim the 3′-end of reads and also determines the quality at which it is sufficiently high enough to trim the 5′-end of reads. This approach finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads. Quality Threshold < 30
The pre-processing operations included a quality check (FastQC), removal of adapter content (used during sequencing), quality thresholding (remove any bad quality reads)
Read quality was checked for each sample using FastQC 0.11.2.
High-quality reads were then imported into a fast splice junction mapper for RNA-Seq reads and this aligns RNA-Seq reads to genomes using the ultra high-throughput short read aligner. The mapping results were then analyzed to identify splice junctions between exons, for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline by the Transcriptomic Analysis Pipeline (proprietary pipeline designed in-house).
Reads were mapped to the reference genome. This aligns RNA-Seq reads to the genome using a short read aligner and discovers the splice sites.The resulting alignment files were used to generate a transcriptome assembly. TopHat (v 2.1.1) used
The major stages of analysis included read mapping to the latest reference genome (GRCM38), assembly of the mapped reads to identify expressed transcripts and genes, followed by quantification and comparison of the assembled transcriptomes between cells.
Gene and transcript expression between the comparing RNASeq samples were quantified and reported as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) units
Genome_build: GRCM38
Supplementary_files_format_and_content: Excel file with FPKM

molecule: polyA RNA

growth_protocol: 5X10^5 cells MC38 (murine colon carcinoma) s.c. into right flank of C57BL/6 mice

extract_protocol:
Sorted into TRIZOL (LS); RNeasy Mini Kit (QIAGEN)
Trizol samples were sent to Admera Health for RNA extraction (RNeasy Mini Kit (QIAGEN)) and to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.

treatment_protocol: Sorting with FACSAria Fusion

tag: tumor model

value: JHU083, pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) on day 14-18 post-implantation (0.3mg/kg/day) then harvested and sorted on day 18

tag: grouping

value: B


title: Rh41 parental, biological rep2


title: Venom gland organoid plate 5


title: NS532_HAT1KD_0h_H2AZ_ChIP_4

description:
CpB_ws1_ss1_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS536_HAT1KD_0h_H2AZ_Input_4_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS532_HAT1KD_0h_H2AZ_ChIP_4_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: IP-449

value: mitotic cohesin, Scc1-3HA (449)


title: pregnant yolk sac miRNA rep 5

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

description:
P5YSmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

data_processing:
Adapter trimming and removal of reads shorter than 17 bp, having a quality score lower than 20 or containing any ambiguities, was done using cutadapt (v1.11).
Feature counting, identification of known miRNAs and prediction of putative novel miRNA were done using the miRPro pipeline.
MicroRNA data from miRBase (release 22) and the corresponding annotated horse genome (EquCab2.0) were used as a reference. All mammalian data in miRBase was used for the prediction of novel miRNA.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: Comma separated count files. Fasta files of the predicted miRNAs.

organism: Equus caballus

source_name: yolk sac

growth_protocol: Samples were collected from cycling or pregnant mares 13 days after ovulation

extract_protocol:
Total RNA was extracted from the UF and the YS fluid samples for miRNA analysis, using the miRNeasy Serum/Plasma kit (Qiagen), according to the manufacturers' instructions. For RNA extraction from the B and the E tissue samples, the RNeasy Mini Kit (Qiagen) was combined with the RNeasy MinElute Cleanup Kit (Qiagen) in order to extract both small RNAs and larger RNAs (>200 nt) separately from the same tissue sample for mRNA- and miRNA-Sequencing respectively.
MicroRNA sequencing libraries were constructed and size-selected with the TailorMix miRNA Sample Preparation Kit V2 (SeqMatic, Fremont, CA, USA) using 100 ng total RNA and amplified by 18 PCR cycles.

treatment_protocol: cyclic mares: no treatment, pregnant mares: inseminated and confirmed to be pregnant

value: yolk sac

tag: Stage

value: pregnant


title: JHU083 CD8TIL5

value: 5X10^5 cells MC38 (murine colon carcinoma) s.c. into right flank of C57BL/6 mice


title: Tissue venom gland [HUB-JP-038]

tag: tissue


title: C-11

value: Bone marrow

value: Pre-leukaemia


title: Input-449


title: pregnant uterine fluid miRNA rep 5

description:
P5UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

source_name: uterine fluid

value: uterine fluid


title: JHU083 CD8TIL4

tag: strain


title: NS531_HAT1KD_0h_H2AZ_ChIP_3

description:
CpB_ws1_ss1_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS535_HAT1KD_0h_H2AZ_Input_3_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS531_HAT1KD_0h_H2AZ_ChIP_3_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: polyclonal affinity-purified H2A.Z rabbit antibody (available from T. N. Siegel)


title: C-1

value: KLG


title: Venom gland organoid plate 7

value: Wildtype

value: Venom gland


title: JHU083 CD8TIL2


title: Tissue venom gland

description:
Bulk rna sequencing from venom gland tissue.
bulk_final.csv


title: pregnant embryo miRNA rep 5

description:
P5EmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

source_name: embryo

value: embryo


title: Tissue pancreas

description:
Bulk rna sequencing from pancreas tissue.
bulk_final.csv

source_name: Tissue pancreas

value: Pancreas


title: NS496_2T1_HAT1_KD_48h_Input_2

description:
CpB_ws1_ss1_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Tissue liver

description:
Bulk rna sequencing from liver tissue.
bulk_final.csv

source_name: Tissue liver

value: Liver


title: pregnant uterus miRNA rep 5

description:
P5BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

source_name: uterus

value: uterus


title: Vehicle CD8TIL6

value: vehicle (PBS) treatment days 14-18 post implanytation then harvested and sorted on day 18

value: A


title: JHU083 CD8TIL1

value: JHU083, pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) on day 14-18 post-implantation (0.3mg/kg/day) then harvested and sorted on day 18

value: B


title: pregnant yolk sac miRNA rep 4

description:
P4YSmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: yolk sac

value: pregnant


title: Venom gland expansion bulk

description:
Bulk rna sequencing from expansion medium venom gland organoids.
bulk_final.csv


title: NS494_2T1_HAT1_KD_0h_Input_2

description:
CpB_ws1_ss1_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Vehicle CD8TIL4

value: 5X10^5 cells MC38 (murine colon carcinoma) s.c. into right flank of C57BL/6 mice


title: NS493_2T1_HAT1_KD_48h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS496_2T1_HAT1_KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS493_2T1_HAT1_KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS495_2T1_HAT1_KD_24h_Input_2

description:
CpB_ws1_ss1_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Vehicle CD8TIL3


title: NS492_2T1_HAT1_KD_24h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS495_2T1_HAT1_KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS492_2T1_HAT1_KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: pregnant uterine fluid miRNA rep 4

description:
P4UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: Venom gland early bulk

description:
Bulk rna sequencing from early passage venom gland organoids.
bulk_final.csv


title: pregnant embryo miRNA rep 4

description:
P4EmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: Venom gland differentiation bulk

description:
Bulk rna sequencing from differentiated venom gland organoids.
bulk_final.csv


title: Vehicle CD8TIL2


title: Vehicle CD8TIL1


title: NS487_2T1_HAT1_KD_0h_Input_1

description:
CpB_ws1_ss1_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: pregnant uterus miRNA rep 4

description:
P4BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: NS491_2T1_HAT1_KD_0h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS494_2T1_HAT1_KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS491_2T1_HAT1_KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Purified Germ Cell - KO 43 °C rep 5

city: Bronx

first: Ayodele

last: Akintayo

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data from purified Germ Cell of 43°C treated Mgat4d KO C57Bl6/J mice

hyb_protocol: 5.2 ug of fragmented and labelled sscDNA were hybridized for 16 hr at 45°C on GeneChip Clariom D, mouse array (49-format array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Thermo Fisher GeneChip™Scanner 3000 7G.

data_processing: The raw data in the .CEL files were normalized to gene and exon level with Affymetrix proprietary Microarray analysis software TAC 4.

source_name: C57BL6/J - KO-43 deg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual Target Preparation for GeneChip™Whole Transcript (WT) Expression Arrays, publication Number MAN0018137, Affymetrix).

extract_protocol: Isolated germ cells were subjected to total RNA extraction using Trizol reagent (Invitrogen) following the manufacturer’s protocol. Germ cell RNA (150 ng, RIN 7-9) was provided to the Genomics Core Facility of the Albert Einstein College of Medicine for conversion to cDNA, labeling and hybridization to a mouse Affymetrix Clariom™ D array previously known as GeneChip™ Mouse Transcriptome Array 1.0 (Affymetrix, Santa Clara, CA).

treatment_protocol: Briefly, male mouse of two months were anaesthetized using isoflurane and the testes were secured in the scrotum by manual massage. The lower one third of the body (hind legs, tail and scrotum) was immersed in a 43ºC or 33°C (no treatment control) water bath for 25 min. The testes and epididymis were harvested 8 hr after treatment. Germ cells were isolated by sequential enzymatic digestion.

value: KO

value: Testis Germ Cell

tag: age

value: 2 months

tag: stress

value: heat stress


title: AI.Treated.105B [reanalysis]

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from baseline (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

value: female

tag: timepoint

value: baseline (B)

value: Negative

value: LumB

tag: accession

tag: reanalysis

value: AI.Treated.105B [reanalysis]


title: pregnant uterine fluid miRNA rep 3

description:
P3UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: uterine fluid


title: NS486_2T1_HAT1_KD_48h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

tag: genotype/variation

tag: time

value: polyclonal affinity-purified H2A.Z rabbit antibody (available from T. N. Siegel)


title: Purified Germ Cell - KO 43 °C rep 4

tag: cell type

tag: genotype


title: pregnant yolk sac miRNA rep 3

description:
P3YSmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: Purified Germ Cell - KO 43 °C rep 3


title: NS485_2T1_HAT1_KD_24h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

tag: chip antibody


title: Liver, GO_rep2

city: Ji'an

first: Guanghua

last: Xiong

address: No. 28 Xueyuan Road, Qingyuan District

country: China

institute: Jinggangshan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to zebrafish GRCz11 whole genome using bowtie2 v2.3.2 with parameters --end-to-end --sensitive -N 1 -p 20
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: Liver

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

value: AB

value: Liver

value: three month old

value: wild type

tag: treatment

value: Graphene oxide nanoparticles (GO)


title: Liver, GO_rep1


title: Purified Germ Cell - KO 43 °C rep 1


title: NS484_2T1_HAT1_KD_0h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS484_2T1_HAT1_KD_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Liver, GO_rep3


title: pregnant embryo miRNA rep 3

description:
P3EmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: embryo

value: pregnant


title: Purified Germ Cell - WT 43 °C rep 3

description: Gene expression data from purified Germ Cell of 43°C treated WT C57Bl6/J mice

source_name: C57BL6/J - WT-43 deg

value: WT

value: Testis Germ Cell


title: NS476_2T1_HAT1_KD_24h_Input_1

description:
CpB_ws1_ss1_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS485_2T1_HAT1_KD_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Liver, CK_rep3

value: control


title: Purified Germ Cell - WT 43 °C rep 2

value: 2 months

value: heat stress


title: NS477_2T1_HAT1_KD_48h_Input_1

description:
CpB_ws1_ss1_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS486_2T1_HAT1_KD_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Liver, CK_rep2


title: pregnant embryo miRNA rep 2

description:
P2EmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: Liver, CK_rep1


title: pregnant uterine fluid miRNA rep 2

description:
P2UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: NS295_HAT2_KD_2T1_Input_72h_2

description:
CpB_ws1_ss1_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Purified Germ Cell - WT 43 °C rep 1


title: NS294_HAT2_KD_2T1_Input_72h_1

description:
CpB_ws1_ss1_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: 438_11258_AP2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to mm10 and Plasmodium berghei whole genomes using hisat2
normalization and comparisons were run using deseq2. Matrix-mouse and matrix_Plasmodium are condensed files of the original with deseq2 normalized reads for each sample listed
Genome_build: mm10 with Plasmodium berghei (ANKA)

organism:
Plasmodium berghei
Mus musculus

source_name: mouse blood

extract_protocol:
on the 9th day the mice were bled from the cheek and 250 ul blood was collected. The blood was immediately transferred to the eppendorf tubes containing 750ul Trizol LS.
RZ Globin/TruSeq mRNA Seq (Poly-dT)

treatment_protocol: 9 weeks old female C57BL/6 mice were injected intraperitoneally with 200ul PBS containing 10^6 infected red blood cells

value: female

tag: mouse strain

tag: plasmodium berghei strain

value: ANKA

tag: agent

value: AP2 Plasmodium berghei


title: NS293_HAT2_KD_2T1_Input_48h_2

description:
CpB_ws1_ss1_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

source_name: T. brucei 2T1 bloodstream form


title: pregnant uterus miRNA rep 2

description:
P2BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

tag: tissue

value: uterus

tag: Stage


title: Purified Germ Cell - KO 43 °C rep 2

value: KO

tag: age


title: Purified Germ Cell - KO 33 °C rep 2

description: Gene expression data from purified Germ Cell of 33°C treated Mgat4d KO C57Bl6/J mice

source_name: C57BL6/J - KO-33 deg

tag: stress


title: 437_11257_AP2

tag: Sex


title: Purified Germ Cell - KO 33 °C rep 3


title: pregnant uterus miRNA rep 3

description:
P3BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: pregnant yolk sac miRNA rep 1

description:
P1YSmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: yolk sac


title: 422_11256_WT

value: wild type Plasmodium berghei


title: NS292_HAT2_KD_2T1_Input_24h_2

description:
CpB_ws1_ss1_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: pregnant uterine fluid miRNA rep 1

description:
P1UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: uterine fluid


title: Purified Germ Cell - KO 33 °C rep 1


title: Purified Germ Cell - WT 33 °C rep 4

description: Gene expression data from purified Germ Cell of 33°C treated WT C57Bl6/J mice

source_name: C57BL6/J - WT-33 deg


title: 421_11255_WT


title: 417_11252_WT


title: NS291_HAT2_KD_2T1_Input_0h_2

description:
CpB_ws1_ss1_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: pregnant yolk sac miRNA rep 2

description:
P2YSmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: Purified Germ Cell - WT 33 °C rep 3


title: pregnant uterus miRNA rep 1

description:
P1BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: NS287_HAT2_KD_2T1_ChIP_72h_2

description:
CpB_ws1_ss1_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS295_HAT2_KD_2T1_Input_72h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS287_HAT2_KD_2T1_ChIP_72h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: polyclonal affinity-purified H2A.Z rabbit antibody (available from T. N. Siegel)


title: Purified Germ Cell - WT 33 °C rep 1


title: Purified Germ Cell - WT 33 °C rep 2


title: cyclic uterine fluid miRNA rep 4

description:
C4UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: cyclic


title: 419_11254_WT


title: 431_11251_AP2


title: 430_11250_AP2


title: NS286_HAT2_KD_2T1_ChIP_72h_1

description:
CpB_ws1_ss1_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS294_HAT2_KD_2T1_Input_72h_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS286_HAT2_KD_2T1_ChIP_72h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS285_HAT2_KD_2T1_ChIP_48h_2

description:
CpB_ws1_ss1_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS293_HAT2_KD_2T1_Input_48h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS285_HAT2_KD_2T1_ChIP_48h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS283_HAT2_KD_2T1_ChIP_0h_2

description:
CpB_ws1_ss1_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS291_HAT2_KD_2T1_Input_0h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS283_HAT2_KD_2T1_ChIP_0h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: cyclic uterus miRNA rep 3

description:
C3BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: cyclic uterus miRNA rep 4

description:
C4BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: NS284_HAT2_KD_2T1_ChIP_24h_2

description:
CpB_ws1_ss1_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS292_HAT2_KD_2T1_Input_24h_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS284_HAT2_KD_2T1_ChIP_24h_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS278_2T1_HAT2_KD_ChIP_48h_1

description:
CpB_ws1_ss1_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS477_2T1_HAT1_KD_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS278_2T1_HAT2_KD_ChIP_48h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: pregnant embryo miRNA rep 1

description:
P1EmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv

value: embryo


title: 433_11253_AP2


title: 427_11249_AP2


title: cyclic uterine fluid miRNA rep 2

description:
C2UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: cyclic uterine fluid miRNA rep 3

description:
C3UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: 412_11248_WT


title: cyclic uterine fluid miRNA rep 1

description:
C1UFmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: RNA-Seq_HCT116_siLUCRCrep

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using STAR version 2.7.0e.
Genome_build: hg19

source_name: colorectal cancer

growth_protocol: HCT116 cells were cultured in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using Trizol (Takara) following the manufacturer’s protocol followed by DNase I digestion to remove residual DNA.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina NovaSeq 6000 platform.

tag: cell line

tag: sirna

value: siLUCRC


title: 411_11247_WT


title: Venom gland organoids

description:
Bulk rRNA sequencing from differentiated venom gland organoids.
NajaNivea_bulk.csv

organism: Naja nivea

source_name: Venom gland organoids

value: Wildtype

value: Venom gland


title: NS263_WT_ChIP_H2AZ

description:
CpB_ws1_ss1_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

source_name: T. brucei WT bloodstream form Lister 427

value: WT


title: cyclic uterus miRNA rep 1

description:
C1BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv


title: RNA-Seq_HCT116_siCTLrep

value: siCTL


title: NS276_2T1_HAT2_KD_ChIP_0h_1

description:
CpB_ws1_ss1_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS487_2T1_HAT1_KD_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS276_2T1_HAT2_KD_ChIP_0h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS277_2T1_HAT2_KD_ChIP_24h_1

description:
CpB_ws1_ss1_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS476_2T1_HAT1_KD_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS277_2T1_HAT2_KD_ChIP_24h_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: J1_uH2A

status: Public on Feb 23 2020

first: Donncha

middle: S

last: Dunican

address: Western General Hospital

institute: IGMM / MRC HGU

description:
Chromatin
non-commercial antibody

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequences assessed for quality using fastQC (v0.11.4)
Sequences trimmed using trimGalore (v0.4.1).
ChIPSeq mapped with bowtie2 (v2.2.6) to mm10.
WGBS mapped with bismark (v0.16.3) (bowtie2) to mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw) file output from bowtie2 (ChIPSeq) or bismark (WGBS). Methylation calls were made with bismark (v0.16.3) , sub-selected for depth n=5 coverage with custom R (v3.6.0) scripts and converted to bigwig format using BEDTools (v2.25.0). ChIPSeq bigwigs were generated using deepTools (v3.2.0).

source_name: Mouse ES cells

growth_protocol:
mESC were cultured on gelatin-coated cell culture flasks using standard mESC culture conditions.
Undifferentiated ES cells were grown in DMEM containing LIF (500U/mL) in pre-gelatinised culture flasks without feeder cells as widely described. Neural progenitors were cultured in neurodifferentiation media (1:1 mix of Neurobasal (Gibco) and DMEM/F-12 media (Gibco) with 0.5% Neuro-2 Supplement (Millipore), 0.5% B27 Supplement (Gibco), 0.2mM L-glutamine and 0.1mM β-mercaptoethanol) and plated onto 0.1% gelatin-coated flasks at a density of 3x105 cells per 75cm2 flask area. Media was changed on day 2 of differentiation and then daily thereafter. Neural progenitor cells (10 days) cultures were enriched using two passes of Magnetic Activated Cell Sorting (MACS) with anti-PSA-NCAM antibody Microbead kit (Miltenyi Biotec).

extract_protocol:
For each sample 9x10^6 cells were harvested by trypsinisation and rinsed well in 1xPBS before being resuspended in 1.5ml of PBS. Each sample was fixed with the addition of 40.5 µl of 37% formaldehyde (Sigma) and incubated for 10minutes at room temperature on rotation. 225 µl of 1M glycine was added to quench the formaldehyde and rotated at room temperature for 5minutes. Samples were then centrifuged at 2000rpm for 4 minutes at 4 oC, supernatant discarded and pellets resuspended in 2ml LB1 (50mM Hepes KOH pH7.9, 140mM NaCl,1mM EDTA, 10% glycerol, 0.5% IPEGAL, 0.25% triton X100, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and rotated at 4 oC for 4 minutes. This process was repeated resuspending in 2 ml LB2 (10mM TrisHcl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and then repeated resuspending in 200 µl LB3 (10mM TrisHCl Ph8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na Deoxycholate, 0.5% LaurylSulphate, 1xComplete EDTA-free protease inhibitor tablet (Roche)). Chromatin was then sheared at 4 oC using a Diagenode bioruptor set on high for 45 cycles at 30seconds on/30seconds off. 20 µl of 10% triton X in LB3 was then added to each sample and mixed by inversion. Samples were then centrifuged at 13000rpm at 4 oC for 10 minutes to remove nuclear debris and supernatant transferred to a fresh tube. In order to check the efficiency of the sonication process, 8 µl of sheared chromatin was taken, mixed with 1 µl 5M NaCl and 16 µl dH2O, incubated at 98 oC for 15minutes and treated with RNase cocktail before being purified with Qiagen PCR Clean up kit as per manufacturer’s instructions . Sheared chromatin was then resolved on 1.5% agarose gel post-stained with EtBr. The DNA smear should be between 100-500bp with peak at 250-300bp.
For immunoprecipitation 25 µl of Protein G Dynabeads (Novex Lifetech) was washed 3 times in block solution and then resuspended in 500 µl of block solution. Beads were then incubated with 5 µl of antibody (H3K27me3(Millipore 07449), IgG (Santa Cruz Biotech sc-2027)) and incubated at 4 oC for 4 hours on a rotator. Beads were then washed 3 times in 500 µl block solution and supernatant removed
For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit.  For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions.
50bp PE sequencing

treatment_protocol: For doxycyline treatment, Dnmt1tet-tet ES cells were incubated with 2ug/mL doxycylcine for 7 days. For reversion/recovery, doxycycline was removed for 7 days.

tag: cell line name

tag: background strain

value: Mouse ES cells