title: H3K27ac_HPC7

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

data_processing:
Reads quality filtered according to the Illumina pipeline
Experimental and input control sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best --trim5 2 mm9.
Chromatin binding sites of MYSM1 were identified using peak detection algorithm MACS (version 1.4.1, default parameters), with comparisons for read enrichment against control input DNA from the same cells.
The resulting binding sites were filtered to remove regions with < 5 fold enrichment compared to the input DNA and < 5 normalized tag counts within 200bp to the peak summit.
Genome_build: mm9
Supplementary_files_format_and_content: filtered bedfile of MYSM1 peak summits
Supplementary_files_format_and_content: bigWig

source_name: HPC7 cell line stably expressing triple-FLAG-tagged murine MYSM1

growth_protocol: The Ba/F3 cell line stably expressing triple-Flag-tagged MYSM1 was maintained at 0.5-2 x 10^6 cells/mL in RPMI-1640 (Wisent) with 10% Fetal Calf Serum (FCS, Wisent), 2mM L-Glutamine, 100μg/mL streptomycin, 100U/mL penicillin (Wisent), 5% WEHI conditioned media as the source of IL-3, and under 2μg/mL puromycin selection (Wisent). The HPC7 cell line stably expressing triple-Flag-tagged MYSM1 was cultured at 0.5-2 x 10^6 cells/mL in IMDM (Life Technologies), with 10% FCS (Gibco, Life Technologies), 100μg/mL streptomycin, 100U/mL penicillin (Wisent), 7.48x10^-5M MTG (M6145, Sigma-Aldrich), 100 ng/mL murine SCF (Shenandoah Biotechnology, Cedarlane), and under 2μg/mL puromycin selection (Wisent).

extract_protocol:
Cells were crosslinked for 10 min at room temperature with 1% formaldehyde added in culture medium. Crosslink was stopped with ice-cold PBS containing 0.125M glycine for 5min. Nuclei were prepared by sequential incubation on ice for 5min in buffer A [10mM Tris-HCl (pH 8), 10mM EDTA, 0.25% Triton X-100], and for 30min in buffer B [10mM Tris-HCl (pH 8), 1mM EDTA, 200mM NaCl] (all buffers include proteases inhibitors). Nuclei were resuspended in sonication buffer [10mM Tris-HCl (pH 8), 1mM EDTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140mM NaCl] and sonicated with a Branson Digital Sonifier (Branson Ultrasonics) to an average size of 250bp (12 cycles of 30 seconds  at 80%, with 30 seconds rest in cooled circulating water). Sonicated chromatin from the equivalent of 5x10^6 cells per ChIP was incubated overnight on a rotating platform at 4°C with 40μL of Dynabeads Protein G (Invitrogen, Life Technologies) conjugated to 3-5μg of antibodies: anti-Flag M2 (Sigma, F1804, for MYSM1-FLAG ChIP), anti-H3K27Ac (Abcam, ab4729) or anti-H2AK119Ub (Cell Signaling Technology, D27C4, Table S10). Immune complexes with anti-Flag M2 antibody was washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash 1 [0.5% NP-40, 150mM KCl, 1mM EDTA, 10mM Tris-HCl pH8]; Wash 2 [0.5% Triton, 0.1% NaDOC, 100mM NaCl, 10mM Tris-HCl pH8]; Wash 3A [0.5% Triton, 0.1% NaDOC, 400mM NaCl, 10mM Tris-HCl pH8]; Wash 3B [0.5% Triton, 0.1% NaDOC, 500mM NaCl, 10mM Tris-HCl pH8]; and Wash 4 [0.5% NaDOC, 0.5% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH8]. Immune complexes with anti-H3K27Ac and anti-H2AK119Ub antibodies were washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash B [1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash C [1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash D [1% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH 8]; and TEN buffer [50mM NaCl, 10mM Tris-HCl pH 8, 1mM EDTA]. After de-crosslinking by overnight incubation at 65°C, the ChIP and Input DNA was purified with Qiaquick PCR Cleanup kit following manufacturer’s instructions (Qiagen).
ChIP-seq libraries were prepared using the Illumina TruSeq kit and sequenced on an Illumina HiSeq 2500 sequencer using a 50bp paired-end configuration. Sonicated input DNA from the same cells were sequenced as negative control.

value: HPC7 cell line

tag: chip antibody

value: anti-H3K27Ac (Abcam, ab4729, Rabbit polyclonal)


title: MYSM1_FLAG_HPC7

status: Public on Jul 28 2020

type: SRA

first: David

country: Canada

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

value: anti-Flag M2 (Sigma, F1804, Mouse monoclonal)


title: Input_HPC7


title: MYSM1_FLAG_BaF3

source_name: Ba/F3 cell line stably expressing triple-FLAG-tagged murine MYSM1

value: Ba/F3 cell line


title: H3K27ac_BaF3


title: Input_BaF3


title: H2AK119ub_BaF3

value: anti-H2AK119Ub (Cell Signaling Technology, D27C4, Rabbit monoclonal)


title: H2AK119ub_HPC7


title: AD_80_Biomek_Input

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
fastq files were demultiplexed on RELACS barcodes and aligned to dm6 (S2 cells) or hg38 (HepG2) using snakePipes v. 1.2.3. QC metrics and further downstream files (bigwig) were also generated using snakePipes (Bhardwaj et al. 2019)
default parameters used for the analysis are available at https://github.com/FrancescoFerrari88/AutoRELACS/tree/master/snakePipes_defaults
Genome_build: dm6 (S2 cells) and hg38 (HepG2)
Supplementary_files_format_and_content: bigWig, normalized coverage

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27 °C. HepG2 liver hepatocellular carcinoma (ATCC, HB-8065TM) were cultured in Eagle’s minimal essential medium (EMEM, Lonza, 06-174) supplemented with 10% fetal bovine serum (Sigma), 2 mM L-glutamine (Lonza), 1.8 mM CaCl2, 1 mM sodium pyruvate (Lonza) and penicillin–streptomycin mixture (100 units/mL, Lonza), at 37 °C at 5% CO2 in 10 cm plates, up to 70%-80% confluency.

extract_protocol:
HepG2 and S2 cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in D-MEM (for HepG2 cells) or Express Five SFM (for S2 cells) for 15 min at room temperature under gentle shaking. Formaldehyde was quenched for 5 min by adding 125 mM glycine final concentration. Cells were rinsed twice with ice-cold PBS, harvested by scraping (HepG2) and pelleted (300 g, 10 min, 4 °C). Cells were processed according to RELACS / AutoRELACS protocols
Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After Illumina adapter ligation, library was PCR amplified. Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on NovaSeq 6000 machine, following manufacturer's protocol.
High-throughput RELACS ChIP-seq and automated high-throughput AutoRELACS ChIP-seq

treatment_protocol: No treatment was applied

tag: cell line

tag: chip ab


title: AD_80_manual_Input


title: AD_80_manual_H3K27me3


title: AD_80_manual_H3K27ac


title: F. trinervia_ctrl (HighLight) 1

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

library_source: transcriptomic

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Supplementary_files_format_and_content: xlsx file contains the transcript abundance of annotated genes
Supplementary_files_format_and_content: fasta file contains the de novo assembled transcripts

molecule: total RNA

organism: Flaveria trinervia

source_name: newly expanded mature leaf

growth_protocol: For low high light experiment, Plants were grown in growth chamber with light intensity to be 200 μmol m-2 s-1 and temperature to be 22oC, 16h/8h light/ dark duration, 70% humidity. . Plant were watered twice a week and fertilized weekly.

extract_protocol:
Total RNA was isolated following the protocol of the PureLInkTM RNA Mini (ThermoFisher Scientific)
Next-generation RNA-seq was performed in the Illumina platform in the pair-ended mode with read length150 bp.

treatment_protocol: The light intensity of hight light condition is 1400 μmol m-2 s-1, and that of control is 500 μmol m-2 s-1.

tag: tissue

value: leaf


title: AD_80_Biomek_H3K27ac


title: AD_80_Biomek_H3K27me3


title: AD_79_manual_Input


title: AD_80_manual_H3K4me3


title: AD_80_Biomek_H3K4me3


title: AD_79_manual_H3K4me3


title: AD_79_manual_H3K27me3


title: AD_79_manual_H3K27ac


title: AD_79_Biomek_H3K4me3


title: AD_79_Biomek_H3K27me3


title: AD_79_Biomek_H3K27ac


title: RNA-seq E85A rep2

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

country: USA

institute: UPENN

data_processing:
Raw reads were mapped to reference genome (hg38) using Hisat2
Afterward, genomic alignments were counted in R using GenomicAlignments package
Gene expression levels were normalized using DEseq2

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK 293T

growth_protocol: HEK 293T cells were cultured in Dulbecco’s Modified Eagle Medium (GIBCO, 11995065) supplemented with 10% FBS (GIBCO, 26140-079) and 1% Pen/Strep (Corning, 30-002-CI) in 37 °C, 5% CO2¬ incubator.

extract_protocol:
Total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen). mRNA was fragmented by sonication.
The library was constructed using TruSeq stranded mRNA samples preparation kit from Illumina.

tag: genotype

value: E85A variant overexpression


title: AD_79_Biomek_Input


title: AD_78_manual_Input


title: AD_78_manual_H3K4me3


title: AD_78_manual_H3K27me3


title: AD_77_Biomek_H3K4me3


title: AD_77_manual_H3K27ac


title: AD_78_manual_H3K27ac


title: AD_77_Biomek_H3K27me3


title: AD_78_Biomek_Input


title: AD_77_Biomek_H3K27ac


title: AD_78_Biomek_H3K4me3


title: AD_74_manual_H3K27me3


title: AD_78_Biomek_H3K27me3


title: AD_74_Biomek_Input


title: AD_74_manual_H3K4me3


title: AD_77_manual_Input


title: AD_78_Biomek_H3K27ac


title: AD_74_Biomek_H3K27ac


title: AD_77_manual_H3K4me3


title: AD_77_Biomek_Input


title: AD_73_manual_H3K4me3


title: AD_73_manual_Input


title: AD_77_manual_H3K27me3


title: AD_74_Biomek_H3K4me3


title: AD_73_manual_H3K27ac


title: AD_73_manual_H3K27me3


title: AD_74_manual_H3K27ac


title: AD_74_manual_Input


title: AD_73_Biomek_Input


title: AD_73_Biomek_H3K4me3


title: AD_73_Biomek_H3K27me3


title: AD_74_Biomek_H3K27me3


title: AD_72_manual_Input


title: AD_73_Biomek_H3K27ac


title: AD_72_manual_H3K4me3


title: AD_72_manual_H3K27me3


title: AD_72_Biomek_H3K4me3


title: AD_72_manual_H3K27ac


title: AD_71_manual_H3K27me3


title: AD_71_manual_Input


title: AD_71_Biomek_Input


title: AD_72_Biomek_H3K27me3


title: AD_71_Biomek_H3K4me3


title: AD_72_Biomek_H3K27ac


title: AD_71_manual_H3K4me3


title: AD_71_manual_H3K27ac


title: AD_72_Biomek_Input


title: AD_71_Biomek_H3K27me3


title: AD_70_manual_H3K27ac


title: AD_70_manual_H3K4me3


title: AD_71_Biomek_H3K27ac


title: AD_70_manual_Input


title: AD_70_Biomek_Input


title: AD_70_Biomek_H3K4me3


title: AD_70_manual_H3K27me3


title: AD_70_Biomek_H3K27ac


title: AD_69_manual_H3K27me3


title: AD_69_Biomek_H3K27me3


title: AD_69_manual_H3K27ac


title: AD_69_manual_H3K4me3


title: AD_69_Biomek_Input


title: AD_69_Biomek_H3K4me3


title: AD_69_manual_Input


title: AD_70_Biomek_H3K27me3


title: AD_69_Biomek_H3K27ac


title: AD_68_manual_H3K27me3


title: AD_68_Biomek_Input


title: AD_68_manual_H3K4me3


title: AD_67_manual_H3K27me3


title: AD_68_Biomek_H3K27me3


title: AD_68_Biomek_H3K4me3


title: AD_67_manual_H3K4me3


title: AD_67_manual_H3K27ac


title: AD_68_Biomek_H3K27ac


title: AD_67_Biomek_Input


title: AD_67_Biomek_H3K4me3


title: AD_66_manual_H3K4me3


title: AD_66_manual_Input


title: AD_66_manual_H3K27me3


title: AD_66_manual_H3K27ac


title: AD_68_manual_H3K27ac


title: AD_66_Biomek_H3K4me3


title: AD_66_Biomek_H3K27me3


title: AD_65_manual_Input


title: AD_67_manual_Input


title: AD_65_Biomek_Input


title: AD_65_manual_H3K4me3


title: AD_67_Biomek_H3K27ac


title: AD_66_Biomek_H3K27ac


title: AD_65_manual_H3K27me3


title: AD_65_Biomek_H3K27me3


title: AD_64_manual_H3K27ac


title: AD_65_manual_H3K27ac


title: AD_64_manual_Input


title: AD_64_Biomek_H3K27ac


title: AD_65_Biomek_H3K4me3


title: AD_63_manual_H3K27me3


title: AD_67_Biomek_H3K27me3


title: AD_64_manual_H3K4me3


title: AD_64_Biomek_H3K27me3


title: AD_65_Biomek_H3K27ac


title: AD_63_manual_Input


title: AD_63_manual_H3K4me3


title: AD_63_Biomek_H3K4me3


title: AD_68_manual_Input


title: AD_62_manual_H3K27ac


title: AD_62_manual_Input


title: AD_64_Biomek_Input


title: AD_61_manual_H3K27ac


title: AD_62_Biomek_H3K27me3


title: AD_63_Biomek_Input


title: AD_62_manual_H3K4me3


title: AD_62_Biomek_H3K27ac


title: AD_61_manual_H3K27me3


title: AD_61_manual_Input


title: AD_61_manual_H3K4me3


title: AD_62_Biomek_H3K4me3


title: AD_61_Biomek_H3K27me3


title: AD_61_Biomek_H3K4me3


title: AD_61_Biomek_H3K27ac


title: AD_60_manual_H3K27me3


title: AD_63_Biomek_H3K27ac


title: AD_60_Biomek_Input


title: AD_62_Biomek_Input


title: AD_61_Biomek_Input


title: AD_60_Biomek_H3K4me3


title: AD_60_manual_H3K27ac


title: AD_60_Biomek_H3K27me3


title: AD_60_Biomek_H3K27ac


title: AD_59_manual_Input


title: AD_60_manual_Input


title: AD_60_manual_H3K4me3


title: AD_59_manual_H3K27ac


title: AD_59_Biomek_H3K4me3


title: AD_59_Biomek_H3K27ac


title: AD_59_Biomek_Input


title: AD_58_manual_Input


title: AD_58_manual_H3K27ac


title: AD_58_Biomek_Input


title: AD_58_manual_H3K27me3


title: AD_58_manual_H3K4me3


title: AD_58_Biomek_H3K27me3


title: AD_58_Biomek_H3K4me3


title: AD_58_Biomek_H3K27ac


title: AD_57_manual_Input


title: AD_57_manual_H3K27ac


title: AD_57_manual_H3K27me3


title: AD_57_Biomek_Input


title: AD_57_Biomek_H3K27me3


title: AD_59_Biomek_H3K27me3


title: AD_59_manual_H3K4me3


title: AD_59_manual_H3K27me3


title: AD_56_manual_H3K27ac


title: AD_57_Biomek_H3K27ac


title: AD_57_Biomek_H3K4me3


title: AD_56_manual_Input


title: AD_56_Biomek_H3K4me3


title: AD_56_Biomek_Input


title: AD_56_Biomek_H3K27me3


title: AD_56_Biomek_H3K27ac


title: AD_57_manual_H3K4me3


title: AD_55_manual_H3K27me3


title: AD_55_manual_H3K4me3


title: AD_55_Biomek_H3K4me3


title: AD_55_manual_H3K27ac


title: AD_56_manual_H3K27me3


title: AD_55_Biomek_H3K27ac


title: AD_56_manual_H3K4me3


title: AD_55_Biomek_Input


title: AD_54_manual_H3K27me3


title: AD_54_manual_Input


title: AD_54_Biomek_Input


title: AD_66_Biomek_Input


title: AD_54_Biomek_H3K27ac


title: AD_53_manual_H3K4me3


title: AD_53_manual_H3K27me3


title: AD_53_Biomek_Input


title: AD_55_Biomek_H3K27me3


title: AD_53_Biomek_H3K27ac


title: AD_54_Biomek_H3K27me3


title: AD_53_Biomek_H3K4me3


title: AD_54_manual_H3K27ac


title: AD_52_manual_H3K4me3


title: AD_53_Biomek_H3K27me3


title: AD_53_manual_Input


title: AD_52_manual_H3K27me3


title: AD_52_Biomek_H3K4me3


title: AD_52_manual_Input


title: AD_54_manual_H3K4me3


title: AD_52_Biomek_Input


title: AD_52_Biomek_H3K27ac


title: AD_51_manual_Input


title: AD_51_manual_H3K27me3


title: AD_54_Biomek_H3K4me3


title: AD_52_Biomek_H3K27me3


title: AD_51_manual_H3K27ac


title: AD_53_manual_H3K27ac


title: AD_55_manual_Input


title: AD_51_manual_H3K4me3


title: Input_60_BCs_Rep2

description: non demultiplexed input chromatin


title: AD_51_Biomek_Input


title: AD_51_Biomek_H3K27ac


title: Input_60_BCs_Rep1

description: non demultiplexed input chromatin


title: AD_52_manual_H3K27ac


title: AD_51_Biomek_H3K27me3


title: 6181

city: Rehovot

first: Jedrzej Jakub Szymanski

middle: Jakub

last: Szymanski

address: 234 Herzl Street, POB 26

country: Israel

institute: Weizmann Institute of Science

description:
2041
Solanum lycopersicum-pennellii
Manually peeled skin tissue

data_processing:
The reads were mapped against a combined file that included the genomes from Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0).
Mapping has been performed with STAR 2.4.2a.
The alignments in resulting SAM file were divided into genomes based on the alignment scores. If the highest scoring alignment is assigned to a certain genome, and is unique in that genome, then it is assigned as “lycopersicum-unique” or “pennellii-unique”. If there is no difference in the scores between the two genomes then the alignment to the S. lycopersicum genome is kept and categorized as “indistinguishable”.
Counting was performed on the TES (Transcript End Site) region of each gene. The TES region is defined as 200 bp downstream from the STOP codon of the gene, and at least 500 bases upstream to the STOP codon of the gene. The reads were counted using htseq-count using stranded method and union mode.
Genome_build: Solanum lycopersicum (ITAG 3.0) and Solanum pennellii (v2.0)
Supplementary_files_format_and_content: Using the htseq-count for each type of genome provide three complementary datasets:
Supplementary_files_format_and_content: (1) lyc-count - containing the count for the reads specific to S. lycopersicum genome (68% of all reads);
Supplementary_files_format_and_content: (2) pen-count - containing the count for the reads specific to S. pennellii genome (28% of all reads);
Supplementary_files_format_and_content: (3) ind-count - containing the count for the reads aligning to both genomes (4% of all reads).

organism: Solanum lycopersicum x Solanum pennellii

source_name: Skin fruit tissue

growth_protocol: Fruit at the breaker and red ripe stages were harvested from the field at the Western Galilee Experimental Station in Akko, Israel. Plants were grown in a randomized design with 4 plants per m2.

extract_protocol:
Standard tri-reagent protocol (Maniatis T., Fritsch E.F., Sambrook J. Cold Springs Harbor; NY: 1982. Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory).
Jaitin, Diego, Ido Amit, and Hadas Keren-Shaul. 2014. High throughput transcriptome analysis. WIPO 2014108850:A2. World Patent, filed January 9, 2014, and issued July 17, 2014. https://www.google.com.na/patents/WO2014108850A2?cl=en

treatment_protocol: Fruits were brought to the lab and skin tissue at the breaker and red, ripe stages was immediately separated from the flesh and frozen in liquid nitrogen.

value: Skin fruit tissue

tag: ripening stage

value: breaker stage of ripening

tag: population

value: BIL


title: 6261

description:
2121
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6319

description:
2179
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6602

description:
2462
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL11-2

description:
2629
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: AD_51_Biomek_H3K4me3


title: 6432

description:
2292
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6399

description:
2259
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6427

description:
2287
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6240

description:
2100
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6242

description:
2102
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6249

description:
2109
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6274

description:
2134
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6306

description:
2166
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6305

description:
2165
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6320

description:
2180
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL8-1

description:
2607
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6628

description:
2488
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6494

description:
2354
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6598

description:
2458
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6704

description:
2564
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6237

description:
2097
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6506

description:
2366
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AD_63_manual_H3K27ac


title: IL10-1

description:
2623
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6679

description:
2539
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AD_62_manual_H3K27me3


title: 6534

description:
2394
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL10-2

description:
2625
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6449

description:
2309
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6532

description:
2392
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6478

description:
2338
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AD_64_Biomek_H3K4me3


title: 6673

description:
2533
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6297

description:
2157
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6347

description:
2207
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6556

description:
2416
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6688

description:
2548
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AD_64_manual_H3K27me3


title: 6617

description:
2477
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL10-3

description:
2627
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6491

description:
2351
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6195

description:
2055
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6595

description:
2455
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6285

description:
2145
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-4-1

description:
2605
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6570

description:
2430
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL5-3

description:
2593
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6188

description:
2048
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6571

description:
2431
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6404

description:
2264
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6303

description:
2163
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6513

description:
2373
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6370

description:
2230
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6366

description:
2226
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6252

description:
2112
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6190b

description:
2050
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6396

description:
2256
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6238

description:
2098
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL4-1-1

description:
2586
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6416

description:
2276
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL2-5

description:
2577
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6546

description:
2406
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL3-3b

description:
2582
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6479

description:
2339
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6191

description:
2051
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6394

description:
2254
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6280

description:
2140
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6176

description:
2036
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6483b

description:
2343
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6557

description:
2417
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL2-3b

description:
2575
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6409

description:
2269
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6212b

description:
2072
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6367b

description:
2227
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6658

description:
2518
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6357

description:
2217
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6362

description:
2222
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6256

description:
2116
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6182

description:
2042
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6179b

description:
2039
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6521b

description:
2381
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6445

description:
2305
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6521a


title: 6175

description:
2035
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6192

description:
2052
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6345

description:
2205
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6289

description:
2149
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL8-1-1

description:
2608
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6420

description:
2280
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6292

description:
2152
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6526

description:
2386
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6262

description:
2122
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6327

description:
2187
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6656

description:
2516
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6383b

description:
2243
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6522

description:
2382
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6178

description:
2038
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6208

description:
2068
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL4-4

description:
2590
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6222b

description:
2082
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6517

description:
2377
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6650

description:
2510
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6429

description:
2289
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6184

description:
2044
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6426

description:
2286
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6601

description:
2461
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6501

description:
2361
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6200

description:
2060
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6169

description:
2029
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6197

description:
2057
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6442

description:
2302
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6194

description:
2054
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6180b

description:
2040
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6589

description:
2449
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6337

description:
2197
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6418

description:
2278
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6580

description:
2440
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6258b

description:
2118
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6632

description:
2492
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6605

description:
2465
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6627

description:
2487
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6692

description:
2552
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6220b

description:
2080
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL8-1-3

description:
2609
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6223b

description:
2083
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6412

description:
2272
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6615

description:
2475
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6342

description:
2202
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6457

description:
2317
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL1-4-18

description:
2571
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6270b

description:
2130
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6199b

description:
2059
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6203

description:
2063
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL5-4

description:
2594
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6502b

description:
2362
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6369

description:
2229
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-5

description:
2606
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6676b

description:
2536
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6392b

description:
2252
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6651

description:
2511
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6239

description:
2099
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6296

description:
2156
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6431

description:
2291
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL2-4

description:
2576
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6398

description:
2258
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6220a

description:
2080
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6397

description:
2257
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6246

description:
2106
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6448

description:
2308
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6585b

description:
2445
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6624

description:
2484
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6441b

description:
2301
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6633

description:
2493
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6317

description:
2177
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6318

description:
2178
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6260

description:
2120
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: AD_63_Biomek_H3K27me3


title: 6180a

description:
2040
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6406

description:
2266
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6582

description:
2442
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6463

description:
2323
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6642

description:
2502
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6352b

description:
2212
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6676a

description:
2536
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6423

description:
2283
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6424

description:
2284
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6477

description:
2337
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6272

description:
2132
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6245

description:
2105
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6475

description:
2335
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6343

description:
2203
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6298

description:
2158
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6687

description:
2547
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL1-4

description:
2570
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL2-6

description:
2578
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6682

description:
2542
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6703

description:
2563
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6270a

description:
2130
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6677

description:
2537
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6410

description:
2270
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6183

description:
2043
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6664

description:
2524
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6231

description:
2091
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6206

description:
2066
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6390

description:
2250
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6236

description:
2096
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL6-3b

description:
2599
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6665

description:
2525
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6585a

description:
2445
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6669

description:
2529
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6258a

description:
2118
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6223a

description:
2083
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6233

description:
2093
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6512

description:
2372
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6281

description:
2141
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6177

description:
2037
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6328

description:
2188
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6326

description:
2186
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6683

description:
2543
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-4

description:
2604
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6381

description:
2241
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6699

description:
2559
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL5-2

description:
2592
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6213a

description:
2073
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6592

description:
2452
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6341

description:
2201
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6211

description:
2071
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6408

description:
2268
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6222a

description:
2082
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6694

description:
2554
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6193

description:
2053
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6483a

description:
2343
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6213b


title: 6657

description:
2517
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6224

description:
2084
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6373

description:
2233
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6392a

description:
2252
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6391

description:
2251
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6350

description:
2210
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6527

description:
2387
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL12-3

description:
2636
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL4-2

description:
2587
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6419

description:
2279
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6291

description:
2151
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6209

description:
2069
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6646

description:
2506
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6216

description:
2076
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL1-3

description:
2569
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6255

description:
2115
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6367a

description:
2227
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6645

description:
2505
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6599

description:
2459
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6660

description:
2520
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6383a

description:
2243
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6504

description:
2364
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6330

description:
2190
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6559

description:
2419
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6593

description:
2453
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6308

description:
2168
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6244

description:
2104
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6441a

description:
2301
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6248

description:
2108
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6199a

description:
2059
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6452

description:
2312
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6348

description:
2208
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6225

description:
2085
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6498

description:
2358
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6250

description:
2110
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL6-3a

description:
2599
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6502a

description:
2362
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6384

description:
2244
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6671

description:
2531
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6351

description:
2211
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6352a

description:
2212
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6573

description:
2433
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6315

description:
2175
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6170

description:
2030
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6528

description:
2388
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL3-1

description:
2580
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6489

description:
2349
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-1

description:
2601
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6471

description:
2331
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6229

description:
2089
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6514

description:
2374
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6336

description:
2196
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6174

description:
2034
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6414

description:
2274
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6271

description:
2131
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6458

description:
2318
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6453

description:
2313
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6626

description:
2486
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6672

description:
2532
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6359

description:
2219
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL12-1-1

description:
2634
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6459

description:
2319
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6668

description:
2528
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6204

description:
2064
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6456

description:
2316
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6508

description:
2368
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6690

description:
2550
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6625

description:
2485
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6647

description:
2507
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6283

description:
2143
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6210

description:
2070
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6702

description:
2562
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6402

description:
2262
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6293

description:
2153
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6290

description:
2150
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6529

description:
2389
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6631

description:
2491
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL9-3-2

description:
2622
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL3-4

description:
2583
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6314

description:
2174
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6401

description:
2261
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6329

description:
2189
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL7-3

description:
2603
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6497

description:
2357
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6254

description:
2114
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6544

description:
2404
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL5-1

description:
2591
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6568

description:
2428
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6681

description:
2541
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6547

description:
2407
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6269

description:
2129
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6230

description:
2090
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6634

description:
2494
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6635

description:
2495
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL1-1-2

description:
2566
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6413

description:
2273
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6700

description:
2560
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6358

description:
2218
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6525

description:
2385
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6299

description:
2159
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6301

description:
2161
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6648

description:
2508
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6523

description:
2383
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6325

description:
2185
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6434

description:
2294
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6368

description:
2228
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6428

description:
2288
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6400

description:
2260
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6344

description:
2204
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6380

description:
2240
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6321

description:
2181
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6466

description:
2326
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6639

description:
2499
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6436

description:
2296
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6311

description:
2171
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6411

description:
2271
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL9-2-5

description:
2618
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6349

description:
2209
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL11-1

description:
2628
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL9-1

description:
2614
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6323

description:
2183
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6654

description:
2514
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: K4C ATAC-Seq

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

description: ATAC-seq

data_processing:
Low-quality bases (Phred <20) and Nextera adapters (5’-CTGTCTCTTATA-3’) were identified and trimmed using FastQC and TrimGalore (v0.4.5).
FASTQ files containing trimmed sequences were then aligned to Rn6 Ensembl genome assembly (v95) to generate binary alignment map (BAM) files with Bowtie2 (v.2.3.4.2) with custom options: `--local --very-sensitive-local`, and `-X 3000`
Post-trimming QC with FastQC
Sequences ordered by genomic position using Samtools (v.1.9)
BAM files for each brain region were merged to generate three metasamples that were used for downstream data analysis. Peaks for each region were called using macs2 (Zhang et al., 2008) callpeak with the options - -qvalue 0.00001 - -gsize 2729862089 - -format BAMPE, ignoring duplicates.
Within each brain region, peaks closer than 1000bps were merged with bedtools and peaks less than 146bp, the specific length of DNA wrapped around a single nucleosome, were removed in R. Finally, peaks from each brain region were merged with bedtools to create an additive peak set containing 192,830 peaks.
Genome_build: rn6
Supplementary_files_format_and_content: BED file cotaining ATAC-seq peaks (output of MACS2). Data are in BED format - columns are chromosome, start, end, and score for how many cell types (of 3) contained the ATAC peak.

organism: Rattus norvegicus

source_name: Cortical neuron culture

growth_protocol: Neurons were removed from cortical, hippocampal, or striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Following treatment, media containing KCl or Vehicle was aspirated, and cells were washed with 1x cold PBS. Then, 600 µl of Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, Molecular Grade H2O) was added to cell culture wells and incubated for 5 mins on ice. Lysed cells were then transferred to a 1.5 ml Eppendorf tube and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, 500 µl of 1x cold PBS was added to each tube, and nuclei were counted using the Countess II (Life Technologies). The approximate volume needed to achieve 50,000 nuclei was then placed in new Eppendorf tube, and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge.
The nuclei pellet was then resuspended in 22.5 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), 0.011% Digitonin, 0.1% Tween-20, followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 1 hr. Following tagmentation, libraries were PCR amplified and purified using the Qiagen Minelute PCR purification kit (Qiagen). To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.8X Ampure beads with 80% ethanol. Libraries were sequenced (75-bp paired end reads) on the NextSeq500 platform (Illumina).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 25mM) for 1hr on DIV 11. 50,000 cells per sample were harvested for ATAC-seq.

tag: strain

value: Sprague-Dawley

tag: age

value: Embryonic day 18, 11 DIV

tag: treatment

value: 25mM KCl


title: K3S ATAC-Seq

description: ATAC-seq

source_name: Striatal neuron culture


title: K4H ATAC-Seq

description: ATAC-seq

source_name: Hippocampal neuron culture


title: K3C ATAC-Seq

description: ATAC-seq


title: 6376

description:
2236
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6331

description:
2191
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6579

description:
2439
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6363

description:
2223
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6198

description:
2058
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6603

description:
2463
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6335

description:
2195
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: K1S ATAC-Seq

description: ATAC-seq


title: K2C ATAC-Seq

description: ATAC-seq


title: 6622

description:
2482
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6524

description:
2384
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: K2H ATAC-Seq

description: ATAC-seq


title: K2S ATAC-Seq

description: ATAC-seq


title: 6638

description:
2498
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V2H ATAC-Seq

description: ATAC-seq

value: Vehicle


title: V4H ATAC-Seq

description: ATAC-seq


title: V3C ATAC-Seq

description: ATAC-seq


title: V2C ATAC-Seq

description: ATAC-seq


title: K1H ATAC-Seq

description: ATAC-seq


title: V2S ATAC-Seq

description: ATAC-seq


title: V1S ATAC-Seq

description: ATAC-seq


title: V4S ATAC-Seq

description: ATAC-seq


title: IL11-4-1

description:
2632
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6540

description:
2400
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6587

description:
2447
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6309

description:
2169
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6454

description:
2314
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6667

description:
2527
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6294

description:
2154
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6652

description:
2512
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6219

description:
2079
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: K7S

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore v0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore v0.4.5
Post-trimming QC with FastQC
Splice-aware alignment to Rn6 genome reference with star v2.6.0c.
Merging of BAM files and index generation with samtools v1.9
Identification of transcriptionally active putative enhancers (TAPEs) with custom processing in Seqmonk v 1.46.0
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with of transcriptionally active putative enhancer (TAPE) expression estimates, in counts per kilobase per million mapped reads for each sample. Columns are TAPE_ID, chromosome, start, end, type, distance, sample values (several columns), TAPE center, nearest gene, and information related to nearest gene.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads; ~12.6-20.4 M reads/sample) on an Illumina sequencing platform (NextSeq500)

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 25mM) for 1hr on DIV 11. Media was removed and RNA was extracted.

value: Striatal neuron culture


title: K5S


title: K1S


title: K2H

value: Hippocampal neuron culture


title: 6555

description:
2415
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: K3C

value: Cortical neuron culture


title: K2C


title: K3H


title: K1H


title: V4S


title: K1C


title: 6234

description:
2094
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6578

description:
2438
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6393

description:
2253
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V8S


title: 6377

description:
2237
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V6S


title: 6583

description:
2443
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V3H


title: V3C


title: V1C ATAC-Seq

description: ATAC-seq


title: V2S


title: 6241

description:
2101
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6389

description:
2249
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V2H


title: 6307

description:
2167
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: V1C


title: V1H ATAC-Seq

description: ATAC-seq


title: V2C


title: V1H


title: 6302

description:
2162
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6566

description:
2426
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6286

description:
2146
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Leaflet: AD_A

city: Riverside

first: Christi Ann

last: Scott

state: CA

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

data_processing:
For HiSeq2000: RTA v1.7, CASAVA v1.7 used for basecalling. For NextSeq500: RTA 2.0 used for basecalling.
Reads aligned to the latest release of each of the genomes used (dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome) and quantified with kallisto (Version: kallisto 0.43.1, Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519) . Only libraries for which we obtained >75 % alignment were used for downstream analysis.
Transcript counts were summarized to gene-level using tximport package (version 1.4.0).
For any instances of detected batch effects, we removed unwanted variation using RuvR in the RuvSeq package (version_1.10.0).
Differentially expressed gene (DEG) analysis was performed with the edgeR package (version 3.18.1), using low count filtering (cpm >0.5) and TMM normalization.
Genome_build: dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited .tsv files including counts TPM normalized read counts for each sample

organism: Arabidopsis thaliana

source_name: Leaflet

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.

value: wild type

value: 28 days

value: 1% diacetyl in PO, 5days

value: leaflet


title: 6385

description:
2245
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: IL5-5

description:
2595
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6364

description:
2224
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6567

description:
2427
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6604

description:
2464
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6273

description:
2133
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Leaflet: AC_A

value: PO, 5 days (control)


title: 6505

description:
2365
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Leaflet: AC_B


title: 6288

description:
2148
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6422

description:
2282
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6480

description:
2340
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6388

description:
2248
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Leaflet: AD_B


title: 6324

description:
2184
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6312

description:
2172
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6450

description:
2310
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [KD18_DAC_Input]

city: Institute

first: Sridhar

middle: A

last: Malkaram

state: West Virginia

address: Barron Drive

department: Mathematics and Computer Sciences

institute: West Virginia State University

description:
KD18_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).

data_processing:
Sequence reads were quality checked using FastQC v0.11.5, and the adapter sequences were removed and low quality (<20) bases at 3-prime ends were trimmed using Trim-galore v0.4.4.
Reads were then aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in an end-to-end alignment mode with default parameters.
Alignments with average phred quality score of < 10, PCR duplicates and those aligning to blacklisted regions of the genome were filtered out using Samtools v1.4.1.
The alignments were converted to bed format using bamtools v2.3.0 and the H3K9ac enriched (peak) regions were identified using diffReps v1.55.6 software with default parameters, using the input samples for background correction.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Bed format alignment files for each sample.
Supplementary_files_format_and_content: Tab-delimited text format differential peaks and hotspot regions for H3K9ac levels between DAC and DMSO.

source_name: Bone marrow mononuclear cells

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FBS for 24 hours prior to the experiment in a humidified incubator with 5% carbon dioxide supply.

extract_protocol:
ChIP-Seq libraries were prepared using SMARTer ThruPLEX DNA-seq kit (Takara Bio USA, Mountain View, CA) according to the manufacturer’s instructions.
1 to 2 ng fragmented double stranded DNAs were used to construct libraries with dual indices.

treatment_protocol: Each patient sample was divided into two groups, one treated with DAC (500 nM) for 72 hours and the other group (control) treated with DMSO.

tag: diagnosis

value: Acute myeloid leukemia (AML)

tag: patient

value: Bone marrow mononuclear cells

value: Decitabine (500nM) for 72 hours


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [JCT19_DMSO_Input]

description:
JCT19_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).

value: DMSO


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [MAV22_DAC_Input]

description:
MAV22_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [KDG8_DMSO_Input]

description:
KDG8_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [KD18_DMSO_Input]

description:
KD18_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [KDG8_DAC_Input]

description:
KDG8_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [JCT19_DAC_Input]

description:
JCT19_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [REB20_DAC_Input]

description:
REB20_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [REB20_DMSO_Input]

description:
REB20_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [MAV22_DMSO_Input]

description:
MAV22_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [GMW2_DMSO_Input]

description:
GMW2_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6405

description:
2265
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: breaker stage of ripening

value: BIL


title: Input ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [GMW2_DAC_Input]

description:
GMW2_DAC_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6518

description:
2378
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [MAV22_DMSO_H3K9]

description:
MAV22_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).

value: H3K9ac (Active Motif, Carlsbad, CA)


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [KDG8_DMSO_H3K9]

description:
KDG8_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6166

description:
2026
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6425

description:
2285
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6185

description:
2045
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [KD18_DMSO_H3K9]

description:
KD18_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6287

description:
2147
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [JCT19_DMSO_H3K9]

description:
JCT19_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6596

description:
2456
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [GMW2_DMSO_H3K9]

description:
GMW2_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6575

description:
2435
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [REB20_DAC_H3K9]

description:
REB20_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6594

description:
2454
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [REB20_DMSO_H3K9]

description:
REB20_DMSO_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [MAV22_DAC_H3K9]

description:
MAV22_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6670

description:
2530
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [KDG8_DAC_H3K9]

description:
KDG8_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6695

description:
2555
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6492

description:
2352
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6629

description:
2489
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6686

description:
2546
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6620

description:
2480
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [JCT19_DAC_H3K9]

description:
JCT19_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6560

description:
2420
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [KD18_DAC_H3K9]

description:
KD18_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: IL9-1-3

description:
2616
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: IL12-1

description:
2633
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6515

description:
2375
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6563

description:
2423
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6346

description:
2206
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6618

description:
2478
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: case12-liver1

city: Boston

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: liver

growth_protocol: Rapid autopsy was performed for samples collection.

extract_protocol:
RNA extraction from FFPE slides was done using the FormaPure Total nucleic acid extraction kit (C16675, Beckman Coulter) according to manufacturer instructions. Three 5 um thin tissue sections from areas devoid of acute inflammation were used per sample
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: Samples were formalin fixed for 3 days prior to embedding in paraffin and sectioning.

tag: case

tag: tissue type

value: Formalin fixed paraffin embedded tissue

tag: pool no


title: case3-liver1


title: case10-liver1


title: 6701

description:
2561
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6266

description:
2126
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6541

description:
2401
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: H3K9ac ChIPseq of Bone marrow mononuclear cells from AML patient – Decitabine treated [GMW2_DAC_H3K9]

description:
GMW2_DAC_H3K9
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).


title: 6558

description:
2418
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6680

description:
2540
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6493

description:
2353
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. robusta_HighLight 3

organism: Flaveria robusta

value: leaf


title: 6472

description:
2332
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. robusta_HighLight 1


title: F. robusta_HighLight 2


title: F. robusta_ctrl (HighLight) 3


title: Y1-positive rep2

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
y1_WT2

data_processing:
Raw HiSeq2000 data files were processed with CASAVA 1.8.2 (Illumina) to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples, if index sequences were non-redundant, we allowed for 1 mismatch or N in the index.
Paired end reads were mapped to the zebrafish genome (GRCz11) using STAR
Mapped reads were quantified using Ensembl (v95), RefSeq (GCF_000002035.6), or a custom annotation (V4.3.gtf, included as processed file) using RSEM
Differentially expressed genes were identified using DEseq2
RNAseq pipeline was run in the DolphinNext environment
Genome_build: GRz11
Supplementary_files_format_and_content: CSV-formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation

organism: Danio rerio

source_name: non-venous endothelial, blood, and arch mesenchyme

extract_protocol: total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA-Seq Kit (Clontech)

treatment_protocol: embryos were dissociated into single cell suspensions, immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2-positive cells were isolated by fluorescence activated cell sorting.

tag: Stage

value: 38 hours post fertilization

tag: source

value: FACS-isolated cells


title: Y1-positive rep1

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
y1_WT1


title: Y1-positive rep3

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
y1_WT3


title: 6403

description:
2263
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Nr2f2andY1-positive rep3

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
Nr2f2_y1_WT3

source_name: venous endothelial cells


title: Nr2f2andY1-positive rep2

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
Nr2f2_y1_WT2


title: 6421

description:
2281
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6168

description:
2028
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: HumanPodocyte_72hr_NG_rep3

type: RNA

city: Zhuhai

first: qiongxia

last: deng

state: Guangdong

address: 52 Meihua Dong Lu, Xiangzhou District, Zhuhai city, Guangdong Province, China

department: 1.	Division of nephrology, Department of medicine

institute: Fifth affiliated hospital Sun Yat-Sen University

description: Gene expression data

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction,6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction and hybridized to Agilent Human Gene Expression（ 8*60K） for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Human Podocyte treated with normal glucose

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 μg RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human podocytes were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, Insulin-Transferrin-Selenium supplement, 2 mM L-glutamine and antibiotic mixture. To stimulate cell proliferation, podocytes were cultivated at 33 °C in 5% CO2. To induce differentiation, they were maintained at 37 °C in 5% CO2 for at least 2 weeks.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Differentiated human podocytes were treated with normal glucose (NG, 5.5 mmol/l) and high glucose (HG, 30 mmol/l) medium for 72 h.

tag: cell type

value: Differentiated podocytes

value: normal glucose


title: 6499

description:
2359
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: HumanPodocyte_72hr_HG_rep2

description: Gene expression data

source_name: Human Podocyte treated with high glucose

value: high glucose


title: 6643

description:
2503
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. robusta_ctrl (HighLight) 2


title: HumanPodocyte_72hr_NG_rep2

description: Gene expression data


title: HumanPodocyte_72hr_HG_rep3

description: Gene expression data


title: HumanPodocyte_72hr_NG_rep1

description: Gene expression data


title: HumanPodocyte_72hr_HG_rep1

description: Gene expression data


title: 6590

description:
2450
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: F. robusta_ctrl (HighLight) 1


title: Nr2f2andY1-positive rep1

description:
ribo-depleted RNA
Nr2f2_Ens95.csv,Nr2f2_RefSeq.csv,Nr2f2_V4.3.csv
Nr2f2_y1_WT1


title: 6586

description:
2446
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6361

description:
2221
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: pdgfrb-positive rep3

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTpdgfrb09

source_name: pdgfrb:citrine-positive cells

extract_protocol: oligo dT primed libraries were constructed using the TotalScript kit (Epicentre)

treatment_protocol: embryos were dissociated into single cell suspensions and transgene expressing cells were isolated by fluorescence activated cell sorting.

value: 5 days post fertilization


title: pdgfrb-positive rep1

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTpdgfrb01


title: scRNA-seq_ac24

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

data_processing:
transcript level counting with cell ranger v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix

source_name: infusion product

extract_protocol: Libraries were prepared according to 10X Genomics Chromium Single Cell 5' Library Construction Kit (1000020) according to manufacturer's protocol.

treatment_protocol: CART cells were washed out from infusion bag by saline, and spin down at 500g for 30min. Cells were resuspended in PBS solution containing 0.4% ultrapure BSA and counted using haemocytometer to determine cell concentration and cell viability.

value: CART cells

tag: histology

value: DLBCL

tag: 3mo pet/ct

value: PD


title: 6433

description:
2293
Solanum lycopersicum-pennellii
Manually peeled skin tissue

tag: tissue


title: 6553

description:
2413
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: pdgfrb-positive rep2

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTpdgfrb06


title: 6251

description:
2111
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6232

description:
2092
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: 6485

description:
2345
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: scRNA-seq_ac23

value: tFL


title: pdgfrb-negative rep3

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTnegative14

source_name: pdgfrb:citrine-negative cells


title: 6588

description:
2448
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: pdgfrb-negative rep2

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTnegative11


title: scRNA-seq_ac22


title: pupal wing, D2_66hAPF_rep3

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Str. 2

department: Faculty of Biology

institute: Ludwig Maximilian University of Munich

data_processing:
Libraries were demultiplexed and then trimmed using trimmomatic
Libraries were then aligned to dm6 genome assembly using Bowtie2
Aligned libraries were then iltered by Picard with following steps: clean sam, FixMate information, MarkDuplicate. The PCR duplicates were subsequently removed by SAMtools
Peak calling was performed on three replicates together using MACS2 (ref) with following settings: --keep-dup all; -q 0.01; --nomodel; --shift -100; --extsize 200; -B –SPMR; --call-summits
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files were converted from corresponding bedGraph files, which were generated by MACS2 using SPMR setting.

source_name: pupal wing

growth_protocol: Flies were cultured at 25˚C

extract_protocol:
The protocol is modified from Omni-ATACseq. 24 pupal wings were then dissected, rinsed in cold PBS for twice, and moved into 100µl cold 1x lysis buffer. The wings were further cut into 3-4 pieces and transferred into a 2ml Dounce homogenizer. They were then disrupted by 12 strokes using pestle A, rest on ice for 5min, then 20 strokes using pestle B. After additional 10min incubation on ice, 900µl 1x wash buffer was added. 20ml syringe and 20 ½ gauge needle were employed here to separate cells from the wing cuticle. The mixture was then filtered with 40µM strainer , and centrifuged at 4°C, 1000g for 10min. Pelleted nuclei were gently resuspended with 45µl ultrapure water and counted using hemocytometer. 50000 nuclei were then centrifuged at 4°C, 1000g for 10min, resuspended with 8ml 2x Tagment DNA buffer. The tagmentation reaction followed the standard ATAC-seq protocol with minor modifications: 10ul 2X TD buffer with nuclei; 2ul Tagment DNA Enzyme; 8ul ultrapure water.
Libary was prepaire using Illunmina standard protocol.

treatment_protocol: White male pupal were selected and grown at 25˚C on wet filter paper for 66h.

tag: developmental stage

value: 66h APF

value: wing

tag: genotype


title: pupal wing, D206KO_66hAPF_rep3


title: pupal wing, D206KO_66hAPF_rep1


title: pupal wing, D206KO_66hAPF_rep2


title: pupal wing, D2_66hAPF_rep2


title: scRNA-seq_ac21


title: 6503

description:
2363
Solanum lycopersicum-pennellii
Manually peeled skin tissue

tag: ripening stage

value: breaker stage of ripening

tag: population

value: BIL


title: 6550

description:
2410
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: pdgfrb-negative rep1

description:
pdgfrbCit_Ens95.csv,pdgfrbCit_RefSeq.csv,pdgfrbCit_V4.3.csv
WTnegative08

tag: strain


title: MPP2_Sham_4

description: rRNA-depleted stranded RNA. Both males and females were used, and sex-matched between experimental groups.

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
Low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.1.2).
Pairwise comparisons were performed between samples across different mouse genotypes (Het and Sham samples were grouped together as WT) and genes with changes in expression ≥ |1.5| folds and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

extract_protocol:
Mouse bone marrow was flushed from femurs, tibiae, humeri, and ilia of mice with a 26-G needle in PBS supplemented with 0.1% BSA and 2 mM EDTA, filtered through 40-μm cell strainers, and subjected to red blood cell lysis in ACK buffer (0.15 M NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA). The samples were stained with biotin anti-mouse Lineage Panel (BioLegend), PE-Cy7 cKit (clone 2B8, BioLegend), APC-Cy7 Sca-1 (D7, BioLegend), FITC CD48 (HM48-1, eBioscience), APC CD150 (TC15-12F12.2, BioLegend), PE Flt3 (A2F10, eBioscience), Brilliant Violet 421 CD34 (RAM34, BD Biosciences), and streptavidin-PECy5 (BioLegend). DAPI was added immediately before sorting for dead cell exclusion. Cell sorting was performed on FACSAria and analyzed with FACS Diva software (BD Biosciences). Specifically, the extracted BM cells were FACS sorted into primary HSC, MPP1, and MPP2 cells, gating on Lin-cKit+Sca1+CD150+Flt3-, and CD34-CD48- for HSCs, CD34+CD48- for MPP1, and CD34+CD48+ for MPP2 cells.
RNA was isolated from FACS-sorted HSCs and MPPs using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech).The libraries were sequenced on an Illumina HiSeq 2000 sequencer in paired-end 50bp configuration.

treatment_protocol: For tamoxifen-induced Mysm1 gene inactivation, the Mysm1 fl/fl CreERT2 mice were injected intraperitoneally with tamoxifen (Sigma T5648) in sterilized corn oil at 0.15mg/gram per injection, with 8 doses in total administered over 16 days. Successful deletion of Mysm1 exon 3 was validated by genotyping of the genomic DNA from hematopoietic and lymphoid organs, and the loss of Mysm1 transcript was further confirmed by qRT-PCR with Lin-cKit+Sca1+ HSC/MPP cells from mouse bone marrow. Mysm1 +/fl CreERT2 mice undergoing identical tamoxifen treatment, as well as Mysm1 fl mice treated with corn-oil only, were used as controls.

tag: age

value: Mice were 8-12 weeks of age.

tag: gender

value: pooled male and female

value: Bone marrow

value: Multipotent Progenitors 2 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48+)

value: Mysm1-WT (Corn oil treated control Mysm1 fl mice)


title: 6354

description:
2214
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Phf7 tKO rep2

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
The raw reads are from 2 instruments (Illumina Nextseq 550 / Novaseq 6000)
SGdev.barcodes.tsv.gz
SGdev.genes.tsv.gz
SGdev.matrix.mtx.gz

data_processing:
Fastq files were generated using bcl2fastq (v2.19.1.403)
The sequenced reads were aligned using cellranger count (v3.0.2; --r1-length 26 --r2-length 75) to cellranger reference mm10 (v 2.1.0).
Aligned files were aggregated with cellranger aggr (v3.0.2; --normalize=mapped)
Genome_build: mm10
Supplementary_files_format_and_content: SGdev.barcodes.tsv' contains the cell identity information which is represented as barcode sequences in the same order as 'SGdev.matrix.mtx' columns. 'SGdev.genes.tsv' include the gene names  in the same order as 'SGdev.matrix.mtx' rows. 'SGdev.matrix.mtx' contains the expression value of each cell and gene.

source_name: testicular cells

extract_protocol:
Mouse testis tissues were digested with collagenase A, DNase I , and trypsin in DMEM-F12. Trypsin was blocked using FBS and cells were filtered by 70 μm and 40 μm strainers. Following centrifugation, red blood cells were removed using RBC lysis buffer. Then, testis cells were washed and resuspended with HBSS.
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3. The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on Nextseq 550.

tag: cell types

value: single cell suspension of testes

value: post natal day 63

value: Stra8-Cre:Phf7 f/f


title: Phf7 tKO rep1


title: MPP2_Sham_2_3


title: scRNA-seq_ac19

value: CART cells


title: 6539

description:
2399
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: scRNA-seq_ac18

value: DLBCL


title: MPP2_Mysm1_Het_4

value: Mysm1-Het (Tamoxifen-treated Mysm1+/fl CreERT2 mice)


title: Phf7 f/f rep2

value: Phf7 f/f


title: 6340

description:
2200
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: IL9-3-1

description:
2621
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: IL


title: scRNA-seq_ac14

value: CR


title: scRNA-seq_ac20

value: PR


title: MPP2_Mysm1_Ko_1

value: Mysm1-KO (Tamoxifen-treated Mysm1fl/fl CreERT2 mice)


title: scRNA-seq_ac17

value: tFL

value: PD


title: MPP2_Mysm1_Het_2_3

value: Mice were 8-12 weeks of age.

value: pooled male and female

value: Bone marrow


title: Phf7 f/f rep1

value: single cell suspension of testes


title: scRNA-seq_ac16


title: CSN8, batch 2

city: Tel Aviv

first: Tamir

last: Tuller

address: Ramat Aviv

department: Biomedical Engineering

institute: Tel Aviv University

description: Gene expression data from young seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 Scanner

data_processing: data analysis was performed by MATLAB:  (i) Expression values were computed from raw CEL files by applying the background adjustment using Robust Multi-array Average (RMA) background correction algorithm, then applying quantile normalization over the multiple arrays, and finally performed the RMA procedure to get final gene expression values.  (ii) In the next step, in each of the samples (Col/Csn5a-1 and Ws/Csn8), we computed significantly over/under-expressed genes based on:   For Col/csn5a-1 we used t-test based on data of six6 chips.   For Ws/csn8 we used ANOVA(Rutherford, 2001), considering batch effects such as the scan date of each chip, etc.

label: biotin

source_name: light grown CSN8 seedlings batch 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Seedlings were grown for 12 days on agar plates containing MS salts, pH 5.7, under a light-and-dark cycle with 16 h of white light at 75 lmol m-2 s-1 and 8 h of darkness.

extract_protocol: Tri-Reagent (Molecular Research Center, Inc., USA)  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After 12 days the seedlings were collected  for RNA extraction with no additional treatment

value: whole seedlings

value: CSN8 mutant


title: Wassilewskija + DTT, batch 2

source_name: light grown DTT treated Wassilewskija seedlings batch 2

value: Wassilewskija wild type


title: CSN8 + DTT, batch 2

source_name: light grown DTT treated CSN8 seedlings batch 2


title: MPP2_Mysm1_Ko_2_3

value: Multipotent Progenitors 2 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48+)


title: 6382

description:
2242
Solanum lycopersicum-pennellii
Manually peeled skin tissue

source_name: Skin fruit tissue

value: breaker stage of ripening

value: BIL


title: MPP2_Mysm1_Het_1

value: Mysm1-Het (Tamoxifen-treated Mysm1+/fl CreERT2 mice)


title: scRNA-seq_ac13

value: CART cells

value: DLBCL


title: pupal wing, D2_66hAPF_rep1

value: 66h APF

value: wing


title: scRNA-seq_ac11

value: tFL


title: 6172

description:
2032
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: scRNA-seq_ac15

value: PD


title: 6614

description:
2474
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: scRNA-seq_ac10

value: CR


title: 6519

description:
2379
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MPP1_Mysm1_Sham_2_3

value: Mice were 8-12 weeks of age.

value: pooled male and female

value: Bone marrow

value: Multipotent Progenitors 1 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48-)

value: Mysm1-WT (Corn oil treated control Mysm1 fl mice)


title: MPP1_Mysm1_Het_4


title: 6447

description:
2307
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MPP2_Mysm1_Ko_4

value: Multipotent Progenitors 2 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48+)

value: Mysm1-KO (Tamoxifen-treated Mysm1fl/fl CreERT2 mice)


title: MPP1_Mysm1_Sham_4


title: scRNA-seq_ac12


title: 6537

description:
2397
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: breaker stage of ripening

value: BIL


title: 6661

description:
2521
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Wassilewskija, batch 2

source_name: light grown Wassilewskija seedlings batch 2

value: whole seedlings

value: Wassilewskija wild type


title: scRNA-seq_ac09

value: CART cells

value: DLBCL


title: Wassilewskija + DTT, batch 1

source_name: light grown DTT treated Wassilewskija seedlings batch 1


title: 6649

description:
2509
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: scRNA-seq_ac08

value: PMBCL


title: CSN8, batch 1

source_name: light grown CSN8 seedlings batch 1

value: CSN8 mutant


title: 6609

description:
2469
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue


title: 6662

description:
2522
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: MPP1_Mysm1_Ko_4

description: rRNA-depleted stranded RNA. Both males and females were used, and sex-matched between experimental groups.


title: scRNA-seq_ac06

value: NE


title: 6562

description:
2422
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: CSN8 + DTT, batch 1

source_name: light grown DTT treated CSN8 seedlings batch 1


title: scRNA-seq_ac05

value: tFL

value: CR


title: scRNA-seq_ac04

value: PD


title: 6265

description:
2125
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Csn5a-1, biological rep2

source_name: light grown csn5a-1 seedlings

value: csn5a-1 mutant


title: 6179a

description:
2039
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: Csn5a-1, biological rep3


title: Csn5a-1, biological rep1


title: Wassilewskija, batch 1

source_name: light grown Wassilewskija seedlings batch 1


title: HSC_Sham_2_3

source_name: HSC

value: Mice were 8-12 weeks of age.

value: pooled male and female

value: Bone marrow

value: Hematopoietic Stem cells (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34-CD48-)

value: Mysm1-WT (Corn oil treated control Mysm1 fl mice)


title: scRNA-seq_ac07


title: Columbia, biological rep3

source_name: light grown Columbia seedlings

value: whole seedlings

value: Columbia wild type


title: Columbia, biological rep2


title: MPP1_Mysm1_Het_1

value: Multipotent Progenitors 1 (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34+CD48-)

value: Mysm1-Het (Tamoxifen-treated Mysm1+/fl CreERT2 mice)


title: 6545

description:
2405
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: breaker stage of ripening

value: BIL


title: MPP1_Mysm1_Het_2_3


title: MPP1_Mysm1_Ko_2_3

value: Mysm1-KO (Tamoxifen-treated Mysm1fl/fl CreERT2 mice)


title: HSC_Mysm1_Het_4


title: scRNA-seq_ac02

value: CART cells

value: DLBCL


title: IL6-2-2

description:
2598
Solanum lycopersicum-pennellii
Manually peeled skin tissue

value: Skin fruit tissue

value: IL


title: scRNA-seq_ac01

value: CR


title: HSC_Sham_4

value: Mice were 8-12 weeks of age.


title: Columbia, biological rep1

description: Gene expression data from young seedlings


title: HSC_Mysm1_Het_1

value: pooled male and female


title: 6313

description:
2173
Solanum lycopersicum-pennellii
Manually peeled skin tissue


title: scRNA-seq_ac03

value: PD


title: HSC_Mysm1_Ko_4

value: Bone marrow

value: Hematopoietic Stem cells (Bone marrow cells sorted by gates Lin-Sca1+cKit+CD150+Flt3-CD34-CD48-)