title: TG_B_Sperm_H3K27me3

status: Public on Oct 15 2020

type: SRA

city: Sainte-Anne-de-Bellevue

first: Sarah

last: Kimmins

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Quality of the FASTQ files were assessed with FastQC (v0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were trimmed using Trimmomatic (v0.32, Bolger et al., 2014) with the parameters TRAILING = 20, and MINLEN = L, where L = (read length x 0.80). Reads were aligned to the mouse reference genome (UCSC version mm10, December 2011) using BWA (v0.7.15, Li et al., 2009) with the settings MEM -MP -t 10 -v 2 -c 100 for paired-end H3K27me3 datasets, or using Bowtie (v1.1.2, Ben et al., 2002) with the settings -t -v 3 -m 100 for single-end H3K4me3 datasets. These parameters were implemented to reduce reads with multiple alignments (Royo et al., 2016). Samtools (v1.3, Li et al., 2012) was used to filter out unaligned reads, sort the alignment file and convert alignment files the BAM format. Read duplicates were marked using PicardTools (v2.4.1; Broad Institute, https://broadinstitute.github.io/picard/), but were not discarded.
DeepTools2 was used to generate Bigwig coverage tracks (Fidel et al., 2016). The coverage was calculated in 10 bp bins genome-wide and normalized using Reads Per Kilobase per Million mapped reads (RPKM).
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse sperm

extract_protocol:
ChIP-Seq on sperm was performed as previously described (Hisano et al., 2013) with slight modifications. Briefly, a total of 12 million sperm cells were pooled from 3 - 4 C57BL/6 CRwt, TG, and nonTG males for H3K4me3 (n = 3 biological replicates per group), and 3 - 4 C57BL/6 CRwt males for H3K27me3 (n = 2 biological replicates per group). Pooled sperm was made accessible through dithiothreitol treatment. Mouse spermatozoa were then lyzed, washed with PBS, and aliquoted into 6 aliquots of 2 million cells per tube. Spermatozoa were lysed again and mononucleosome fragments were generated using 15U MNase per tube (Roche, Switzerland, #10107921001). After 5 minutes at 37°C, MNase digestion was stopped using EDTA and chromatin was recovered by centrifugation at 17 000 x g. Chromatin was precleared with protein-A Dynabeads (Invitrogen, USA; Cat#10001D) for 1 hour. Samples were immunoprecipitated using 5 µg of H3K4me3 antibody (Cell Signalling Technologies, USA; #CST9751) or H3K27me3 antibody (Cell Signalling Technologies; USA, #CST9733) bound to 50µL protein-A Dynabeads overnight. The next day, bead-antibody complexes were washed and transferred to Eppendorf LoBind tubes on the last wash (Eppendorf, Germany; Cat# 0030108051). Samples were eluted twice using 125 µL of elution buffer and 400 rpm shaking for 10 minutes at 65°C. Elutes were then treated with RNaseA and Proteinase K. Immunoprecipitated DNA was recovered using Zymogen ChIP-Clean and Concentrator Kit (Zymo Research, USA; Cat# D5205). DNA quality and concentration were assessed using the Bioanalyzer High Sensitivity DNA kit (Agilent, USA; Cat# 5067-4626) and 3 - 5ng of 147 bp mononucleosomes were size selected using Agencourt AMPure XP magnetic beads (Beckman Coulter, USA; Cat#A63880) following manufacturer’s recommendations.
H3K4me3 and H3K27me3 libraries were prepared using Kapa BioSystems HTP Library Preparation kit (Roche, Switzerland; Cat# 07138008001). Sequencing was performed on Illumina HiSeq 2500 and multiplexed with 6 samples per lane. H3K4me3 libraries were sequenced using single-end 100 bp reads and H3K27me3 was sequenced using paired-end 100 bp reads.

tag: strain

tag: developmental stage

value: Mature sperm

tag: chip antibody

value: H3K27me3, Cell Signalling Technologies, #CST9733


title: CRwt_B_Sperm_H3K27me3


title: CRwt_A_Sperm_H3K27me3


title: TG_A_Sperm_H3K27me3


title: nonTG_B_Sperm_H3K27me3


title: nonTG_C_Sperm_H3K4me3

value: H3K4me3, Cell Signalling Technologies, #CST9751


title: nonTG_A_Sperm_H3K4me3


title: CRwt_C_Sperm_H3K4me3


title: TG_B_Sperm_H3K4me3


title: CRwt_A_Sperm_H3K4me3


title: TG_A_Sperm_H3K4me3


title: nonTG_A_Sperm_H3K27me3


title: nonTG_B_Sperm_H3K4me3


title: WT_MC38_4

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: 234, Herzl

country: Israel

institute: The Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Reads were trimmed using FastX toolkit,  fastx_trimmer -f 7 -Q33 -i ${sample} -o ${sample}_trimmed (https://www.lexogen.com/sense-data-analysis/)
Low quality tails were removed by fastq_quality_trimmer -t 10 -l 20 -Q33 -v -i ${sample} -o ${sample}_clean (https://www.lexogen.com/sense-data-analysis/)
Reads were mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Counting was done using STAR. Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: total RNA

source_name: Liver from WT (C57BL/6) mice

growth_protocol: 16 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions

extract_protocol:
Livers were dissociated by Bead ruptor elite (OMNI international) with metal beads in Micro-tube (Sarstedt #72.694.006). RNA isolation was performed by RNeasy fibrous tissue mini kit (Qiagen #74704) according to manufacturer’s instructions.
Libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen USA) according to the instructions of the manufacturer.
RNA-Seq , based on poly-A

treatment_protocol: Per2-/- or WT C57Bl/6 male mice were injected at the age of 16 weeks with 20,000 MC38 cells (n=4 mice per genotype) and PBS (n=2 control mice per genotype) into the hepatic portal vein (under anesthesia by isoflurane 2.5%). To prevent bleeding, light pressure was applied to the injection site with a cotton applicator for 4 min. Then, the muscle and skin were sutured using 6/0 polypropylene monofilament sutures. At day 7 post-injection, mice were sacrificed and livers  were then dissociated and sequenced.

tag: treatment

value: MC38 (colon cancer) into the hepatic portal vein

tag: tissue

value: Liver

tag: mouse age

value: 16 weeks


title: Per2-/-_MC38_2

source_name: Liver from Per2-/- mice

value: PER2 -/- mice (Binhai Zheng et al. 2001) backcrossed to a C57BL/6 background (provided by Gad Asher, WIS)


title: WT_MC38_2


title: Per2-/-_MC38_3


title: Per2-/-_MC38_1


title: Per2-/-_MC38_4


title: WT_MC38_1


title: WT_PBS_2

value: PBS into the hepatic portal vein


title: KO7

status: Public on Sep 30 2020

city: Aarhus

first: Abdel-Rahman

last: Al-Absi

address: Palle Juul Jensens Boulevard 99

country: Denmark

institute: Aarhus University

data_processing:
BGISeq-500 platform was used to perfrom Single-end read RNA sequencing .
Sequence data were filtered to remove the adaptor sequence and low-quality sequence.
The first 5 bases were removed from the start of the read using using Trimmomatic
Reads that passed the quality control are mapped using HISAT2 to the mouse genome (Mus_musculus.GRCm.38.95).
Transcript assembly and quantification was performed using StringTie. Number of transcripts are normalized by gene length and sequencing depth (in millions) in the sample to produce Transcripts Per Kilobase Million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: TPM values for each sample

source_name: PFC

extract_protocol:
Micro punch from PFC region was collected using mouse brain slicer.Total RNA was exctracted from the punches using LEV simply and RNA Tissue Kit (Promega, USA). RNA quality was checked using Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer.
BGISeq-500 Library preparation kit

tag: age

value: 8-10 weeks


title: WT_MC38_3


title: TG_C_Sperm_H3K4me3


title: KO4


title: Per2-/-_PBS_1


title: Per2-/-_PBS_2


title: KO6


title: KO2


title: CRwt_B_Sperm_H3K4me3


title: KO3


title: KO5


title: KO8


title: KO1


title: WT3


title: WT_PBS_1


title: WT1


title: WT7


title: WT5


title: WT2


title: WT6


title: WT4


title: Interlobular hTERT_2

city: Copenhagen

first: Mikkel

last: Morsing

state: Nørrebro

address: Blegdamsvej 3b

department: Department of Cellular and Molecular Medicine and Danish Stem Cell Center

institute: University of Copenhagen

description:
Interlobular_hTERT-VS-lobular_hTERT.DEseq2_Method.GeneDiffExp
AllSamples.GeneExpression.FPKM.xls

data_processing:
Used SOAPnuke software to filter reads
Data processing included removing adaptors, any contamination and low-quality reads from raw reads.
After reads filtering, we map clean reads to reference genome using HISAT
13.7 M clean reads were generated for each sample. Mapped clean reads to reference using Bowtie 2 tool were then used to calculate gene expression with the RSEM package
Genome_build: hg19

organism: Homo sapiens

source_name: Human breast fibroblastic cells

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fischer) and a spin column method according to the manufacturer’s instructions (Zymo Research)
DNAse treated total RNA samples were enriched for mRNAs using oligo dT magnetic beads. mRNAs were fragmented into 200 bp-size fragments and the first strands of cDNAs were synthesized by using random-hexamers. In order to generate the library products, after the second strand synthesis, double strands cDNAs were purified by magnetic beads followed by addition of adenine to the 3’ends and ligation of sequencing adaptors to the fragments. These fragments were amplified by PCR using ABI StepOnePlus Real-Time PCR System, and the quantity and quality was checked by Agilent 2100 Bioanalyzer. Sequencing was performed using BGISeq 500

tag: cell type

value: Interlobular fibroblastic cells

tag: htert immortalized

value: Yes

tag: passage #


title: Interlobular hTERT_1


title: Primary interlobular cells_2

description:
Primary interlobular-VS-primary lobular.DEseq2_Method.GeneDiffExp
AllSamples.GeneExpression.FPKM.xls

value: No


title: X21_3

city: Taian

first: chuansong

last: quan

state: - Select -

address: yingsheng road 2

department: School of Basic Medical Sciences

country: China

institute: shandong first medical university

description: RNAseq data

data_processing:
Reads with low quality or adaptor contamination were filtered out, and the clean reads were aligned to Genome Reference Consortium Human genome build 38 using HISAT2.The featureCounts package was used to count reads aligned to each gene in order to quantify gene expression levels.
The filtered reads were aligned to BCR germline sequences using MiXCR. VDJtools52 was used for downstream analysis including clonotype filtering, diversity analysis, and repertoire overlap.
Genome_build: human GRCh38
Genome_build: IMGT Repertoire
Supplementary_files_format_and_content: featruecounts

source_name: PBMC

extract_protocol:
RNA was purified from PBMCs using the RNeasy Plus Mini Kit (Qiagen, Germany). RNA concentration and integrity number were determined with the RNA Bioanalyzer (Agilent).As for BCR sequencing, the third complementary determining region (CDR3) of BCR H chain was amplified in a multiplex PCR.
Libraries were generated according to the manufacturer’s instructions.

tag: patient group

value: moderate

tag: time period

value: recovered

tag: disease

value: Hemorrhagic fever with renal syndrome


title: X18_1

description: RNAseq data

value: severe

value: acute


title: X21_4

description: RNAseq data


title: X14_1

description: RNAseq data


title: N2

description: RNAseq data

value: healthy control

value: healthy


title: X21_1

description: RNAseq data


title: N6

description: RNAseq data


title: X7_4

description: RNAseq data


title: X37_1

description: RNAseq data


title: X18_3

description: RNAseq data


title: N1

description: RNAseq data


title: X7_2

description: RNAseq data


title: X9_2

description: RNAseq data


title: X37_3

description: RNAseq data


title: X9_1

description: RNAseq data


title: X18_2

description: RNAseq data


title: Lobular hTERT_1

value: Lobular fibroblastic cells


title: Primary interlobular cells_1


title: Primary lobular cells_1


title: Primary lobular cells_2


title: DZNeP-3

city: Shanghai

first: Yan

last: Jiang

address: Yixueyuan Rd. 138

department: Institutes of biomedical sciences

institute: Fudan Universtiy

data_processing:
The raw data was trimmed, filtered and qualified using FASTX (http://hannonlab.cshl.edu/fastx toolkit/), then the clean data was aligned to rat referential genome sequence (rn5) using Tophat2 soft.
The expression level of every gene was evaluated by RPKM method (expected number of reads per kilobase of transcript sequence per millions base pairs sequenced).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: hepatic stellate cell

extract_protocol:
The primary rat HSCs were isolated and purified using the method of in situ perfusion with pronase and collagenase IV and density gradient centrifugation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD

value: primary HSCs

value: DZNeP at 1 uM


title: X14_3

description: RNAseq data


title: X7_1

description: RNAseq data


title: DMSO-3

value: DMSO


title: DMSO-2


title: Lobular hTERT_2


title: DMSO-1


title: DZNeP-2


title: DZNeP-1


title: abaM::Tn26 3

city: Nottingham

first: Mario

last: López-Martín

address: Centre for Biomolecular Sciences, Biodiscovery, Institute

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Data assessment (Error rate, AT and GC content distribution, daat filtration)
Mapping to reference genome (Bowtie2 software)
Expression quantification (HTSeq software)
RNA-seq advanced QC (Pearson correlation coefficient)
Differential expression analysis. (Differential expression between either the abaI::Tn26 or the abaM::Tn26 mutant compared to the wild-type strain, performed using the DESeq software)
Genome_build: GCF_000963815.1
Supplementary_files_format_and_content: readcount txt contains the expression level for every mapped gene in each of the different samples. abaIvsWT.DEG.txt and abaMvsWT.DEG.txt contain the differential expression for each gene between either the abaI::Tn26 or the abaM::Tn26 mutant compared to the wild-type strain.

organism: Acinetobacter baumannii

source_name: Liquid culture

growth_protocol: Opaque phases of each strain were grown to OD600=0.5 in LS-LB at 200 rpm and 37ºC and diluted to OD600=0.05. Bacteria were cultured in LS-LB under static conditions at 37ºC for 18h.

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (QIAGEN) following the manufacturer instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent  Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM Directional  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was  synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I  and RNase H.

treatment_protocol: Two mililiters of each culture were centrifuged at 12000 rpm in a bench centrifuge and pellets were resuspended in RNAprotect (Qiagen) prior RNA extraction.

tag: background strain

tag: taxonomy id

tag: genotype

tag: phase

value: Opaque


title: H-N-16 [miRNA-Seq]

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with  H-N-16 in the column of processed data file

data_processing:
The 50nt sequence tags from HiSeq sequencing went through the data cleaning first,
which included getting rid of the low quality tags and several kinds of contaminants from the
50nt tags. Length distribution of clean tags was then summarized. Afterwards, the standard
bioinformatics analysis was used to annotate the clean tags into different categories and to take
those which cannot be annotated to any category to predict the novel miRNA and base edit of potential known miRNA
Genome_build: Sscrofa11.1

organism: Sus scrofa

extract_protocol:
Pig intestine samples were isolated for small RNA. Then small RNA samples were sequenced.
small  RNA was used for the library.

tag: breed

value: Big white

value: Intestine cells

tag: group

value: Weaning2 (After 21 days of age, weaning for 3 days)


title: H-N-18 [miRNA-Seq]

description: The group information is prefixed with  H-N-18 in the column of processed data file


title: H-N-4 [miRNA-Seq]

description: The group information is prefixed with H-N-4 in the column of processed data file

value: Weaning1 (After 21 days of age, weaning for 1 day)


title: H-N-6 [miRNA-Seq]

description: The group information is prefixed with H-N-6 in the column of processed data file


title: AB5075 wild-type 3

value: Wild-type


title: abaI::Tn26 1


title: AB5075 wild-type 2


title: H-N-28 [miRNA-Seq]

description: The group information is prefixed with  H-N-28 in the column of processed data file

value: Weaning3 (After 21 days of age, weaning for 7 days)


title: H-N-3 [miRNA-Seq]

description: The group information is prefixed with  H-N-3 in the column of processed data file

value: Feeding  (After 21 days of age, breast feeding)


title: abaM::Tn26 2


title: H-N-1 [miRNA-Seq]

description: The group information is prefixed with H-N-1 in the column of processed data file


title: H-N-14 [miRNA-Seq]

description: The group information is prefixed with  H-N-14 in the column of processed data file


title: AB5075 wild-type 1


title: abaI::Tn26 2


title: H-N-5 [miRNA-Seq]

description: The group information is prefixed with H-N-5 in the column of processed data file


title: H-N-26

description: The group information is prefixed with  H-N-26 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: Sscrofa11.1

extract_protocol:
Pig intestine samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: strain


title: abaI::Tn26 3


title: abaM::Tn26 1


title: H-N-26 [miRNA-Seq]


title: H-N-16


title: H-N-30 [miRNA-Seq]

description: The group information is prefixed with  H-N-30 in the column of processed data file


title: H-N-18


title: H-N-28


title: H-N-2 [miRNA-Seq]

description: The group information is prefixed with  H-N-2 in the column of processed data file


title: H-N-14


title: H-N-30


title: H-N-6


title: H-N-4


title: H-N-2


title: H-N-5


title: H-N-3


title: LCL DNA Methylation Sample 67

type: genomic

city: Los Angeles

first: Anil

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

country: USA

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software and Methylumi R package

label: biotin

source_name: Methylation  24h exposure  2uM clozapine

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LCL samples using Qiagen DNeasy Kit according to standard instructions

value: lymphoblast cell line model

tag: trio

tag: Sex

value: M

tag: plate


title: LCL DNA Methylation Sample 79

source_name: Methylation  96h exposure  40uM clozapine

tag: tissue


title: LCL DNA Methylation Sample 73

source_name: Methylation  24h exposure  40uM clozapine


title: LCL DNA Methylation Sample 82

source_name: Methylation  24h exposure  120uM clozapine


title: LCL DNA Methylation Sample 91

source_name: Methylation  24h exposure  0.05% DMSO


title: LCL DNA Methylation Sample 80

source_name: Methylation  96h exposure  0.05% DMSO


title: LCL DNA Methylation Sample 78

source_name: Methylation  364h exposure  40uM clozapine


title: LCL DNA Methylation Sample 83

source_name: Methylation  24h exposure  control

value: F

value: CONT


title: LCL DNA Methylation Sample 84

source_name: Methylation  96h exposure  control


title: LCL DNA Methylation Sample 72

source_name: Methylation  364h exposure  2uM clozapine


title: LCL DNA Methylation Sample 81


title: LCL DNA Methylation Sample 70

source_name: Methylation  96h exposure  2uM clozapine


title: LCL DNA Methylation Sample 74


title: LCL DNA Methylation Sample 66


title: LCL DNA Methylation Sample 90

source_name: Methylation  96h exposure  80uM clozapine


title: LCL DNA Methylation Sample 71

source_name: Methylation  364h exposure  0.05% DMSO


title: LCL DNA Methylation Sample 69

source_name: Methylation  96h exposure  120uM clozapine


title: LCL DNA Methylation Sample 87


title: LCL DNA Methylation Sample 86


title: LCL DNA Methylation Sample 75


title: LCL DNA Methylation Sample 77


title: LCL DNA Methylation Sample 68


title: LCL DNA Methylation Sample 89

source_name: Methylation  364h exposure  control


title: LCL DNA Methylation Sample 92


title: LCL DNA Methylation Sample 88

source_name: Methylation  24h exposure  80uM clozapine


title: LCL DNA Methylation Sample 76


title: LCL DNA Methylation Sample 64


title: LCL DNA Methylation Sample 65


title: LCL DNA Methylation Sample 85


title: LCL DNA Methylation Sample 39


title: LCL DNA Methylation Sample 50


title: LCL DNA Methylation Sample 49


title: LCL DNA Methylation Sample 55


title: LCL DNA Methylation Sample 38


title: LCL DNA Methylation Sample 46


title: LCL DNA Methylation Sample 51

source_name: Methylation  364h exposure  80uM clozapine


title: LCL DNA Methylation Sample 48


title: LCL DNA Methylation Sample 52


title: LCL DNA Methylation Sample 43

source_name: Methylation  364h exposure  120uM clozapine


title: LCL DNA Methylation Sample 57


title: LCL DNA Methylation Sample 44


title: LCL DNA Methylation Sample 54


title: LCL DNA Methylation Sample 59


title: LCL DNA Methylation Sample 53

source_name: Methylation  24h exposure  2uM clozapine


title: LCL DNA Methylation Sample 62


title: LCL DNA Methylation Sample 37


title: LCL DNA Methylation Sample 63


title: LCL DNA Methylation Sample 35


title: LCL DNA Methylation Sample 56

source_name: Methylation  24h exposure  40uM clozapine


title: LCL DNA Methylation Sample 47


title: LCL DNA Methylation Sample 61


title: LCL DNA Methylation Sample 58


title: LCL DNA Methylation Sample 42


title: LCL DNA Methylation Sample 34

source_name: Methylation  24h exposure  120uM clozapine


title: LCL DNA Methylation Sample 36


title: LCL DNA Methylation Sample 45

source_name: Methylation  96h exposure  40uM clozapine


title: LCL DNA Methylation Sample 41

source_name: Methylation  24h exposure  0.05% DMSO


title: LCL DNA Methylation Sample 40


title: LCL DNA Methylation Sample 33


title: LCL DNA Methylation Sample 28


title: LCL DNA Methylation Sample 29


title: LCL DNA Methylation Sample 60


title: LCL DNA Methylation Sample 30

source_name: Human fully methylated control


title: LCL DNA Methylation Sample 23


title: LCL DNA Methylation Sample 26


title: LCL DNA Methylation Sample 24


title: LCL DNA Methylation Sample 27


title: IL33 DNLS C4

type: RNA

city: Calgary

first: Stephen

middle: M

last: Robbins

state: Alberta

address: 3330 Hospital Drive N.W.

department: Oncology

institute: University of Calgary

description: Gene expression data of IL33 DNLS overexpressing U87 human glioma cells clone 4

hyb_protocol: Following fragmentation, 15 ug cRNA were hybridized to Affymetrix GeneChip Human PrimeView Arrays at 45ºC for 16 hours. Arrays were stained using Affymetrix GeneChip Fluidics_450 following manufacturer's protocol

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

data_processing: Affymetrix GeneChip array data files were generated using GeneChip Command Console Software (AGCC) and statistical analysis was carried out using Partek Genomics Suite 6.0 (Partek Incorporated)

label: Biotin

source_name: IL33 DNLS C4

label_protocol: 100 ng of RNA with a RIN higher than 9 was labeled with 3’ IVT Express Kit (Ambion)

extract_protocol: RNA was extracted from 500,000 cells using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's protocol. Total RNA was purified with RNeasy Plus Micro Kit (Qiagen) and RNA integrity number (RIN) was measured using the Agilent RNA 6000 NanoChip on 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

tag: cell type

value: Human glioma cell line

tag: over-expression

value: IL33 DNLS


title: LCL DNA Methylation Sample 22


title: LCL DNA Methylation Sample 25


title: LCL DNA Methylation Sample 13


title: LCL DNA Methylation Sample 21


title: LCL DNA Methylation Sample 16


title: LCL DNA Methylation Sample 15


title: LCL DNA Methylation Sample 18


title: LCL DNA Methylation Sample 17

source_name: Methylation  364h exposure  40uM clozapine


title: LCL DNA Methylation Sample 20


title: LCL DNA Methylation Sample 14


title: LCL DNA Methylation Sample 10


title: LCL DNA Methylation Sample 19


title: LCL DNA Methylation Sample 9

source_name: Methylation  24h exposure  control


title: LCL DNA Methylation Sample 12


title: LCL DNA Methylation Sample 31


title: LCL DNA Methylation Sample 11

source_name: Methylation  364h exposure  2uM clozapine


title: HSC treated with PU-1 Y244D mutant protein replicate 3

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description: Gene expression after 5days of treatment.

hyb_protocol: cRNA was hybridized to human whole genome array chip (8x60k array) using Agilent’s In situ Hybridzation kit 5190-6420.

scan_protocol: scanned using agilent microarray scanner (agilent technologies, part number G2600D)

data_processing: The data was normalized by percentile shift normalization method using GeneSpring GX11 (Agilent technologies, India).

source_name: Hematopoetic stem CD34+ cells,

label_protocol: Cy3 labeled cRNA was formed by cDNA by T7 promoter based linear amplification using Agilent’s Quick amp labeling kit and quantified in Nanodrop Spectrophotometer and their integrity was checked by Bioanalyser

growth_protocol: Hematopoetic stem cells were grown in IMDM supplemented with 0.2% heat-inactivated fetal bovine serum.   The cultures were incubated for 5 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was isolated by Qiagen’s RNeasy mini kit and was reverse transcribed into cDNA.

treatment_protocol: Cells were incubated with 30ng/ml GMCSF, 83ng/ml MCSF, 3ng/ml IL-3, 3ng/ml SCF, 150ng/ml FLT-3, 3ng/ml IL-6 and  for 5days

value: hematopoetic stem cells

tag: marker


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 Y244D protein replicate 2


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF replicate 3


title: LCL DNA Methylation Sample 5

source_name: Methylation  96h exposure  2uM clozapine


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 protein replicate 1


title: HSC treated with PU-1 Y244D mutant protein replicate 2


title: LCL DNA Methylation Sample 7


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 protein replicate 2


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 Y244D protein replicate 1


title: HSC treated with PU-1 protein  replicate 1


title: HSC treated with PU-1 protein  replicate 3


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 protein replicate 3


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF,PU-1 Y244D protein replicate 3


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF replicate 2


title: HSC treated with PU-1 protein  replicate 2


title: LCL DNA Methylation Sample 2

source_name: Methylation  96h exposure  120uM clozapine


title: LCL DNA Methylation Sample 3


title: LCL DNA Methylation Sample 6

source_name: Methylation  96h exposure  80uM clozapine


title: control hematopoetic stem cells replicate 1


title: control hematopoetic stem cells replicate 3


title: GMCSF and MCSF treated THP-1 cells replicate 3

description:
SG13134300_253949447902_S001_GE1_1105_Oct12_2_1
Gene expression after 24hrs GMCSF and MCSF treatment.

scan_protocol: scanned using agilent microaaray scanner(Agilent Technologies, part number G2600D)

source_name: THP-1 cells

growth_protocol: THP-1 cells were grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: Cells were incubated with 30ng/ml GMCSF and 83ng/ml MCSF for 24hrs

value: human monocytic cell line


title: control hematopoetic stem cells replicate 2


title: LCL DNA Methylation Sample 4


title: GMCSF and MCSF treated THP-1 cells replicate 1

description:
SG13134300_253949447902_S001_GE1_1105_Oct12_1_4
Gene expression after 24hrs GMCSF and MCSF treatment.


title: 18T1E

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

description: 16216X5:18T1E (column header information  in raw counts file)

data_processing:
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to mm10 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Perform differential expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: tumor

growth_protocol: genetically induced tumors

extract_protocol:
harvested and snap frozen at primary tumor morbidity
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold
ribosomal RNA depletion

treatment_protocol: no pharmacological treatments

value: HprtCre; Ewsr1-loxP; Atf1-loxP


title: 68C1

description: 16216X6: 68C1 (column header information  in raw counts file)

source_name: skeletal muscle

value: WT


title: 4T1

description: 16216X7: 4T1 (column header information  in raw counts file)


title: N107

description: 16216X8: N107 (column header information  in raw counts file)


title: 44T1

description: 16216X4:44T1 (column header information  in raw counts file)


title: LCL DNA Methylation Sample 1


title: N105

description: 16216X9: N105  (column header information  in raw counts file)


title: N26

description: 16216X10: N26  (column header information  in raw counts file)


title: 99482

description: 16216X12: 99482 (column header information  in raw counts file)


title: 99481

description: 16216X11: 99481 (column header information  in raw counts file)


title: control THP-1 cells replicate 3

description:
SG13134300_253949447900_S001_GE1_1105_Oct12_1_2
Gene expression after 24hrs GMCSF and MCSF treatment.


title: control THP-1 cells replicate 2

description:
SG13134300_253949447900_S001_GE1_1105_Oct12_1_3
Gene expression after 24hrs GMCSF and MCSF treatment.


title: HSC treated with IL-3, SCF, FLT-3,GMCSF,MCSF replicate 1


title: 18T1

description: 16216X2: 18T1 (column header information  in raw counts file)


title: HSC treated with PU-1 Y244D mutant protein replicate 1


title: 65T1

description: 16216X3: 65T1 (column header information  in raw counts file)


title: IL33 DNLS C3

description: Gene expression data of IL33 DNLS overexpressing U87 human glioma cells clone 3

source_name: IL33 DNLS C3


title: 18T1 [wgs]

description: low-read-depth whole genome sequencing

data_processing:
Library strategy: whole genome sequencing
BWA mem mm10 alignments, GATK recalibration/realignment, unique observation read coverage estimation and comprehensive data quality control
CNVkit with the CBS method and a bin size of 100 kb
Genome_build: mm10
Supplementary_files_format_and_content: vcf

extract_protocol:
harvested and snap frozen at primary tumor morbidity
nextera dna flex library prep with udi


title: 18X8 [wgs]

description: low-read-depth whole genome sequencing

source_name: muscle


title: 65T1 [wgs]

description: low-read-depth whole genome sequencing


title: 44T1 [wgs]

description: low-read-depth whole genome sequencing


title: 68T1 [wgs]

description: low-read-depth whole genome sequencing


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H9_ad002

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

value: male

tag: age


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H9_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H9_ad007


title: 68T1

description: 16216X1: 68T1 (column header information  in raw counts file)


title: LCL DNA Methylation Sample 32

source_name: Human fully unmethylated control


title: control THP-1 cells replicate 1

description:
SG13134300_253949447900_S001_GE1_1105_Oct12_1_1
Gene expression after 24hrs GMCSF and MCSF treatment.


title: GMCSF and MCSF treated THP-1 cells replicate 2

description:
SG13134300_253949447902_S001_GE1_1105_Oct12_1_3
Gene expression after 24hrs GMCSF and MCSF treatment.


title: LCL DNA Methylation Sample 8

source_name: Methylation  364h exposure  control


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H8_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H7_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H8_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H7_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H9_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H8_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H8_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H8_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H7_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H7_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H7_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H5_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H5_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H6_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H5_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H9_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H4_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H4_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H4_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H4_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H3_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H3_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H3_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H12_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H12_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H12_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H2_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H3_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H11_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H5_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H11_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H11_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H10_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H10_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H10_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H10_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H10_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H3_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad012


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H4_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H11_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G8_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G8_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G8_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H1_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G7_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G6_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G6_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G6_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G6_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G6_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G8_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G8_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G9_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G4_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G5_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G4_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G2_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G4_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G3_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G10_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G10_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G10_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G10_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G10_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_H5_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F9_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G11_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G1_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F8_ad008


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad006


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F6_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F6_ad002


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F6_ad007


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G4_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_G12_ad001


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F7_ad010


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F5_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F6_ad004


title: CEMBA190131_6D_3_CEMBA190131_6D_4_F5_ad001


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title: CEMBA190131_6D_1_CEMBA190131_6D_2_D8_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D8_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D8_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D8_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D8_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D9_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D7_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D6_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_E11_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D5_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D4_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D12_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D12_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D3_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D12_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D12_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D2_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C9_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D11_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C8_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D10_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_D1_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C7_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C6_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C5_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C3_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C2_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C4_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C12_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad010


title: CNS_Nkx2.2-/-_12

city: odense

first: mads

last: thomassen

address: soender boulevard 29

institute: odense university hospital

hyb_protocol: According to Affymetrix protocol

scan_protocol: Affymetrix

data_processing: The microarray data were normalized at probe set level by using the variance stabilization and normalization (vsn) package in R, before the expression indexes were calculated by use of the Robust Multiarray Average (RMA) package in R

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Postnatal day 1.5-2

extract_protocol: TRIzol reagent (Ambion).

treatment_protocol: P1.5-2 mice were deeply anaesthetised with an overdose of pentobarbital and perfused transcardially with phosphate buffered saline (PBS). Brains for studies in un-fixed tissue were frozen immediately in CO2 snow, and stored at -80ºC until cut into sagittal serial sections of 20μm thickness in a -20ºC cryostat.

tag: genotype/variation

value: Pons, medulla, and rostral spinal cord were dissected from parallel sections of 20µm.


title: CNS_Nkx2.2-/-_29


title: CNS_Nkx2.2-/-_22


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad004


title: CNS_WT_21

source_name: WT

value: wild type


title: CNS_Nkx2.2-/-_43


title: CNS_WT_18


title: T040B

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Gene expression data from T040B

hyb_protocol: The labeled RNA samples were hybridized onto a Affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, CA) at 48°C and 60 rpm for 16 hours.

scan_protocol: Chips were scanned using the GeneChip Scanner 3000

data_processing: Background-adjusted signals were normalized by three steps: Robust Multichip Analysis (RMA), median polish method, and quantile normalization algorithm.

source_name: peripheral blood

label_protocol: Biotin

extract_protocol: Total RNA of PBMCs was purified using TRIzol® reagent (Invitrogen). Quantification of RNA was performed using a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

tag: individual

value: Male

tag: treatment

value: Atorvastatin

tag: sampling time

value: before treatment

value: peripheral blood


title: CNS_WT_15


title: CNS_Nkx2.2-/-_11


title: CNS_WT_16


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad006


title: T038B

description: Gene expression data from T038B

value: Female

value: Pitavastatin


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad008


title: T042B

description: Gene expression data from T042B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C10_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C11_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_C1_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad004


title: T039B

description: Gene expression data from T039B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B9_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad010


title: T036B

description: Gene expression data from T036B


title: T035B

description: Gene expression data from T035B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad006


title: T033B

description: Gene expression data from T033B


title: T034B

description: Gene expression data from T034B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad004


title: T031B

description: Gene expression data from T031B


title: T029B

description: Gene expression data from T029B


title: T032B

description: Gene expression data from T032B


title: T030B

description: Gene expression data from T030B


title: T024B

description: Gene expression data from T024B


title: CNS_WT_14


title: T025B

description: Gene expression data from T025B


title: T023B

description: Gene expression data from T023B


title: T022B

description: Gene expression data from T022B


title: T021B

description: Gene expression data from T021B


title: T026B

description: Gene expression data from T026B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B8_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad002


title: T015B

description: Gene expression data from T015B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad001


title: T013B

description: Gene expression data from T013B


title: T012B

description: Gene expression data from T012B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad004


title: T018B

description: Gene expression data from T018B


title: T017B

description: Gene expression data from T017B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B7_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B6_ad002


title: T006B

description: Gene expression data from T006B


title: T007B

description: Gene expression data from T007B


title: T004B

description: Gene expression data from T004B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad010


title: T009B

description: Gene expression data from T009B


title: T040

description: Gene expression data from T040

value: after treatment


title: T008B

description: Gene expression data from T008B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad006


title: T001B

description: Gene expression data from T001B


title: T042

description: Gene expression data from T042


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad004


title: T011B

description: Gene expression data from T011B


title: T010B

description: Gene expression data from T010B


title: T003B

description: Gene expression data from T003B


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B5_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad012


title: T039

description: Gene expression data from T039


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad007


title: T036

description: Gene expression data from T036


title: T033

description: Gene expression data from T033


title: T034

description: Gene expression data from T034


title: T038

description: Gene expression data from T038


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad004


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad007


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad001


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad010


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad006


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B4_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad004


title: T032

description: Gene expression data from T032


title: T035

description: Gene expression data from T035


title: T030

description: Gene expression data from T030


title: T026

description: Gene expression data from T026


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad012


title: T029

description: Gene expression data from T029


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad002


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B2_ad012


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B3_ad008


title: CEMBA190131_6D_1_CEMBA190131_6D_2_B2_ad001


title: T024

description: Gene expression data from T024


title: T031

description: Gene expression data from T031