title: HCEC bait 5 low cell input, rep9

description: Sample name: NW045.NWHCECH009ent9_MID09


title: HCT116, 35 pg input, bait 5, replicate A18

status: Public on Sep 30 2019

type: SRA

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
Sequence reads were mapped using bwa 0.7.12-r1039 to a reference genome composed of PhiX, BDGP5 (Drosophila), K12 (E. coli) and human (HG19). Alignments with mapping quality greater than 10 of the read 2 were used to determine the probe position. An extension region (region from the probe’s end to the first restriction site) was used to discriminate valid from mis-annealing events. The total number of alignments in the read 1 with the proper probe extension in the second read was reported by restriction fragment. Next the number of distinct transposon integration sites was also reported to remove PCR duplicates.
Genome_build: hg19/BDGP5/PhiX/K12
Supplementary_files_format_and_content: tab-delimited text files

molecule: genomic DNA

organism:
Drosophila melanogaster
Homo sapiens

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10 % Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5 % CO2 circumstance at 37 C.

extract_protocol:
Chromosome Conformation Capture (3C) was performed as described before with slight modification. Briefly, 1 million of the cells were fixed with 1 % monomeric formaldehyde for 10 min at RT and excess amount of the formaldehyde was captured by 0.125 M Glycine. Then cells were collected and suspended in 10 ml of nuclear isolation buffer (0.2 % NP-40, 10 mM Tris-cl, pH 7.5, 10 mM NaCl, x1 Proteinase inhibitor (Roche, 04693116001)) and incubated for 10 min on ice. Isolated nuclei were precipitated and washed with 1 ml of Buffer 2 (New England Biolabs, B7002S). Next, nuclei were re-suspended in 500 ul of x1.2 buffer 2. Un-crosslinked fraction was removed by adding 5 ul of 10 % SDS and incubated for 1 hr at 37 °C. Then excess amount of SDS was captured by TritonX-100. The chromatin DNA was fragmented by the incubation at 37 °C for overnight with HindIII (1 U/ul, New England Biolabs, R0104T). As a spiking control, same amount of chromatin was isolated from Drosophila S2 cell with same method and mixed with chromatin for analysis. After the inactivation of the enzyme, the solution was transferred to 50 ml tube containing 7 ml of ligation buffer (50 mM Tris-cl, pH 7.5, 10 mM MgCl2, 1 % Triton X-100) and incubate for 1 hr at 37 °C. Then 70 ul of 100 mM ATP, 70 ul of 1 M DTT and 2000 U of T4 DNA ligase were added. Then the solution was incubated at 16 °C for overnight followed by for 1 hr at RT. Crosslink was reversed with conventional methods. Finally, DNA was collected by ethanol precipitation followed by the purification with MSB Spin PCRapace (Stratec, 1020220200) and Zymo Clean & Concentrator-5 (Zymo Research, D4013). The digestion efficiency was estimated by qPCR. The quality of 3C DNA was visualized on 1 % agarose gel.
3C DNA was tagmented and adapter DNA which equipped with T7 RNA polymerase promoter was incorporated by limited cycle PCR using either Nextera or Nextera XT DNA sample prep kit (Illumnia, FC-121-1031, FC-131-1024). The resulting product was amplified by in vitro transcription (Maxiscript T7 kit, Life technology, AM1312M). The template DNA was fragmented by Turbo DNase I (Life technology, AM2239) prior to the RNA purification by RNeasy (Qiagen, 74104). For primer annealing, 1 ug of template RNA with 0.2uM of bait specific primer was denatured at 75 °C for 3 min and then mixed with x2 buffer of Platinum Quantitative RT-PCR ThermoScript One-Step System (Life technology, 11731-015) and 0.5U/ul of SUPERase In RNase inhibitor (Life technology, AM2694). The solution was incubated at 4 °C for 44-48 hrs. Then following the incubation at 65 °C for 5 min, the primer was extended by adding Thermoscript Plus/Platinum Taq mix at 60 °C for 30 min. After the inactivation of reverse transcriptase, bait-interactor chimeric DNA is enriched by PCR with Illumina P5 and bait specific primer. At last Illumina P7 sequence was incorporated with Nextera DNA sample prep kit by following manufacture’s instruction.

treatment_protocol: For Flavopiridol treatment, cells were incubated with 2 mM Flavopiridol (Sigma Aldrich, F3055) at growing condition for 6 hrs.

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

tag: probes


title: HCT116, 35 pg input, bait 5, replicate A12


title: HCEC bait 5 low cell input, rep7

description: Sample name: NW045.NWHCECH009ent7_MID07

data_processing:
Library strategy: 3C-seq
Sequence reads were mapped using bwa 0.7.12-r1039 to a reference genome composed of PhiX, BDGP5 (Drosophila), K12 (E. coli) and human (hg19). Alignments with mapping quality greater than 10 of the read 2 were used to determine the probe position. An extension region (region from the probe’s end to the first restriction site) was used to discriminate valid from mis-annealing events. The total number of alignments in the read 1 with the proper probe extension in the second read was reported by restriction fragment. Next, the number of distinct transposon integration sites was also reported to remove PCR duplicates.
Genome_build: hg19/BDGP5/PhiX/K12
Supplementary_files_format_and_content: Tab-delimited text files.

source_name: HCEC, bait 5, low cell input

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5% CO2 circumstance at 37 C.

extract_protocol:
Chromosome Conformation Capture (3C) was performed as described before with slight modification. Briefly, 1 million of the cells were fixed with 1% monomeric formaldehyde for 10 min at RT and excess amount of the formaldehyde was captured by 0.125 M Glycine. Then, cells were collected and suspended in 10 ml of nuclear isolation buffer (0.2% NP-40, 10 mM Tris-cl, pH 7.5, 10 mM NaCl, x1 Proteinase inhibitor (Roche, 04693116001)) and incubated for 10 min on ice. Isolated nuclei were precipitated and washed with 1 ml of Buffer 2 (New England Biolabs, B7002S). Next, nuclei were re-suspended in 500 ul of x1.2 buffer 2. Un-crosslinked fraction was removed by adding 5 ul of 10% SDS and incubated for 1 hr at 37 °C. Then, excess amount of SDS was captured by TritonX-100. The chromatin DNA was fragmented by the incubation at 37 °C for overnight with HindIII (1 U/ul, New England Biolabs, R0104T). As a spiking control, same amount of chromatin was isolated from Drosophila S2 cells with same method and mixed with chromatin for analysis. After the inactivation of the enzyme, the solution was transferred to 50 ml tube containing 7 ml of ligation buffer (50 mM Tris-cl, pH 7.5, 10 mM MgCl2, 1% Triton X-100) and incubated for 1 hr at 37 °C. Then, 70 ul of 100 mM ATP, 70 ul of 1 M DTT and 2000 U of T4 DNA ligase were added. Then, the solution was incubated at 16 °C for overnight followed by for 1 hr at RT. Crosslink was reversed with conventional methods. Finally, DNA was collected by ethanol precipitation followed by the purification with MSB Spin PCRapace (Stratec, 1020220200) and Zymo Clean & Concentrator-5 (Zymo Research, D4013). The digestion efficiency was estimated by qPCR. The quality of 3C DNA was visualized on 1% agarose gel.
3C DNA was tagmented and adapter DNA which equipped with T7 RNA polymerase promoter was incorporated by limited cycle PCR using either Nextera or Nextera XT DNA sample prep kit (Illumina, FC-121-1031, FC-131-1024). The resulting product was amplified by in vitro transcription (Maxiscript T7 kit, Life Technology, AM1312M). The template DNA was fragmented by Turbo DNase I (Life Technology, AM2239) prior to the RNA purification by RNeasy (Qiagen, 74104). For primer annealing, 1 ug of template RNA with 0.2uM of bait-specific primer was denatured at 75 °C for 3 min and then mixed with x2 buffer of Platinum Quantitative RT-PCR ThermoScript One-Step System (Life Technology, 11731-015) and 0.5U/ul of SUPERase In RNase inhibitor (Life Technology, AM2694). The solution was incubated at 4 °C for 44-48 hrs. Then, following the incubation at 65 °C for 5 min, the primer was extended by adding Thermoscript Plus/Platinum Taq mix at 60 °C for 30 min. After the inactivation of reverse transcriptase, bait-interactor chimeric DNA was enriched by PCR with Illumina P5 and bait-specific primer. At last, Illumina P7 sequence was incorporated with Nextera DNA sample prep kit by following manufacturer's instruction.

value: HCEC

value: human colonic epithelial cell line

tag: spiking control

value: Drosophila S2 cell chromatin


title: HCEC bait 5 low cell input, rep8

description: Sample name: NW045.NWHCECH009ent8_MID08


title: HCT116 half of 300 cells input, bait 5, replicate 6


title: HCT116 half of 300 cells input, bait 5, replicate 7


title: HCT116 half of 300 cells input, bait 5, replicate 4


title: HCEC bait 5 low cell input, rep1

description: Sample name: NW045.NWHCECH009ent1_MID01


title: HCEC bait 5 low cell input, rep3

description: Sample name: NW045.NWHCECH009ent3_MID03


title: HCEC bait 5 low cell input, rep4

description: Sample name: NW045.NWHCECH009ent4_MID04


title: HCEC bait 1

description: Sample name: NW044.NWHCECH077ent150306_MID8

source_name: HCEC, bait 1


title: HCEC bait 5 low cell input, rep6

description: Sample name: NW045.NWHCECH009ent6_MID06


title: HCEC bait 7

description: Sample name: NW044.NWHCECH075ent150306_MID6

source_name: HCEC, bait 7


title: HCEC bait 2

description: Sample name: NW044.NWHCECH076ent150306_MID7

source_name: HCEC, bait 2


title: HCT116 bait 2

description: Sample name: NW044.NW28H076ent150306_MID2

source_name: HCT116, bait 2


title: HCT116 bait 7

description: Sample name: NW044.NW28H075ent150306_MID1

source_name: HCT116, bait 7


title: HCT116 bait 5 low cell input, rep8

description: Sample name: NW042.NW28Hent009h150223_MID08

source_name: HCT116, bait 5, low cell input


title: HCT116 bait 5 low cell input, rep6

description: Sample name: NW042.NW28Hent009f150223_MID06


title: HCT116 bait 5 low cell input, rep7

description: Sample name: NW042.NW28Hent009g150223_MID07


title: HCT116 bait 1

description: Sample name: NW044.NW28H077ent150306_MID3

source_name: HCT116, bait 1


title: HCT116 bait 5 low cell input, rep5

description: Sample name: NW042.NW28Hent009e150223_MID05


title: HCT116 bait 5 low cell input, rep4

description: Sample name: NW042.NW28Hent009d150223_MID04


title: HCT116 bait 5 low cell input, rep3

description: Sample name: NW042.NW28Hent009c150223_MID03


title: HCT116 bait 5 low cell input, rep1

description: Sample name: NW042.NW28Hent009a150223_MID01


title: HCT116 bait 5 low cell input, rep2

description: Sample name: NW042.NW28Hent009b150223_MID02


title: HCEC bait 5

description: Sample name: NW039.NWHCECH009ent150131

source_name: HCEC, bait 5


title: HCT116 bait 5, rep2

description: Sample name: NW037.NW28H009ent2150114_MID01

source_name: HCT116, bait 5


title: HCT116 bait 5, rep1

description: Sample name: NW036.NW28H009ent1150114_MID01


title: HCEC bait 5 low cell input, rep2

description: Sample name: NW045.NWHCECH009ent2_MID02


title: HCEC bait 3, bait 4, bait 6, bait 9, bait 10

description: Sample name: NW033.NWHCECHmix141210

source_name: HCEC, bait 3, bait 4, bait 6, bait 9, bait 10


title: HCT116 bait 9

description: Sample name: NW035.NONE

source_name: HCT116, bait 9


title: HCEC bait 8

description: Sample name: NW032.NWHCECH063ent141127

source_name: HCEC, bait 8


title: HCT116 bait 8

description: Sample name: NW032.NW28H063ent141127

source_name: HCT116, bait 8


title: R3: released 0.5 hours

city: Worcester

first: Kristin

last: Abramo

state: MA

address: 368 Plantation Street

country: USA

institute: University of Massachusetts Medical School

data_processing:
Mapped to hg19 human reference genome using distiller-nf mapping pipeline. For more details see methods of Abramo et al, BioRxiv 2019 (https://www.biorxiv.org/content/10.1101/678474v1) and https://github.com/mirnylab/distiller-nf.
Data was binned and balanced using cooler to obtain '.cool' contact matrices. For more details see methods of Abramo et al, BioRxiv 2019 (https://www.biorxiv.org/content/10.1101/678474v1), Abdennur & Mirny, 2019, and Imakaev et al, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: Proccessed data files are in cooler format. https://cooler.readthedocs.io/en/latest/api.html

organism: Homo sapiens

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin

extract_protocol:
For each Hi-C library, approximately 5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation
Hi-C was performed according to published protocol (Belagzhal et al., 2017)

treatment_protocol: Cells were harvested as non-synchrous without treatment, arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole (G2/M samples: t = 0 hours), or synchronized in mitosis and released for x hours.

tag: protocol

value: Hi-C

tag: enzyme

value: DpnII

value: Human adenocarcinoma cells


title: R3: asynchronous control


title: HCEC bait 5 low cell input, rep5

description: Sample name: NW045.NWHCECH009ent5_MID05


title: HCT116 bait 5 low cell input, rep9

description: Sample name: NW042.NW28Hent009i150223_MID09


title: HCT116 bait 5 low cell input, rep10

description: Sample name: NW042.NW28Hent009j150223_MID10


title: R3: G2/M sample (t = 0 hours)


title: R3: released 1.5 hours


title: R3: released 2 hours


title: R3: released 2.5 hours


title: R3: released 2.25 hours


title: R3: released 2.75 hours


title: R3: released 3.25 hours


title: R3: released 3.5 hours


title: R3: released 3 hours


title: R3: released 4.5 hours


title: R3: released 4 hours


title: R3: released 1.75 hours


title: R2: released 1 hour


title: R3: released 6 hours


title: R3: released 1 hour


title: HCT116 bait 3, bait 6, bait 10

description: Sample name: NW031.NW28HTier2mix141119

source_name: HCT116, bait 3, bait 6, bait 10


title: R2: G2/M sample (t = 0 hours)


title: R3: released 5 hours


title: R2: released 0.5 hours


title: R2: asynchronous control


title: R2: released 2 hours


title: R1: released 1.5 hours


title: R2: released 1.5 hours


title: R1: released 0.5 hours


title: R1: released 1 hour


title: R2: released 12 hours


title: R2: released 9 hours


title: R2: released 6 hours


title: R2: released 11 hours


title: R2: released 7 hours


title: R2: released 5 hours


title: R2: released 3.5 hours


title: R2: released 8 hours


title: R2: released 3 hours


title: R2: released 2.5 hours


title: R1: asynchronous control


title: R1: G2/M sample (t = 0 hours)


title: R2: released 4.5 hours


title: R2: released 4 hours


title: R2: released 10 hours


title: R1: released 1.75 hours


title: R1: released 2 hours


title: R1: released 3.25 hours


title: R1: released 3 hours


title: R1: released 2.75 hours


title: R1: released 2.5 hours


title: R1: released 2.25 hours


title: R1: released 3.5 hours


title: R1: released 4 hours


title: R1: released 5 hours


title: R1: released 6 hours


title: R1: released 8 hours


title: R1: released 4.5 hours


title: R1: released 7 hours


title: R1: released 9 hours


title: Lineage low cKit+ Sca1+ cells, SF_1630

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

library_source: transcriptomic

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCM38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
BM LKS+ from  Scl-CreERT, Scl-CreERTxCdx2, Scl-CreERT x FLT3 ITD/+ and Scl-CreERT x Cdx2 x FLT3 ITD/+ mice four weeks after tamoxifen induction
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500 Sequencer High Output mode (1 × 75 bp).

value: Lineage low cKit+ Sca1+

tag: strain

tag: tissue

value: bone marrow

tag: time point

value: 4 weeks post tamoxifen

tag: genotype

value: Scl-CreERT x FLT3 ITD/+


title: R1: released 11 hours


title: R1: released 10 hours


title: Chick_HH18_flank_rep3

city: Boston

first: John

last: Young

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: chromatin accessibility assay using Tn5 enzyme

data_processing:
Sequencing and basecalling was carried out on NextSeq_2_1_0.
Raw ATAC-seq reads were trimmed using NGmerge (https://github.com/jsh58/NGmerge) with adapter mode (-a) and a minumum overlap of 20 bases (-e 20).
Trimmed reads were aligned to droNov1 for emu and galGal4 for chicken using Bowtie2.2.4 with -X 2000.
Mitochondrial reads were removed with removeChrom (https://github.com/jsh58/harvard/blob/master/removeChrom.py) .
ATAC-seq peaks were called using MACS2 (v 2.1.0) first on individual libraries and then on pools for each species and tissue.  Significant peaks were determined as described in the supplemental methods.
Homologous regions for emu peaks were identified using halLiftover (v2.1) as described in the supplementary methods.
Young_Grayson_2019_ATAC-seq_Matrix.txt was generated using bedtools annotate (v2.25.0).  Columns are as follows: Chromosome, Start, Stop, and Size all pertain the the galGal4 genomic position of the peak; geneName is the closest annotated gene to the peak; the next 6 columns are the Chicken (C) and Emu (E) strict peak calls for flank (K), forelimb (FL), and hindlimb (HL), where the value is the proportion of the entire peak region that is overlapped by that dataset; the next 18 columns are the individual libraries for each species and tissue as described for the strict datasets; the next 15 columns are the porportion of the entire peak region that overlaps with previously-published ChIP-seq datasets for chicken (Seki et al. 2017); CNEE is the porportion of overlap of the entire peak region with Conserved Non-Exonic Elements described in Sackton et al. 2019.
Genome_build: droNov1, galGal4
Supplementary_files_format_and_content: strict_(species)_(tissue)_annotate.txt files represent peaks that were present across all three biological replicates for a given species and tissue,

organism: Gallus gallus

source_name: embryonic HH18 flank somatopleure

extract_protocol:
Tissue was dissected from each embryo in cold PBS.  Tissue was immediately transferred to 1x Trypsin in EDTA Solution (Sigma) for 10-15 minutes at room temperature. Following trypsinization, the tissue was transferred to a neutralizing culture media (DMEM (Gibco) with 10% FBS (Gibco) and 1% Pen Strep (Gibco)) and pipette-mixed until homogenized. Homogenate was filtered through 35µm nylon mesh filters and filtrate was taken immediately to cell counting.
50,000 live cells were utilized for ATAC-seq tagmentation as described in Buenrostro et al. (2015).  Following tagmentation clean-up, 11 cycles of PCR were carried out and PCR products were cleaned using the Minelute PCR Purification Kit (QIAGEN).

tag: developmental stage

value: flank somatopleure


title: Chick_HH18_forelimb_rep1

source_name: embryonic HH18 forelimb somatopleure

value: forelimb somatopleure


title: Chick_HH18_hindlimb_rep2

source_name: embryonic HH18 hindlimb somatopleure

value: hindlimb somatopleure


title: Chick_HH18_flank_rep1


title: Untreated rep1

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
fastq: Illumina's HiSeq Control Software
Scan and trim bridge linker of paired-end reads using the trimLinker program (part of ChIA-PET2) with options, reads containing at least one instance of the bridge-linker sequence at either end are adapted for the next step.
For BAT Hi-C data, mapping, pair-matching and filtering were done using the HiC-Pro pipeline
Convert HiC-pro output *allValidPairs files into the Juicer compatible .hic format using the hicpro2juicebox function
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (.hic) were generated useing juicebox pre

source_name: mouse embryonic stem cells

growth_protocol: For cells grown to proper confluency, harvest the cells in 10 ml volume of fresh culture medium with 1 million cells per milliliter. Add 278 μl of 37% methanol-free formaldehyde solution to obtain a final concentration of 1% (vol/vol), and gently shake at room temperature for 10 min

extract_protocol:
BAT Hi-C experiment were conducted in two biological replicates using AluI, and we used a final concentration of 1% formaldehyde to crosslink DNA-DNA interactions bridged by proteins. DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Jie et al. Methods 2019
Given that PCR overamplification would reduce the complexity of BAT Hi-C libraries, we selected an optimal amount of PCR cycles by PCR titration

value: mES

tag: restriction enzyme

value: AluI


title: Chick_HH18_flank_rep2


title: BSPP_targeted_bisulfIte_methyl_Seq 136

city: la jolla

first: Brian

last: Reilly

state: CA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

data_processing:
Raw sequencing reads were trimmed for 1) BSPP capture arm sequences, 2) any illumina adapter sequences and 3) low quality base-calls using TrimGalore v.0.4.0 with settings ‘--stringency 5 –phred33 –suppress_warn –dont_gzip --paired --clip_R1 27 --clip_R2 27’
BSPP reads were aligned to hg19 genome using BisReadMapper v.1.4 which utilized the Burroughs-Wheeler algorithm mem version 0.7.12 with options ‘-B2 -c1000’
overlapping read segments were clipped using BamUtils (v.1.0.13) ClipOverlaps function
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: methylScore files were generated using custom scripts from BAM files; each methylScore file has columns for chromosome=“chr”; genomic coordinate = “base”;  genome strand = “strand”; read coverage of base = “coverage”; frequency that base was observed to be methylated =  “freqC”; frequency that base was observed to be unmethylated = “freqT”

source_name: Bone marrow mononuclear cells

extract_protocol:
Bone marrow aspirates were processed by Ficoll-Hypaque to isolate mononuclear cell fractions which were then processed for genomic DNA extraction.
Bisulfite padlock probe libraries were constructed following published protocols (Diep et al., Nature Methods volume 9, pages 270–272 (2012) ) to produce sequencing libraries compatible with the Illumina sequencing platform.

tag: gender

value: M

tag: karyotype

value: Normal

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: BMMC

value: intermediate

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: Chick_HH18_hindlimb_rep1

tag: developmental stage

tag: tissue


title: Untreated rep2

tag: cell type

tag: restriction enzyme


title: Chick_HH18_forelimb_rep3


title: BSPP_targeted_bisulfIte_methyl_Seq 137

tag: gender

tag: karyotype

tag: fab

value: CMML

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: low

tag: treatment

value: Dec x1

tag: atrx

tag: bcor


title: BSPP_targeted_bisulfIte_methyl_Seq 140

value: F

value: MDS-U

value: high

value: Azacitidine

value: NR

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb


title: BSPP_targeted_bisulfIte_methyl_Seq 141

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 138

value: RCMD

tag: hgb

tag: platelet

tag: treatment

value: SD

tag: atrx

tag: bcor

tag: braf

tag: cbl


title: BSPP_targeted_bisulfIte_methyl_Seq 134

value: Complex

value: HI

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: Chick_HH18_forelimb_rep2

tag: developmental stage

tag: tissue

value: forelimb somatopleure


title: R1: released 12 hours

tag: protocol

value: Hi-C

tag: enzyme

value: DpnII

tag: cell line

value: Human adenocarcinoma cells


title: Chick_HH18_hindlimb_rep3

value: hindlimb somatopleure


title: BSPP_targeted_bisulfIte_methyl_Seq 132

tag: gender

value: M

tag: karyotype

tag: fab

value: RCUD

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: BMMC

tag: treatment

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 131

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 130

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

value: intermediate


title: BSPP_targeted_bisulfIte_methyl_Seq 135

tag: platelet

tag: treatment

value: PR

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 133

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 139

tag: gender

value: F

tag: karyotype

tag: fab

tag: wbc

tag: anc

value: high

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 129

value: Normal

value: RARS

tag: mono

tag: hgb

tag: platelet

value: low

tag: treatment

value: Azacitidine

tag: atrx

tag: bcor

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 128

value: RAEB

value: Decitabine

value: NR

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 126

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

value: CRp

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 127

value: CMML

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: CR

tag: atrx

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 124

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: pten


title: GAR020413.F17.F2.106b

type: RNA

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Array hybridization were performed per recommended specifications

scan_protocol: Scanning were performed per recommended specifications

data_processing: Raw data in .CEL were processed using the R/Bioconductor package affy; background correction: normexp; quantile normalization: RMA

label: biotin

label_protocol: Biotin labeling per Affymetrix Protocol

extract_protocol:
Sample collection protocol: Blood samples were collected from COMET-IPF participants at study entry
Trizol extraction / Qiagen RNeasy Micro cleanup; Blood samples were collected from IPF patients enrolled in COMET cohort at study entry. PBMCs were isolated by Ficoll-Paque Plus (GE Healthcare Life Science, Pittsburgh, PA) and stored in TRIzol reagent (Thermo Fisher Sci., Waltham, MA). RNA was extracted following manufacturer’s protocol and was re-precipitated by sodium acetate/ethanol.

tag: age

tag: gender

value: M

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

tag: tissue

value: PBMC


title: BSPP_targeted_bisulfIte_methyl_Seq 123

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: BMMC

tag: treatment

value: PD

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: GAR082812.148.COMET.105.PrimeView.101812

tag: age

tag: gender

tag: ethnicity

tag: smoker

value: Baseline


title: GAR082812.149.COMET.105.FU1.PrimeView.101812

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413.F05.COMET.106


title: GAR020413.F12.F1.107

value: F


title: GAR020413.F16.F2.104


title: GAR082812.150.COMET.105.FU2.PrimeView.101812


title: BSPP_targeted_bisulfIte_methyl_Seq 122

tag: karyotype

value: Normal

tag: fab

tag: wbc

tag: anc

value: SD

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: mpl

tag: nras

tag: pten


title: GAR020413.F06.COMET.107

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.147.COMET.102.FU3.PrimeView.101812

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413.F19.F3.104


title: GAR020413.F10.F1.104


title: GAR020413.F04.COMET.104


title: GAR082812.143.COMET.101.FU2.PrimeView.101812


title: GAR020413.F18.F2.107


title: GAR020413.F11.F1.106


title: GAR082812.146.COMET.102.FU2.PrimeView.101812


title: GAR082812.145.COMET.102.FU1.PrimeView.101812


title: BSPP_targeted_bisulfIte_methyl_Seq 125

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: high

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: GAR082812.144.COMET.102.PrimeView.101812

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.142.COMET.101.FU1.PrimeView.101812

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.141.COMET.101.PrimeView.101612


title: GAR020413.F20.F3.106


title: BSPP_targeted_bisulfIte_methyl_Seq 121

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: mpl

tag: nras

tag: pten


title: GAR082812.138.COMET.100.FU1.PrimeView.101612

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 118

tag: karyotype

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: Azacitidine

value: HI

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 119

tag: fab

value: RA

tag: wbc

tag: anc

value: low

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: mpl


title: BSPP_targeted_bisulfIte_methyl_Seq 117

tag: gender

tag: karyotype

value: RAEB

tag: mono

tag: hgb

tag: platelet

value: intermediate

value: Decitabine

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 116

value: M

tag: fab

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: GAR082812.140.COMET.100.FU3.PrimeView.101612

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 115

tag: gender

tag: karyotype

value: Other

tag: wbc

tag: anc

tag: mono

tag: hgb

value: PR

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: mpl


title: GAR082812.139.COMET.100.FU2.PrimeView.101612

tag: age

tag: ethnicity

tag: smoker

value: PBMC


title: BSPP_targeted_bisulfIte_methyl_Seq 120

tag: fab

tag: platelet

value: BMMC

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: nras

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 114

tag: gender

tag: karyotype

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: BSPP_targeted_bisulfIte_methyl_Seq 112

tag: fab

tag: platelet

tag: treatment

value: mCR

tag: atrx

tag: cebpa

tag: eed

tag: mpl


title: BSPP_targeted_bisulfIte_methyl_Seq 113

tag: gender

tag: gnas

tag: kras

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR082812.136.COMET.99.FU3.PrimeView.102612

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.134.COMET.99.FU1.PrimeView.102612


title: GAR082812.132.COMET.98.FU3.PrimeView.101212


title: GAR082812.133.COMET.99.PrimeView.102612

value: Baseline


title: GAR082812.137.COMET.100.PrimeView.101612


title: GAR082812.122.COMET.95.FU1.PrimeView.101612


title: GAR082812.121.COMET.95.PrimeView.101212


title: GAR082812.130.COMET.98.FU1.PrimeView.101212


title: GAR082812.135.COMET.99.FU2.PrimeView.102612


title: GAR082812.131.COMET.98.FU2.PrimeView.101212


title: GAR082812.127.COMET.97.FU2.PrimeView.101212


title: GAR082812.119.COMET.91.FU3.PrimeView.100912

value: F


title: GAR082812.129.COMET.98.PrimeView.101212


title: GAR082812.128.COMET.97.FU3.PrimeView.101212


title: GAR082812.124.COMET.95.FU3.PrimeView.101612


title: GAR082812.125.COMET.97.PrimeView.101212


title: GAR082812.118.COMET.91.FU2.PrimeView.100912


title: BSPP_targeted_bisulfIte_methyl_Seq 110

tag: karyotype

value: Normal

tag: fab

value: RARS

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: SD

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: BSPP_targeted_bisulfIte_methyl_Seq 107

tag: gender

value: NA  (complex)

value: CR

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR082812.116.COMET.91.PrimeView.100912

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 106

tag: karyotype

tag: fab

value: RA

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: HI

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: GAR082812.115.COMET.89.FU3.PrimeView.100912

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.117.COMET.91.FU1.PrimeView.100912

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.112.COMET.89.PrimeView.100912


title: GAR082812.113.COMET.89.FU1.PrimeView.100912


title: GAR082812.126.COMET.97.FU1.PrimeView.101212


title: BSPP_targeted_bisulfIte_methyl_Seq 109

tag: karyotype

tag: fab

value: CMML

tag: wbc

tag: anc

value: Decitabine

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413.E06.COMET.88

tag: age

tag: gender

value: M

tag: ethnicity

tag: smoker

value: IPF


title: GAR082812.114.COMET.89.FU2.PrimeView.100912

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413.E16.F2.88.PrimeView.082213


title: BSPP_targeted_bisulfIte_methyl_Seq 104

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: NE

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: BSPP_targeted_bisulfIte_methyl_Seq 105

tag: gender

value: RAEB

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413.E10.F1.88b.PrimeView.082213

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue

value: PBMC


title: BSPP_targeted_bisulfIte_methyl_Seq 108

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: BMMC

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: BSPP_targeted_bisulfIte_methyl_Seq 103

tag: gender

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413E.catchup.86.FU1.PrimeView.NL.100113

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413.E05.COMET.86c.PrimeView.082213

value: Baseline


title: GAR082812.123.COMET.95.FU2.PrimeView.101612


title: BSPP_targeted_bisulfIte_methyl_Seq 111

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: GAR020413.E15.F2.86.PrimeView.082213

tag: age

tag: gender

value: F

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 100

tag: karyotype

value: Other

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413.E20.F3.85.PrimeView.082213

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.111.COMET.84.FU3.PrimeView.100512

tag: age


title: GAR082812.110.COMET.84.FU2.PrimeView.100512

tag: gender


title: BSPP_targeted_bisulfIte_methyl_Seq 101

value: Normal

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: GAR020413.E04.COMET.85.PrimeView.082213

tag: ethnicity

tag: smoker

tag: diagnosis


title: BSPP_targeted_bisulfIte_methyl_Seq 98

tag: karyotype

value: SD

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 99

tag: gender

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor


title: BSPP_targeted_bisulfIte_methyl_Seq 97

tag: karyotype

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas


title: BSPP_targeted_bisulfIte_methyl_Seq 96

tag: gender

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: Aptamer-3

city: Coimbatore

first: Nikhil

last: Maroli

state: TAMIL NADU

address: Bharathiar University

department: Physics

country: India

institute: DRDO BU CLS

description: The aptamer-3 processed from the forward and reverse scanned raw file

data_processing:
ssDNA sequence retrieval from sequence scanner software v2.0
ssDNA linear chain generation using Discover studio 2016 version
MD simulation of the linear ssDNA using Gromacs 2018 version and generation of 3D structure
MD simulation of aptamer against amyloid-β peptide
Supplementary_files_format_and_content: PDB files contains the three dimensional structure of the aptamer

source_name: Aptamer library

extract_protocol:
ssDNA aptamers specific towards amyloid-β was selected by SELEX strategy from random aptamer library.
The amyloid-β specific ssDNA selected was cloned into pGMET vector by TA cloning strategy and sequenced.

tag: sample type

value: synthetic construct

tag: molecule subtype

value: ssDNA


title: Aptamer-2

description: The aptamer-2 processed from the forward and reverse scanned raw file


title: 6_751: NPC

city: Guangzhou

first: Ying

last: Sun

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer. The mixture was heated at 60 °C for 30 min. 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed LncRNAs and mRNAs between the high and low metastatic potential cell lines (5-8F vs. 6-10B and S18 vs. S26) were identified through Fold Change and Normalized Intensities filtering.

source_name: nasopharyngeal carcinoma tissue

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each mRNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing random priming. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the 6 tissues using QIAGEN FFPE RNeasy kit (QIANGEN, Hilden, Germany) according to the manufacturer’s instructions. mRNA was purified from the total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: tissue

value: nasopharyngeal carcinoma


title: BSPP_targeted_bisulfIte_methyl_Seq 95

tag: karyotype

value: Complex

tag: fab

value: RARS

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor


title: GAR082812.109.COMET.84.FU1.PrimeView.100512

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time


title: GAR082812.108.COMET.84.PrimeView.100512

tag: tissue


title: GAR020413.E14.F2.85.PrimeView.082213


title: Aptamer-1

description: The aptamer-1 processed from the forward and reverse scanned raw file

tag: sample type

tag: molecule subtype


title: GAR020413C.C17b.F2.83b.PrimeView.080213


title: 2_GX6: Normal

source_name: normal nasopharynx tissues

value: normal nasopharynx tissues


title: 4_662: NPC


title: GAR020413C.C11b.F1.82.PrimeView.080213


title: 5_667: NPC


title: 1_GX5: Normal


title: BSPP_targeted_bisulfIte_methyl_Seq 102

value: M

tag: karyotype

tag: fab

tag: wbc

value: Decitabine

value: PD

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 93

tag: gender

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

value: HI

tag: atrx

tag: bcor


title: BSPP_targeted_bisulfIte_methyl_Seq 94

tag: karyotype

tag: fab

value: CMML

tag: wbc

value: mCR

tag: braf

tag: cbl

tag: cblb

tag: cebpa


title: GAR020413C.C6b.COMET.83B.PrimeView.080213

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

value: Baseline

tag: tissue

value: PBMC


title: BSPP_targeted_bisulfIte_methyl_Seq 91

tag: gender

value: F

value: RAEB

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 90

tag: karyotype

tag: fab

value: RA

tag: wbc

value: high

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa


title: BSPP_targeted_bisulfIte_methyl_Seq 89

tag: gender

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: eed

tag: gnas


title: BSPP_targeted_bisulfIte_methyl_Seq 92

tag: karyotype

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413C.C5b.COMET.82.PrimeView.080213

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413C.C12b.F1.83.PrimeView.080213

tag: gender


title: BSPP_targeted_bisulfIte_methyl_Seq 88

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa


title: BSPP_targeted_bisulfIte_methyl_Seq 84

tag: karyotype

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 86

tag: gender

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet


title: GAR082812.104.COMET.81b.PrimeView.100212

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.106.COMET.81.FU2.PrimeView.100212


title: GAR082812.103.COMET.79.FU3.PrimeView.0928.12


title: GAR020413C.C22b.F3.82.PrimeView.080213


title: BSPP_targeted_bisulfIte_methyl_Seq 85

tag: karyotype

value: RAEBT

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: GAR082812.101.COMET.79.FU1.PrimeView.0928.12

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.105.COMET.81.FU1.PrimeView.100212

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.107.COMET.81.FU3.PrimeView.100212


title: GAR082812.102.COMET.79.FU2.PrimeView.0928.12


title: BSPP_targeted_bisulfIte_methyl_Seq 83

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: intermediate

tag: treatment

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: AE05_JINB-exosome2_mRNA

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols. For microRNAs, 1 microgram of total RNAs was labeled with Affymetrix FlashTag kit using normal affymetrix procedure for labeling, hybridization, staining and scanning.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: JinB8 exosome

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: WT (JK) and CD47- (JINB8) T cells (25x106) were cultured using HITES medium (90% Ham's F-12, 10% RPMI 1640 medium, 5 mM HEPES, 2 mM glutamine, 0.1% BSA, 5 μg/ml insulin, 5 ng/ml sodium selenite, 5 μg/ml transferrin (Thermo Fisher Scientific, Waltham, MA), 200 nM hydrocortisone Sigma Aldrich, St. Louis, MO) for 24-48 h at 37°C. The cells were harvested by centrifugation at 1300 RPM for 5 minutes. Cell pellets were washed with 1X PBS for 5 minutes and used for total RNA extraction. Cell supernatants were collected into new tubes and centrifuged at 395xg (1300 RPM) for 5 minutes. Cell supernatants were collected into new tubes and centrifuged for 10 minutes at 2103xg using using Thermo Sorvall Legend XTR (3000 RPM). The supernatants were concentrated using Centrcon-YM-10 filters to 500 µl. The EVs were precipitated using the Exo-quick kit (SBI System Bioscience, Palo Alto, CA) or Exo-spin™ kit (Cell Guidance Systems, St. Louis, MO ) according to the manufacturer’s instructions. The precipitated EVs were used for isolating total RNA and/or miRNA for real time PCR analysis.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

tag: cell line

tag: cell compartment

value: exosome

tag: cell type

value: T lymphocyte

tag: genotype

tag: diet

value: ND


title: AE06_JINB-exosome3_mRNA


title: AE04_JINB-exosome1_mRNA


title: GAR082812.98.COMET.75.FU2.PrimeView.0928.12

tag: age

tag: gender

value: M

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.99.COMET.75.FU3.PrimeView.0928.12


title: BSPP_targeted_bisulfIte_methyl_Seq 81

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: low

tag: treatment

tag: atrx

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: GAR082812.97.COMET.75.FU1.PrimeView.0928.12

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: 3_GX8: Normal

value: normal nasopharynx tissues


title: GAR082812.96.COMET.75.PrimeView.0928.12


title: BSPP_targeted_bisulfIte_methyl_Seq 87

tag: karyotype

tag: fab

value: RARS

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: AE03_JK-exosome3_mRNA

source_name: JK exosome

tag: cell line

value: JK

tag: cell compartment

tag: cell type

tag: genotype

tag: diet


title: AE01_JK-exosome1_mRNA


title: GAR082812.100.COMET.79b.PrimeView.0928.12

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 82

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 80

tag: gender

tag: karyotype

tag: fab

tag: bcor

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 78

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx


title: AE02_JK-exosome2_mRNA

tag: cell line

tag: cell compartment

tag: cell type

tag: genotype

tag: diet


title: BSPP_targeted_bisulfIte_methyl_Seq 77

tag: gender

tag: karyotype

value: negY

tag: fab

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 79

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: GAR082812.94.COMET.74.FU2.PrimeView.092112

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue

value: PBMC


title: BSPP_targeted_bisulfIte_methyl_Seq 76

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: GAR082812.95.COMET.74.FU3.PrimeView.092112

tag: age

tag: gender

value: F

tag: ethnicity

tag: smoker


title: GAR082812.93.COMET.74.FU1.PrimeView.092112

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 75

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 74

tag: gender

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 73

tag: karyotype

tag: fab

value: RAEB

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet


title: BSPP_targeted_bisulfIte_methyl_Seq 72

tag: gender

tag: treatment

tag: atrx

tag: bcor

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 71

value: RA

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 70

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: mpl

tag: nras


title: GAR082812.92.COMET.74.PrimeView.092112

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

value: Baseline

tag: tissue


title: GAR082812.86.COMET.72.FU2.PrimeView.011713


title: GAR082812.85.COMET.72.FU1.PrimeView.011713


title: GAR082812.87.COMET.72.FU3.PrimeView.011713


title: BSPP_targeted_bisulfIte_methyl_Seq 69

value: Normal

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: pten

tag: flnb

tag: utx


title: GAR082812.82.COMET.71.FU2.PrimeView.091312

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.81.COMET.71.FU1.PrimeView.091312

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413C.C21b.F3.69.PrimeView.080213


title: GAR020413C.C16b.F2.69.PrimeView.080213


title: BSPP_targeted_bisulfIte_methyl_Seq 63

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 68

tag: gender

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 67

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet


title: BSPP_targeted_bisulfIte_methyl_Seq 64

tag: gender

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: mpl

tag: nras


title: GAR082812.83.COMET.71.FU3.PrimeView.091312

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.84.COMET.72.PrimeView.011713


title: GAR082812.80.COMET.71.PrimeView.091312


title: BSPP_targeted_bisulfIte_methyl_Seq 66

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 60

tag: gender

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 61

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl


title: BSPP_targeted_bisulfIte_methyl_Seq 59

tag: gender

tag: cblb

tag: cebpa

tag: eed

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 65

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 58

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 57

tag: gender

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: pten


title: GAR020413C.C4b.COMET.69.PrimeView.080213

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 62

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: GAR082812.78.COMET.67.FU2.PrimeView.091312

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.76.COMET.67b.PrimeView.091312

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413C.C10b.F1.69.PrimeView.080213


title: GAR082812.77.COMET.67.Fu1.PrimeView.091312


title: GAR020413.D15.F1.68.PrimeView.082013


title: BSPP_targeted_bisulfIte_methyl_Seq 53

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 52

tag: gender

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: gnas

tag: kras

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 55

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl


title: GAR020413.D07.COMET.68b.PrimeView.082013

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 54

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 51

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: flnb

tag: utx


title: GAR020413.D24.F3.68.PrimeView.082013

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413.D14.F1.66.PrimeView.082013


title: GAR020413.D06.COMET.66.PrimeView.082013


title: GAR082812.79.COMET.67.FU3.PrimeView.091312


title: GAR020413.D18.F2.65.PrimeView.082013


title: GAR082812.75.COMET.64.FU3.PrimeView.101612


title: BSPP_targeted_bisulfIte_methyl_Seq 56

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR082812.74.COMET.64.FU2.PrimeView.101612

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 50

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: bcor

tag: braf

tag: cbl

tag: flnb

tag: utx


title: GAR020413.D19.F2.66b.PrimeView.082013

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 49

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR020413.D23.F3.65.PrimeView.082013

tag: age

tag: gender


title: GAR082812.72.COMET.64b.PrimeView.101612

tag: ethnicity

tag: smoker

tag: diagnosis


title: BSPP_targeted_bisulfIte_methyl_Seq 48

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 47

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR020413.D13.F1.65.PrimeView.082013

tag: age

tag: gender

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 46

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: flnb

tag: utx


title: Sirena1_MII_WT_r3

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Reads were mapped onto indexed mm10 genome using STAR 2.5.3a: STAR --readFilesIn ${FILE}.txt.gz --genomeDir $ REF_GENOME_INDEX --runThreadN 10 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz -c --outFileNamePrefix ${FILE}. --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.2 --sjdbScore 2
Counts of reads over genomic coordinates were computed in R over exon coordinats from .gtf annotation file downloaded from Ensembl Release 93: GenomicAlignments::summarizeOverlaps(features = ensembl_gtf.genomicRangesList reads = bamfiles, mode = "Union", singleEnd = TRUE, ignore.strand = FALSE)
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC: genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content:
ensembl.93.GRCm38.p6.Sirena1_KO.raw_counts.csv:
- .csv table with counts of reads over exon coordinats from Ensembl Release 93 .gtf file
- samples are in columns, genes in rows
coverage genome browser tracks files:
- .bigWig format
- generated in a non-stranded mode.
- not normalized for library size

molecule: polyA RNA

source_name: MII egg, WT, replicate 3

growth_protocol: Fully grown, germinal vesicle (GV)-intact oocytes rom superovulated C57Bl6/J or C57BL/6NCrl mice as described previously (Nagy A, (2003) Manipulating the mouse embryo: a laboratory manual pp Cold Spring Harbor Laboratory Press). GV Oocytes were collected in M2 medium (Sigma-Aldrich) with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX; Sigma). MII eggs are collected in M2 media, 12-14hrs post HCG injection. 25 GV oocytes and MII eggs were collected per sample.

extract_protocol:
Total RNA was extracted from 25 oocytes using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific). Each sample was spiked in with 0.2 pg synthesized Renilla luciferase mRNA before extraction as a normalization control.
Libraries were constructed using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN). RNA-Seq libraries were pooled and sequenced by 65 bp single-end reading using Illumina HiSeq

treatment_protocol: LncRNA deletion mutant models were produced in the Transgenic Unit of the Institute of Molecular Genetics ASCR, Czech Centre for Phenogenomics using Cas9-mediated deletion of lncRNA promoters. Sequences of guide RNAs are listed in the publication. To produce guide RNAs, synthetic 128 nt guide RNA templates including T7 promoter, 18nt sgRNA and tracrRNA sequences were amplified using T7 and TracrRNA primers. Guide RNAs were produced in vitro using the Ambion mMESSAGE mMACHINE T7 Transcription Kit, and purified using the mirPremier™ microRNA Isolation Kit (Sigma). The Cas9 mRNA was synthesized from pSp Cas9-puro plasmid using Ambion mMESSAGE mMACHINE T7 Transcription Kit, and purified using the Qiagen RNasy mini kit. A sample for microinjection was prepared by mixing two guide RNAs in ultra-pure water at a concentration of 25ng/μl for each one together with Cas9 RNA (100 ng/μl). Five picoliters of the microinjection mixture were injected into male pronuclei of C57Bl/6 zygotes and transferred into pseudo pregnant recipient mice. After two generations of breeding with C57BL/6NCrl animals, the heterozygotes were used for producing Sirena1–/– animals for phenotype analysis.

tag: developmental stage

value: MII egg

tag: genotype

value: WT

tag: strain


title: GAR082812.73.COMET.64.FU1.PrimeView.101612

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis


title: BSPP_targeted_bisulfIte_methyl_Seq 43

tag: karyotype

tag: fab

tag: wbc

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 44

tag: gender

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 42

tag: karyotype

tag: fab

tag: wbc

tag: platelet

tag: treatment

tag: atrx

tag: cblb


title: BSPP_targeted_bisulfIte_methyl_Seq 41

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 40

tag: gender

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl


title: Sirena1_MII_WT_r1

source_name: MII egg, WT, replicate 1

tag: developmental stage

tag: genotype

tag: strain


title: Sirena1_MII_Null_r4

source_name: MII egg, Sirena1 Null, replicate 4

value: Sirena1 Null


title: Sirena1_MII_Null_r3

source_name: MII egg, Sirena1 Null, replicate 3


title: BSPP_targeted_bisulfIte_methyl_Seq 45

tag: karyotype

tag: fab

tag: wbc

tag: platelet

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: flnb

tag: utx


title: GAR082812.69.COMET.62.PrimeView.020113

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: Sirena1_MII_WT_r2

source_name: MII egg, WT, replicate 2

tag: developmental stage

tag: genotype

tag: strain


title: BSPP_targeted_bisulfIte_methyl_Seq 39

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: bcor

tag: braf

tag: cbl

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: Sirena1_MII_Null_r1

source_name: MII egg, Sirena1 Null, replicate 1

tag: developmental stage

tag: genotype

tag: strain


title: Sirena1_MII_Null_r2

source_name: MII egg, Sirena1 Null, replicate 2


title: BSPP_targeted_bisulfIte_methyl_Seq 37

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: treatment

tag: atrx

tag: cblb

tag: cebpa

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 38

tag: anc

tag: mono

tag: hgb

tag: platelet

value: high

tag: bcor

tag: braf

tag: cbl

tag: eed

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 36

tag: gender

value: M

tag: karyotype

tag: fab

tag: wbc

tag: mpl

tag: nras

tag: pten


title: GAR082812.66.COMET.61.FU1.PrimeView.101612

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.65.COMET.61b.PrimeView.101612


title: GAR082812.70.COMET.62.FU1.PrimeView.020113


title: GAR082812.64.COMET.59.FU3.PrimeView.101212


title: GAR020413.D04.COMET.60.PrimeView.082013


title: GAR020413.D22.F3.60.PrimeView.082013


title: Sirena1_GV_WT_r2

source_name: GV oocyte, WT, replicate 2

tag: developmental stage

value: GV oocyte

tag: genotype

tag: strain


title: GAR082812.68.COMET.61.FU3.PrimeView.101612


title: GAR020413.D11.F1.60.PrimeView.082013


title: GAR082812.67.COMET.61.FU2.PrimeView.101612


title: BSPP_targeted_bisulfIte_methyl_Seq 35

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: flnb

tag: utx


title: Sirena1_GV_WT_r1

source_name: GV oocyte, WT, replicate 1

tag: developmental stage

tag: genotype

tag: strain


title: GAR082812.63.COMET.59.FU2.PrimeView.100912

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 34

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: mpl

tag: nras

tag: pten


title: Sirena1_GV_Null_r3

source_name: GV oocyte, Sirena1 Null, replicate 3

tag: developmental stage

tag: genotype

tag: strain


title: Sirena1_GV_WT_r3

source_name: GV oocyte, WT, replicate 3


title: BSPP_targeted_bisulfIte_methyl_Seq 33

source_name: Bone marrow mononuclear cells

tag: gender

tag: karyotype

tag: fab

tag: wbc

value: low

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: flnb

tag: utx


title: Sirena1_GV_Null_r2

source_name: GV oocyte, Sirena1 Null, replicate 2


title: BSPP_targeted_bisulfIte_methyl_Seq 32

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: GAR082812.62.COMET.59.FU1.PrimeView.101212

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 31

tag: karyotype

tag: fab

tag: wbc

tag: anc

value: intermediate

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: Miz1 deltaPOZ CD4+ T cell Tumor 76953

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

description: mRNA

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10.
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: _HTSeqCount.txt: Tab-delimited text files containing counts on GRCm38 v77 Ensembl genes.

source_name: Spleen CD4+ T cell tumour

extract_protocol:
RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with a RNA 6000 Pico kit (Agilent).
RNA-Seq libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS.

tag: strain/background

tag: genotype/variation

value: Miz1 deltaPOZ

value: Spleen CD4+ T cell tumour

tag: mouse id number


title: BSPP_targeted_bisulfIte_methyl_Seq 30

tag: gender

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb


title: GAR082812.61.COMET.59.PrimeView.100912

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

value: IPF

tag: follow-up time

tag: tissue


title: Miz1 deltaPOZ CD4+ T cell Tumor 76952

description: mRNA

tag: strain/background

tag: genotype/variation

tag: mouse id number


title: GAR082812.71.62.FU2.PrimeView.NL.093013

tag: gender

value: PBMC


title: GAR082812.60.COMET.58.FU3.PrimeView.100912


title: GAR082812.59.COMET.58.FU2.PrimeView.100912


title: BSPP_targeted_bisulfIte_methyl_Seq 28

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: cebpa

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: Miz1 wt CD4+ T cell Tumor 76971

description: mRNA

tag: strain/background

tag: genotype/variation

value: Miz1 wt

tag: tissue

tag: mouse id number


title: GAR082812.57.COMET.58b.PrimeView.100912

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time


title: Miz1 wt CD4+ T cell Tumor 76962

description: mRNA


title: Miz1 wt B cell tumor 58465

description: mRNA

source_name: Spleen B cell tumour

value: Spleen B cell tumour


title: BSPP_targeted_bisulfIte_methyl_Seq 27

value: F

tag: karyotype

tag: fab

value: RAEBT

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: cebpa

tag: eed

tag: gnas


title: Sirena1_GV_Null_r1

source_name: GV oocyte, Sirena1 Null, replicate 1

tag: developmental stage

tag: genotype

tag: strain


title: Miz1 wt B cell tumor 55996

description: mRNA

tag: strain/background

tag: genotype/variation

tag: tissue

tag: mouse id number


title: GAR020413G.23.57.FU3.PrimeView.NL.100113

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time


title: BSPP_targeted_bisulfIte_methyl_Seq 25

tag: karyotype

value: Normal

tag: fab

value: RAEB

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: Miz1 deltaPOZ B cell tumor 44969

description: mRNA

tag: strain/background

tag: genotype/variation

tag: tissue

tag: mouse id number


title: BSPP_targeted_bisulfIte_methyl_Seq 24

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: cebpa

tag: eed

tag: gnas


title: Miz1 deltaPOZ B cell tumor 44287

description: mRNA


title: BSPP_targeted_bisulfIte_methyl_Seq 29

value: RA

tag: treatment

tag: atrx

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb


title: BSPP_targeted_bisulfIte_methyl_Seq 21

tag: gender

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 22

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: eed

tag: gnas


title: BSPP_targeted_bisulfIte_methyl_Seq 26

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: kras

tag: mpl

tag: nras


title: GAR020413G.22.57.FU1.PrimeView.NL.100113

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413G.21.COMET.57b.PrimeView.NL.100113

value: Baseline


title: GAR082812.55.COMET.55.FU2.PrimeView.101212


title: GAR082812.54.COMET.55.FU1.PrimeView.101212


title: BSPP_targeted_bisulfIte_methyl_Seq 19

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

value: high

tag: treatment

tag: atrx

tag: cebpa

tag: pten

tag: flnb

tag: utx


title: GAR082812.56.COMET.55.FU3.PrimeView.101212

tag: age

tag: gender

value: M

tag: ethnicity

tag: smoker


title: GAR082812.53.COMET.55.PrimeView.101212

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 20

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: gnas

tag: kras

tag: mpl

tag: nras


title: GAR082812.58.COMET.58.FU1.PrimeView.100912

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 16

tag: karyotype

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 15

tag: fab

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: gnas

tag: kras


title: BSPP_targeted_bisulfIte_methyl_Seq 18

tag: gender

tag: karyotype

tag: mono

tag: hgb

tag: platelet

tag: mpl

tag: nras


title: BSPP_targeted_bisulfIte_methyl_Seq 17

tag: fab

tag: treatment

tag: atrx

tag: cebpa

tag: pten

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 23

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed


title: GAR082812.49.COMET.54.PrimeView.020113

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 13

tag: karyotype

tag: fab

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 14

tag: gender

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: flnb

tag: utx


title: GAR020413G.20.53.FU3.PrimeView.NL.100113

tag: age

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 12

tag: karyotype

tag: fab

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR020413.D17.F2.60.PrimeView.082013

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 11

tag: karyotype

tag: wbc

tag: anc

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: flnb

tag: utx


title: GAR020413G.19.53.FU2.PrimeView.NL.100113

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR082812.50.COMET.54.FU1.PrimeView.020113

tag: age


title: GAR020413G.17.COMET.53.PrimeView.NL.100113

tag: gender


title: GAR082812.52.COMET.54.FU3.PrimeView.020113

tag: ethnicity


title: BSPP_targeted_bisulfIte_methyl_Seq 10

tag: fab

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR020413G.18.53.FU1.PrimeView.NL.100113

tag: smoker

tag: diagnosis

tag: follow-up time


title: GAR020413G.16.51.FU3.PrimeView.NL.100113

tag: age

tag: gender

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 9

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: flnb

tag: utx


title: BSPP_targeted_bisulfIte_methyl_Seq 8

tag: hgb

tag: platelet

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: GAR020413G.14.51.FU1.PrimeView.NL.100113

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 6

tag: karyotype

value: -5q inv3q

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed

tag: flnb

tag: utx


title: GAR020413G.13.COMET.51.PrimeView.NL.100113

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: BSPP_targeted_bisulfIte_methyl_Seq 5

tag: karyotype

tag: platelet

value: low

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten


title: BSPP_targeted_bisulfIte_methyl_Seq 4

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed


title: GAR020413B.B17.F2.50.PrimeView.071913

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413G.15.51.FU2.PrimeView.NL.100113


title: BSPP_targeted_bisulfIte_methyl_Seq 2

tag: karyotype

tag: fab

tag: platelet

value: intermediate

tag: treatment

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413B.B6.50B.PrimeView.071913

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR082812.51.COMET.54.FU2.PrimeView.020113

tag: diagnosis

tag: follow-up time

tag: tissue


title: BSPP_targeted_bisulfIte_methyl_Seq 7

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed


title: GAR020413B.B12.F1.50.PrimeView.071913

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR020413B.B21.F3.48.PrimeView.071913

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413B.B16.F2.49.PrimeView.071913


title: BSPP_targeted_bisulfIte_methyl_Seq 1

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: atrx

tag: cebpa

tag: gnas

tag: kras

tag: mpl

tag: nras

tag: pten

tag: flnb

tag: utx


title: GAR020413B.B22.F3.49.PrimeView.071913

tag: age

tag: gender

tag: ethnicity

tag: smoker


title: GAR020413B.B11.F1.49.PrimeView.071913

tag: diagnosis

tag: follow-up time

tag: tissue


title: GAR020413B.B5.49.PrimeView.071913


title: GAR020413B.B23.FU3.50.PrimeView.071913


title: BSPP_targeted_bisulfIte_methyl_Seq 3

tag: karyotype

tag: fab

tag: wbc

tag: anc

tag: mono

tag: hgb

tag: platelet

tag: treatment

tag: bcor

tag: braf

tag: cbl

tag: cblb

tag: eed


title: HCT116 H3K27me3, rep2

data_processing:
Reads were aligned to hg19 using bwa v0.7.12 (bwasw) using default settings. Reads with MAPQ > 30 were summarized over windows of 1,000 bp.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: .bed: Coverage

source_name: HCT116, H3K27me3 ChIP

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life Technologies). Cells were cultured under 5% CO2 circumstance at 37 C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at RT and excess amount of formaldehyde was captured by 0.125 M Glycine. DNA-protein complexes were immunopurified using antibodies to H3K27me3 (Diagenode, CS-069-100), and Dynabeads Protein G (21004D, Invitrogen) by conventional method with slight modification with biological replicate. The immune-complex was reverse crosslinked and associated DNA was purified with ChIP DNA Clean and Concentrator (Zymo research, D5205).
Sequencing library construction was performed using TruSeq ChIP sample prep kit (Illumina, IP-202-1012) by following the manufacturer's instruction with 6-8 ng of ChIPed DNA. To assess the quality of the library, amplified DNA was subjected on DNA 1000 chip (Agilent, 5017-1504).

tag: cell line

tag: cell type

value: human colorectal carcinoma cell line

tag: chip antibody


title: GAR020413B.B15.F2.48.PrimeView.071913

tag: age

tag: gender

tag: ethnicity

tag: smoker

tag: diagnosis

tag: follow-up time

tag: tissue


title: HCT116 H3K27me3, rep1


title: GAR020413.Comet.47.FU3.PrimeView.022013


title: GAR020413A.Comet.47.FU1.PrimeView.021513


title: GAR020413.Comet.46.FU2.PrimeView.022013


title: GAR020413A.Comet.46.PrimeView.021513


title: GAR020413.Comet.45.FU2.PrimeView.022013


title: GAR020413.Comet.47.FU2.PrimeView.022013


title: GAR020413.Comet.46.FU3.PrimeView.022013


title: GAR020413A.Comet.46.FU1.PrimeView.021513


title: GAR020413.Comet.45.FU3.PrimeView.022013


title: GAR020413B.B10.F1.48.PrimeView.071913


title: GAR020413.F03.COMET.44


title: GAR020413.F09.F1.44


title: GAR082812.44.COMET.40.FU1.PrimeView.100512


title: GAR020413.F15.F2.44


title: GAR020413A.Comet.45.FU1.PrimeView.021513


title: GAR020413.F14.F2.43


title: GAR082812.43.COMET.40.PrimeView.100512


title: GAR020413.F02.COMET.43c


title: GAR020413A.Comet.45.PrimeView.021513


title: GAR020413.F13.F2.39


title: STAT3 knock out hESCs-intestinal organoid + IL-2

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: Gene expression of IL-2 treated human intestinal organoids differentiated from STAT3 knock out human embryonic stem cells using CRISPR/Cas9-mediated gene editing

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

source_name: Human embryonic stem cell, STAT3 knock out, hIO differentiation

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Intestinal organoid


title: GAR020413.F07.F1.39

value: IPF


title: GAR020413.F08.F1.43

value: PBMC


title: Human small intestine

description: Gene expression of adult human small intestine tissue

source_name: Human small intestine

value: Small intestine


title: STAT3 knock out hESCs-intestinal organoid + co-culture

description: Gene expression of co-cultured human intestinal organoids differentiated from STAT3 knock out human embryonic stem cells using CRISPR/Cas9-mediated gene editing


title: GAR020413.F01.COMET.39


title: GAR082812.45.COMET.40.FU3.PrimeView.100512


title: Wild type hESCs-intestinal organoid + IL-2

description: Gene expression of IL-2 treated human intestinal organoids differentiated from wild type human embryonic stem cells

source_name: Human embryonic stem cell, wild type, hIO differentiation


title: GAR020413.E19.F3.38.PrimeView.082213


title: STAT3 knock out hESCs-intestinal organoid

description: Gene expression of human intestinal organoids differentiated from STAT3 knock out human embryonic stem cells using CRISPR/Cas9-mediated gene editing


title: GAR020413.E09.F1.38.PrimeView.082213


title: GAR020413.E13.F2.38.PrimeView.082213


title: Array24_pig # 2 dye swap 2

city: Orient

first: James

middle: J.

last: Zhu

state: NY

department: Foreign Animal Disease Research Unit

institute: USDA-ARS

hyb_protocol: Oligoarray DNA microarrays and hybridization chambers were manufectured by Agilent Technologies.  Array hybridization was conducted using hybridization buffer (Agilent In Situ Hybridization Kit Plus), washing buffers and protocols provided by Agilent Technologies.

scan_protocol: Scanned on an Genpix 4000B scanner (Molecular devices). Images were quantified using Genepix Pro Software (version 7).

data_processing: LIMMA package running in R was used for background subtraction, LOWESS normalization and statistical analyses of differential expression using Log 2 transformed signal intensities.

organism: Sus scrofa

source_name: mock infected_18h_macrophages_Cy3

label_protocol: 1 µg of total RNA per sample per reaction were used in labeling reaction using Agilent Quick Amp Gene Expression Labeling Kits, two-color (5190-0444)

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L

extract_protocol: Total RNA extracted using Qiagen Rneasy Mini Kit (Cat. No. 74104) following manufacturer's instructions

tag: infection

value: mock infected

tag: hour post infection

value: macrophages

source_name: ASFV infected_18h_macrophages_Cy5

value: ASFV infected


title: GAR020413.E03.COMET.38.PrimeView.082213


title: Array35_pig # 3 dye swap 1

source_name: ASFV infected_18h_macrophages_Cy3

source_name: mock infected_18h_macrophages_Cy5


title: Array36_pig # 3 dye swap 2


title: Wild type hESCs-intestinal organoid + co-culture

description: Gene expression of co-cultured human intestinal organoids differentiated from wild type human embryonic stem cells


title: Wild type hESCs-intestinal organoid

description: Gene expression of human intestinal organoids differentiated from wild type human embryonic stem cells


title: GAR020413.E12.F2.37.PrimeView.082213


title: Array11_pig # 1 dye swap 1


title: Array34_pig # 3 dye swap 2

source_name: mock infected_15h_macrophages_Cy3

source_name: ASFV infected_15h_macrophages_Cy5


title: Array12_pig # 1 dye swap 2


title: GAR020413.E08.F1.37.PrimeView.082213


title: GAR020413C.C20.F3.35.PrimeView.080213


title: Array10_pig # 1 dye swap 2


title: Array9_pig # 1 dye swap 1

source_name: ASFV infected_15h_macrophages_Cy3

source_name: mock infected_15h_macrophages_Cy5


title: GAR020413.E02.COMET.37.PrimeView.082213


title: Array23_pig # 2 dye swap 1


title: GAR020413C.C19.F3.32.PrimeView.080213


title: Array22_pig # 2 dye swap 2


title: Array21_pig # 2 dye swap 1


title: GAR020413C.C9.F1.35.PrimeView.080213


title: GAR020413.E18.F3.37.PrimeView.082213


title: GAR020413C.C15.F2.35.PrimeView.080213


title: GAR020413C.C3.COMET.35.PrimeView.080213


title: Array32_pig # 3 dye swap 2

source_name: mock infected_12h_macrophages_Cy3

source_name: ASFV infected_12h_macrophages_Cy5


title: GAR020413C.C14.F2.32.PrimeView.080213


title: GAR020413C.C18.F3.30.PrimeView.080213

value: F


title: Array8_pig # 1 dye swap 2


title: GV_WT_r3

data_processing:
Reads were mapped onto indexed rn6 genome using STAR 2.5.3a:   STAR --readFilesIn ${FILE}_1.txt.gz ${FILE}_2.txt.gz --genomeDir $ REF_GENOME_INDEX --runThreadN 10 --genomeLoad LoadAndRemove --limitBAMsortRAM  20000000000 --readFilesCommand unpigz -c --outFileNamePrefix ${FILE}. --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.2 --sjdbScore 2
Counts of reads over genomic coordinates were computed in R over exon coordinats from .gtf annotation file downloaded from Ensembl Release 93:  GenomicAlignments::summarizeOverlaps(features = ensembl_gtf.genomicRangesList reads = bamfiles, mode = "Union", singleEnd = FALSE, ignore.strand = FALSE)
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: rn6
ensembl.93.Rnor_6.0.rat_WT.raw_counts.csv:
- .csv table with counts of reads over exon coordinats from Ensembl Release 93 .gtf file
- samples are in columns, genes in rows
coverage genome browser tracks files:
- .bigWig format
- generated in a non'-stranded mode.
- not normalized for library size

organism: Rattus norvegicus

source_name: GV oocyte, WT, replicate 3

growth_protocol: Fully grown, germinal vesicle (GV)-intact oocytes from Sprague Dawley rat were collected using the same procedure as for isolation of mouse oocytes without superovulation (Nagy A, (2003) Manipulating the mouse embryo: a laboratory manual pp Cold Spring Harbor Laboratory Press). GV Oocytes were collected in M2 medium (Sigma-Aldrich) with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX; Sigma). 25 GV oocytes were collected per sample.

extract_protocol: Total RNA was extracted from 25 oocytes using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific). Libraries were constructed using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN). RNA-Seq libraries were pooled and sequenced by 250 bp paied-end reading using Illumina HiSeq

tag: developmental stage

value: GV oocyte

tag: genotype

value: WT

tag: strain

value: Sprague Dawley


title: Array19_pig # 2 dye swap 1

source_name: ASFV infected_12h_macrophages_Cy3

source_name: mock infected_12h_macrophages_Cy5


title: GV_WT_r4

source_name: GV oocyte, WT, replicate 4


title: Array18_pig # 2 dye swap 2

source_name: mock infected_9h_macrophages_Cy3

source_name: ASFV infected_9h_macrophages_Cy5


title: GAR020413C.C8.F1.32.PrimeView.080213


title: Array17_pig # 2 dye swap 1

source_name: ASFV infected_9h_macrophages_Cy3

source_name: mock infected_9h_macrophages_Cy5


title: Array20_pig # 2 dye swap 2


title: GAR020413.D10.F1.29.PrimeView.082013


title: Array5_pig # 1 dye swap 1


title: GAR020413.D03.COMET.29.PrimeView.082013

value: Baseline


title: Array28_pig # 3 dye swap 2

source_name: mock infected_6h_macrophages_Cy3

source_name: ASFV infected_6h_macrophages_Cy5


title: GAR020413.D21.F3.27.PrimeView.082013

value: M


title: Array7_pig # 1 dye swap 1


title: Array30_pig # 3 dye swap 2


title: Array29_pig # 3 dye swap 1


title: Array31_pig # 3 dye swap 1


title: GAR020413.D16.F2.29.PrimeView.082013


title: GAR020413C.C13.F2.30.PrimeView.080213


title: GAR020413C.C7.F1.30.PrimeView.080213


title: GAR020413C.C2.COMET.32.PrimeView.080213


title: Array6_pig # 1 dye swap 2


title: GV_WT_r2

source_name: GV oocyte, WT, replicate 2


title: GAR020413C.C1.COMET.30.PrimeView.080213


title: GV_WT_r1

source_name: GV oocyte, WT, replicate 1


title: GAR020413.D09.F1.27.PrimeView.082013


title: GAR020413.D02.COMET.27.PrimeView.082013


title: GAR020413B.B4.48.PrimeView.071913


title: Array27_pig # 3 dye swap 1

source_name: ASFV infected_6h_macrophages_Cy3

source_name: mock infected_6h_macrophages_Cy5


title: Array16_pig # 2 dye swap 2


title: GAR020413G.12.25.FU3.PrimeView.NL.100113


title: GAR020413G.11.25.FU2.PrimeView.NL.100113


title: Array15_pig # 2 dye swap 1


title: GAR020413G.8.23.FU3.PrimeView.NL.100113


title: GAR020413G.10.25.FU1.PrimeView.NL.100113


title: Array3_pig # 1 dye swap 1


title: Array14_pig # 2 dye swap 2

source_name: mock infected_3h_macrophages_Cy3

source_name: ASFV infected_3h_macrophages_Cy5


title: Control_10

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Partek GS 6.4 software (St. Louis, MO) using GCRMA normalization algorithm

source_name: Placenta

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

extract_protocol: Qiagen Rneasy FFPE kit used according to the manufacturer's protocol

tag: disease

value: Control


title: Control_5


title: Control_4


title: Array26_pig # 3 dye swap 2


title: Control_8


title: Array25_pig # 3 dye swap 1

source_name: ASFV infected_3h_macrophages_Cy3

source_name: mock infected_3h_macrophages_Cy5


title: Control_9


title: GAR020413G.6.23.FU1.PrimeView.NL.100113


title: GAR020413G.9.COMET.25.PrimeView.NL.100113


title: GAR020413G.7.23.FU2.PrimeView.NL.100113


title: Control_3


title: Control_7


title: Array13_pig # 2 dye swap 1


title: Array4_pig # 1 dye swap 2


title: Control_2


title: Array2_pig # 1 dye swap 2


title: Array1_pig # 1 dye swap 1


title: Control_1


title: Ch317

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1317

data_processing:
FASTQ files were checked for quality control metrics using FastQC (version 0.11.5) and RSeqQC (version 2.6.4)
Post-Quality control, raw reads were mapped to the reference genome using Hisat2 (version 2.1.0) proceeded by exon-counting using featureCounts (version 1.6.0)
Genome_build: Ensembl GRCz11, build 94
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts

organism: Danio rerio

source_name: Adult zebrafish heart_Uninjured_RFP

extract_protocol:
0.2% RNase inhibitor in Triton X-100 plus Dilute the oligo-dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo-dT primers and 90 µl of nuclease-free water to a tube and mix well. Cells were isolated in the lowest possible volume, possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer, 1 ul of oligo dT primeres and dNTP mix. Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )
Smart-seq2 (Picelli, S., et al. Nature Protocols 2014 )

tag: condition

value: Uninjured

value: Adult zebrafish heart

tag: sorted cell population

value: RFP


title: CoBFP333

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1333

source_name: Adult zebrafish heart_Uninjured_BFP

value: BFP


title: GAR020413G.5.COMET.23.PrimeView.NL.100113

value: IPF


title: Ch313

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1313


title: CICh281

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1281

source_name: Adult zebrafish heart_Cryoinjury_RFP

value: Cryoinjury


title: CoBFP257

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1257


title: VUE_pt9 [Low]

tag: immune cell inflitration

value: Low

value: Villitis of unknown etiology


title: GAR020413G.1.COMET.22.PrimeView.NL.100113

value: PBMC


title: VUE_pt7 [Low]


title: Ch249

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1249


title: VUE_pt8 [Low]


title: VUE_pt10 [High]

value: High


title: VUE_pt10 [Low]


title: GAR020413G.3.22.FU2.PrimeView.NL.100113


title: VUE_pt9 [High]


title: GAR020413B.B20.F3.21.PrimeView.071913


title: GAR020413B.B3.COMET.21C.PrimeView.071913


title: VUE_pt8 [High]


title: Ch241

description: HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1241


title: GAR020413B.B19.F3.20.PrimeView.071913


title: VUE_pt7 [High]


title: GAR020413A.Comet.47.PrimeView.021513


title: GAR020413B.B14.F2.21.PrimeView.071913


title: GAR020413B.B8.F1.20.PrimeView.071913