title: WBJPE171125358


title: WBJPE171125348

status: Public on Jan 01 2020

type: SRA

city: Hangzhou

first: Yixiao

last: Liu

state: 浙江

address: Yuhangtang road

country: China

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

molecule: total RNA

organism: Mus musculus

source_name: skeleton muscle

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

treatment_protocol: 563 mice skeletal muscle derived single cells were form  6~8 weeks old male C57BL/6 mice.

tag: tissue

value: mice skeletal muscle

tag: strain

tag: gender

value: male


title: WBJPE171125347


title: Liver of CPT-treated HFD mouse 5

type: RNA

city: Nanjing

first: YITING

last: WANG

address: No. 100, Shizi Street, Maogaoqiao Street

institute: Department of Natural Medicinal Chemistry & State Key Laboratory of Natural Medicines, China Pharmaceutical University

description: Gene expression data from livers of C57/BL6J mouse feeding with high fat diet for 12 weeks, and then Cyclocarya paliurus triterpenic acids for 8 weeks

hyb_protocol: cDNA was hybridized onto a GeneChip Mouse Gene 2.0 ST Array in a GeneChip Hybridization Oven 645, washed and stained in a GeneChip Fluidics Station 450, according to the protocols with the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA)

scan_protocol: Chips were scanned in a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

source_name: Livers of Cyclocarya paliurus triterpenic acids (CPT)-treated HFD mouse

label_protocol: 250 ng total RNA were converted to sense strand cDNA for fragmentation with the Ambion® WT Expression Kit (Affymetrix), and cDNA was labeled using the Affymetrix® GeneChip WT Terminal Labeling and controls Kit

growth_protocol: Liver samples were collected and frozen at -80 °C for later analysis after mice were anesthetized by 10% chloral hydrate and sacrificed after starving for 12 h at the end of the experiments

extract_protocol: Total RNA was extracted from liver tissue with TRIzol Reagent (Life technology) in accordance to the standard protocol.

treatment_protocol: Liver samples were unfroze from -80 °C and then used for RNA extraction

value: liver

tag: diet


title: SkeletalMuscleCell_miR_Subj3

city: Stockholm

first: Anna

last: Krook

address: von Eulers väg 4a

country: Sweden

institute: Karolinska Institutet

description: Gene expresison data from human skeletal muscle cells (subject 3) transfected with a miR-19b-3p mimic

hyb_protocol: ssDNA was hybridized to Clariom S gene array chips according to manufacturer's protocols (Affymetrix, CA).

scan_protocol: Array chips were washed, stained and scanned using a Gene Titan instrument (Thermo Fisher Scientific).

data_processing: Preprocessing of data was performed using Robust Multiarray Average (RMA) using the oligo package with R/Bioconductor. After removal of non-annotated genes, the probe level expression was collapsed to gene level (“average” method) using the WGCNA package. Differentially expressed genes were determined with the linear models for microarray (limma) package.

label: Biotin

organism: Homo sapiens

source_name: Differentiated human skeletal muscle cells

label_protocol: Total RNA (100 ng) was used to generate amplified sense strand DNA followed by fragmentation and biotinylation using the WT Plus Reagent kit (Thermo Fisher Scientific).

growth_protocol: Human skeletal muscle cells (extracted from human vastus lateralis muscle) was cultured in Dulbecco's Modified Eagle Medium (DMEM):Nutrient Mixture F-12 supplemented with 20% FBS, and 1% penicillin-streptomycin/amphotericin B (anti-anti)). Cultures were subcultured with trypsin before reaching 70% confluence. Differentiation of myoblasts into myotubes were induced by switching to fusion medium (DMEM/M199 (4:1), 1% FBS, 1% anti-anti, 20 mM HEPES, 0.03 μg/mL ZnSO4, 1.4 μg/mL vitamin B12, 10 μg/mL insulin, and 100 μg/mL apo-transferrin) for 4 days when cells were approximately 90% confluent. Thereafter cells were cultured in differentiation media (DMEM/M199 (4:1), 1% FBS, 1% anti-anti, 20 mM HEPES, 0.03 μg/mL ZnSO4, and 1.4 μg/mL vitamin B12). Cultures were incubated at 37°C in 7.5% CO2 humidified chambers and media was changed every other day.

extract_protocol: Extraction of total RNA by TRIzol (Invitrogen). Modifications of manufacturer's protocol include addition of 0.75 ml isopropanol (compared to 0.5 ml) containing glycogen with 20 minutes incubation at -20°C to precipitate RNA.

treatment_protocol: Human skeletal muscle cells were transfected 6 days after induction of differentiation when myotubes had formed (4 days on fusion media and 2 days on differentiation media). Cells were transfected twice, first after 6 days and a second transfection after 8 days. Transfection with 25 nM miRNA Pre-miR™ miRNA Precursors (Thermo Fisher Scientific) was performed for 5 hours in OptiMEM reduced serum media with Lipofectamine® RNAiMAX whereafter cells were switched back to differentiation media. Two days after the second transfection (i.e., 4 days after overexpression was initiated) cells were rinsed with PBS before being scraped in TRIzol.

tag: subject id

tag: cell type

value: Skeletal muscle

tag: genotype

value: miR-19b-3p overexpression


title: Liver of HFD mouse 5

description: Gene expression data from livers of C57/BL6J mouse feeding with high fat diet for 20 weeks

source_name: Livers of high fat diet-induced (HFD) mouse

value: high fat diet for 20 weeks


title: SkeletalMuscleCell_NC_Subj3

description: Gene expresison data from human skeletal muscle cells (subject 3) transfected with a negative control miRNA mimic

value: negative control mimic


title: SkeletalMuscleCell_NC_Subj4

description: Gene expresison data from human skeletal muscle cells (subject 4) transfected with a negative control miRNA mimic


title: Liver of CPT-treated HFD mouse 3

value: high fat diet for 12 weeks, and then Cyclocarya paliurus triterpenic acids for 8 weeks


title: Liver of CPT-treated HFD mouse 1


title: SkeletalMuscleCell_miR_Subj4

description: Gene expresison data from human skeletal muscle cells (subject 4) transfected with a miR-19b-3p mimic


title: SkeletalMuscleCell_miR_Subj2

description: Gene expresison data from human skeletal muscle cells (subject 2) transfected with a miR-19b-3p mimic


title: Liver of CPT-treated HFD mouse 2


title: NK0069_Mf

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Dirofilaria Repens assembly, submitted to  NCBI BioProject N. PRJNA527192
Genome annotation: MAKER2 with the following evidence: a) protein sequences from D. immitis (www.nematodes.org, release nDi v2.2.2); b)  de novo assembled transcripts (see lines 45,48 and 59) as EST evidence; c) D. immitis GenBank transcript file (www.nematodes.org, release nDi v2.2.2) was used to train the etraining Augustus and the resulting models for the species were used as ab initio gene predictions.
De novo transcriptome assembly: De novo transcriptome assembly was performed using the Trinity software suite v.2.2.0 using default parameters. The likely coding DNA sequences (CDS) and corresponding proteins were predicted with Transdecoder (http://transdecoder.sourceforge.net/) following the “Running TransDecoder” procedure described at https://github.com/TransDecoder/TransDecoder/wiki and using the output of a homology search with D.Immitis as homology options. Potential redundancy was further decreased by applying the clustering-based method cd-hit-est  with default settings (http://weizhongli-lab.org/cd-hit/)
Supplementary_files_format_and_content: tab-delimited, raw counts; fasta and Gtf annotation

organism: Dirofilaria repens

source_name: Mf

extract_protocol:
RNA was isolated by extraction with the Trizol LS kit (Invitrogen), followed by column purification using the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions.
TruSeq RNA stranded protocol

tag: Stage

value: Microfilaria (Mf)


title: Liver of HFD mouse 4


title: Liver of HFD mouse 3


title: Liver of NC mouse 5

description: Gene expression data from livers of C57/BL6J mouse feeding with normal diet for 20 weeks

source_name: Livers of normal diet control (NC) mouse

value: control


title: Liver of HFD mouse 2


title: Liver of HFD mouse 1


title: NK001_Mf


title: WBJPE171125345


title: SkeletalMuscleCell_NC_Subj2

description: Gene expresison data from human skeletal muscle cells (subject 2) transfected with a negative control miRNA mimic


title: WBJPE171125342


title: NK0021_Mf


title: WBJPE171125343


title: 354_L3_M44

value: Third larva (L3)


title: WBJPE171125340


title: 49_L3_M23


title: WBJPE171125344


title: WBJPE171125341


title: 150_L3_M11


title: WBJPE171125338


title: WBJPE171125339


title: E9.5 Nanog dox+_RNAseq [MTcD1]

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description:
Nanog_E9.5_dox+_1
NanogE95_MTcD1
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

data_processing:
Libraries sequenced using Illumina GAIIx single end 61nt and HiSeq 2500.
Base-calling was produced by Illumina RTA Software v 1.13.48.
Demultiplexed fastq files were generated from the bcl files using picard tools.
Sequencing adaptor contaminations were removed using cutadapt.
Reads were mapped and gene expression quantified using rsem v1.17.
Counts were normalized using voom from Limma R package.
Genome_build: NCBIm37.v65
Supplementary_files_format_and_content: ALLSamples.NCBIM37.v65.rsem.genes.results.txt: Tab-separated text file. Contains estimated counts quantified with rsem.

source_name: E9.5 embryos, high Nanog levels

growth_protocol: Standard mouse growth conditions. Females between 6-7 weeks are mated with double homozygotes males until plug is observed.

extract_protocol:
Total RNA was purified from E7.5 pull of embryos per triplicate (8-12 embryos/replicate) or E9.5 pull of embryos per triplicate (3 embryos/replicates) following Arcturus PicoPure RNA isolation Kit protocol (Thermo Fisher Scientific).
A cDNA library was prepared according to Illumina recommendations and sequenced in a GAII analyzer or HiSeq 2500.

treatment_protocol: Doxycycline was injected at E4.5 intraperitoneally in the pregnant mother and then continued with the doxycycline treatment in the drinking water until E7.5, when embryos are extracted. For E9.5 embryos, females are treated with doxycycline in the drinking water from E6.5 to E9.5, when embryos are extracted.

tag: strain/background

tag: genotype/variation

value: ROSA26tg/+; Nanogtg/+

tag: developmental stage

value: whole embryo

tag: doxycycline induction

value: dox+


title: E9.5 Nanog dox+_RNAseq [MTcD2]

description:
Nanog_E9.5_dox+_2
NanogE95_MTcD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: E9.5 Nanog Control_RNAseq [MTsD3]

description:
Nanog_E9.5_dox-_3
NanogE95_MTsD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E9.5 embryos, control Nanog levels

value: dox-


title: E9.5 Nanog dox+_RNAseq [MTcD3]

description:
Nanog_E9.5_dox+_3
NanogE95_MTcD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: SkeletalMuscleCell_NC_Subj1

description: Gene expresison data from human skeletal muscle cells (subject 1) transfected with a negative control miRNA mimic


title: Sample 59_LC59

city: Corvallis

first: Kristina

middle: M

last: Smith

state: OR

department: Biochemisty and Biophysics

country: USA

institute: Oregon State University

description:
processed data file:
LC36-60_fpkm.txt

data_processing:
Fastq files were input to Tophat and mapped to the F. graminearum genome with options -a 5 -m 1 -i 30 -I 2000
Cufflinks was used to quantify gene expression values as reads per kilobase of exon per million reads (RPKM) using gene annotation from MIPS ftp://ftpmips.gsf.de/fungi/Fusarium/F_graminearum_PH1_v32/.
cuffdiff was used to identify differentially expressed genes
Genome_build: GCA_000240135.3
Supplementary_files_format_and_content: processed data is cuffdiff output

organism: Fusarium graminearum

growth_protocol: To generate Fusarium macroconidia, a small amount of frozen conidia or tissue was inoculated into 50 ml flasks containing CMC medium (Capellini, 1965, Mycologia) and shaken at 150 rpm for 3-4 days at room temperature (RT, ~22C). Conidia were collected by filtration through cheesecloth and stored at -80C in 25% glycerol. To isolate RNA, strains were inoculated into 50-100 ml YPD (0.3% yeast extract, 1% bacto-peptone, 2% dextrose) and incubated at 28C at 150 rpm for 24-36 hrs. Tissue was harvested by filtration and flash-frozen in liquid nitrogen until total RNA isolation.

extract_protocol:
Total RNA was assessed with Agilent 2100 Bioanalyzer to determine RNA integrity; only high quality total RNA (integrity number between 9 - 10) were used. An Ribo-Zero rRNA removal Kit (Epicentre, #MRZY1324) was used for enrichment of transcripts.
For sample 1-60 The SOLiD total RNA-seq kit (ABI SOLiD, #4445374) was used to construct template cDNA.
For sample 61-68 Illumina TruSeq RNA Sample Preparation kits were used to make RNA-seq libraries.

treatment_protocol: Total RNA was isolated as described in Wu et al, 2014 G3

tag: strain background

value: mycelia

tag: library construction

value: SOLiD total RNA-seq kit


title: Sample 60_LC60

description:
processed data file:
LC36-60_fpkm.txt


title: SkeletalMuscleCell_miR_Subj1

description: Gene expresison data from human skeletal muscle cells (subject 1) transfected with a miR-19b-3p mimic


title: Liver of NC mouse 3


title: Liver of CPT-treated HFD mouse 4


title: WBJPE171125336

value: mice skeletal muscle


title: E9.5 Nanog Control_RNAseq [MTsD2]

description:
Nanog_E9.5_dox-_2
NanogE95_MTsD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: Sample 58_LC58

description:
processed data file:
LC36-60_fpkm.txt


title: Liver of NC mouse 4


title: Sample 57_LC57

description:
processed data file:
LC36-60_fpkm.txt


title: Liver of NC mouse 2


title: E9.5 Oct4 dox+_RNAseq [MTcD5]

description:
Oct4_E9.5_dox+_5
Oct4E95_MTcD5
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E9.5 embryos, high Oct4 levels

value: ROSA26tg/+; Oct4tg/+


title: WBJPE171125335

value: male


title: WBJPE171125334


title: Sample 55_LC55

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 56_LC56

description:
processed data file:
LC36-60_fpkm.txt


title: E9.5 Oct4 dox+_RNAseq [MTcD4]

description:
Oct4_E9.5_dox+_4
Oct4E95_MTcD4
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: E9.5 Oct4 dox+_RNAseq [MTcD3]

description:
Oct4_E9.5_dox+_3
Oct4E95_MTcD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: WBJPE171125333


title: E9.5 Oct4 Control_RNAseq [MTsD3]

description:
Oct4_E9.5_dox-_3
Oct4E95_MTsD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E9.5 embryos, control Oct4 levels


title: E9.5 Oct4 Control_RNAseq [MTsD1]

description:
Oct4_E9.5_dox-_1
Oct4E95_MTsD1
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: WBJPE171125331


title: E9.5 Oct4 Control_RNAseq [MTsD2]

description:
Oct4_E9.5_dox-_2
Oct4E95_MTsD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: WBJPE171125332


title: E7.5 Nanog dox+_RNAseq [MTcD4]

description:
Nanog_E7.5_dox+_4
MTcD4
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E7.5 embryos, high Nanog levels


title: WBJPE171125330


title: WBJPE171125329


title: E7.5 Nanog dox+_RNAseq [MTcD3]

description:
Nanog_E7.5_dox+_3
MTcD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: E7.5 Nanog dox+_RNAseq [MTcD1]

description:
Nanog_E7.5_dox+_1
MTcD1
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: E7.5 Nanog Control_RNAseq [MTsD3]

description:
Nanog_E7.5_dox-_3
MTsD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E7.5 embryos, control Nanog levels


title: WBJPE171125346


title: WBJPE171125325


title: E7.5 Nanog Control_RNAseq [MTsD2]

description:
Nanog_E7.5_dox-_2
MTsD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: b_PAD_3

city: Changchun

first: xiang

last: yu

state: Jilin Provine

address: Xinzhu Road

institute: Jilin University

data_processing:
The data is processed using the following steps:Remove low quality tags, tags with 5' primer contaminants, tags without 3' primer,tags without insertion,tags with poly A,tags shorter than 18nt and summarize the length distribution of the clean tags.
After filtering, the remaining tags are called 'clean tags' and stored in FASTQ format
Bowtie2 is used to map clean reads to the reference genome and to other sRNA databases. The default alignment parameters are as follows:  Bowtie2  : -q -L 16 --phred64 -p 6.
Genome_build: NCBI GCF_000003055.6_Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: tab-delimited text files include  TPM values for each Sample …

organism: Bos taurus

source_name: adipose tissue

growth_protocol: Bovine preadipocytes were cultured with F12/DMEM including 10% FBS and 1% antibiotics. Preadipocytes were induced with insulin, dexamethasone, rosiglitazone and IBMX.

extract_protocol:
RNA was extracted with Trizol.
Experiment Pipeline Steps for Small RNA Sequencing: 1) Filter small RNA: separate 18-30nt RNA segment by PAGE gel; 2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3' end of selected small RNAs from step 1; 3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is cross-linked to the 3' adapter of RNAs and excessive free 3' adapter; 4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The connection (5鈥 adaptor) will be attached to the 5鈥 end only, but it is not c onnected to the 3' adaptor or RT primer hybrid chain. This greatly reduces self-ligation; 5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand cDNA; 6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with both 3' and 5' adaptor; 7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts; 8) Library quantitative and pooling cyclization.

tag: breed

value: holstein

tag: passage

value: preadipocytes


title: b_PAD_2


title: WBJPE171125324


title: b_PAD_1


title: WBJPE171125321


title: WBJPE171125322


title: Liver of NC mouse 1

description: Gene expression data from livers of C57/BL6J mouse feeding with normal diet for 20 weeks

value: liver


title: Sample 44_LC43

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 47_LC46

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 45_LC44

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 54_LC53

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 52_LC51

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 50_LC49

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 48_LC47

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 43_LC42

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 53_LC52

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 49_LC48

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 46_LC45

description:
processed data file:
LC36-60_fpkm.txt


title: WBJPE171125328


title: Sample 51_LC50

description:
processed data file:
LC36-60_fpkm.txt


title: b_AD_3

value: adipocytes


title: WBJPE171125327


title: WBJPE171125320


title: b_AD_2


title: WBJPE171125326


title: WBJPE171125337


title: WBJPE171125319


title: b_AD_1


title: Sample 42_LC41

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 41_LC40

description:
processed data file:
LC36-60_fpkm.txt


title: WBJPE171125318


title: WBJPE171125317


title: Sample 40_LC38

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 39_LC37

description:
processed data file:
LC36-60_fpkm.txt


title: WBJPE171125315


title: WBJPE171125314


title: Sample 37_LC35

description:
processed data file:
LC1-35_fpkm.txt

value: Z3639 (Kim, 2012, FEMS Micro.)


title: WBJPE171125316


title: WBJPE171125311


title: WBJPE171125312


title: WBJPE171125310


title: Sample 36_LC34

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 38_LC36

description:
processed data file:
LC36-60_fpkm.txt


title: Sample 34_LC32

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 35_LC33

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125309


title: Sample 32_LC30

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125308


title: Sample 31_LC29

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125313


title: WBJPE171125307


title: Sample 33_LC31

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 30_LC28

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 28_LC26

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 29_LC27

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125306


title: WBJPE171125305


title: WT-I

city: SENDAI

first: Kan

last: Saito

state: Miyagi

address: 4-1 Seiryo-machi

department: Oral Health and Development Sciences

country: Japan

institute: Tohoku University

description: Gene expression of WT mouse incisor

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Fragmentation Buffer and 10x Blocking Agent following the manufacturers instructions.   On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE Microarray 8 x 60K(G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: P0 wildtype incisor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit

value: incisor

tag: age

value: P0 day


title: Sample 27_LC25

description:
processed data file:
LC1-35_fpkm.txt

source_name: eed(UV1-8) F1

value: eed(UV1-8) F1

tag: tissue


title: WBJPE171125304

tag: strain


title: WBJPE171125302

tag: gender


title: KO-I

description: Gene expression of Sox21KO mouse incisor

source_name: P0 Sox21KO incisor


title: Sample 25_LC23

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125301


title: WBJPE171125300


title: MCF7_Input_For_ChIP_seq

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to either the hg19 (Human) or mm9 (Mouse) genome assembly using Bowtie program (http://bowtie-bio.sourceforge.net) with default parameters
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) and MACS2 (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (MACS) to call sub-peaks, summit of peaks and improve peak resolution.
RNA-seq reads were aligned  to UCSC Human reference (build mm9) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
RNA-seq aligned reads (BAM files) were analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build mm9). The expression of each transcript was quantified as the number of reads mapped to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19 (for human), mm9 (for mouse)
Supplementary_files_format_and_content: Narrow peak (bed), bdg, and wig files were generated either by MACS or MACS2

molecule: genomic DNA

source_name: Breast Cancer Cell Line

growth_protocol: K562 and MCF7 cell lines (obtained from ATCC) were grown in Dulbecco's modified Eagle medium (DMEM) supplemented with 10 % fetal calf serum and penicillin-streptomycin. CH12, B-cell lymphoma, cell line was maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol. CH12 wild type (wt) and mutant (mut) cells were described previously in (PMID: 29706548 ) and obtained as a gift from Dr. Rafael Casellas.

extract_protocol:
Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch). DNA concentration was assessed with a Qubit4 (ThermoFisher) and 5–10 ng was used to generate sequencing libraries using a TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA).
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For ChIP-seq 60 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.

tag: cell line

value: wild type (wt)

tag: expressed vector

tag: treatment


title: WBJPE171125299

source_name: skeleton muscle


title: MCF7_ChIP-seq_with_RAD21_Abs_Rep2

tag: genotype

tag: chip antibody

value: RAD21 ABs Abcam (ab992)


title: Sample 24_LC21

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 23_LC20

description:
processed data file:
LC1-35_fpkm.txt


title: MCF7_ChIP-seq_with_RAD21_Abs_Rep1


title: WBJPE171125298


title: Sample 22_LC19

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 26_LC24

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 21_LC18

description:
processed data file:
LC1-35_fpkm.txt


title: MCF7_ChIP-seq_with_CTCF_Abs_Rep2

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: Sample 20_LC17

description:
processed data file:
LC1-35_fpkm.txt


title: MCF7_ChIP-seq_with_CTCF_Abs_Rep1


title: K562_ChIP-seq_with_Mix_of_CTCF_PolyC_Abs

source_name: Human chronic myelogenous leukemia

value: Mix of CTCF rabbit polyclonal ABs(Novus Biologicals:NB100-56494, NB100-947, NB500-194, Abcam:ab70303; Bethyl Laboratories:A300-543A, A300-544A, A300-542A).


title: K562_ChIP-seq_with_CTCF_MonoN_Abs_Rep1

description:
CTCF_K562_MonoN_Rep1_treat_pileup.bdg.gz
CTCF_K562_MonoN_Rep2_treat_pileup.bdg.gz


title: K562_ChIP-seq_with_CTCF_MonoN_Abs_Rep2


title: Sample 17_LC14

description:
processed data file:
LC1-35_fpkm.txt

value: mycelia


title: Sample 16_LC13

description:
processed data file:
LC1-35_fpkm.txt

value: SOLiD total RNA-seq kit


title: Sample 18_LC15

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125297

value: mice skeletal muscle


title: WBJPE171125291


title: WBJPE171125293


title: WBJPE171125292


title: time 0; biological replicate 2

city: Dijon

first: Pascal

last: Piveteau

address: 17 rue Sully

country: France

institute: Université de Bourgogne INRA

description:
This sample is Listeria monocytogenes EGD-e time 0. It is the second of three biological replicates used in this experiment, each from separate cultures.
som04LV4

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Listeria monocytogenes EGD-e

source_name: time 0

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Listeria monocytogenes EGD-e was grown to O.D.600nm 0.4 anerobically at 25°C in TSB, centrifuged and resuspended in soil extracts.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Courtaboeuf, France) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined spectrophotometrically and denaturing gel electrophoresis.

value: EGD-e


title: time 30 minutes; soil extract DA; biological replicate 1

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract DA. It is the first of three biological replicates used in this experiment, each from separate cultures.
somo03ZWW

source_name: time 30 minutes; soil extract DA


title: time 30 minutes; soil extract DA; biological replicate 2

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract DA. It is the second of three biological replicates used in this experiment, each from separate cultures.
som03ZWX


title: time 30 minutes; soil extract TA; biological replicate 2

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract TA. It is the second of three biological replicates used in this experiment, each from separate cultures.
som03ZX2

source_name: time 30 minutes; soil extract TA


title: time 15 minutes; soil extract DA; biological replicate 1

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract DA. It is the first of three biological replicates used in this experiment, each from separate cultures.
som03ZWS

source_name: time 15 minutes; soil extract DA


title: WBJPE171125290

value: male


title: time 15 minutes; soil extract TA; biological replicate 3

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract TA. It is the third of three biological replicates used in this experiment, each from separate cultures.
som03ZWZ

source_name: time 15 minutes; soil extract TA


title: WBJPE171125294


title: time 30 minutes; soil extract DA; biological replicate 3

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract DA. It is the third of three biological replicates used in this experiment, each from separate cultures.
som03ZWY


title: time 15 minutes; soil extract TA; biological replicate 1

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract TA. It is the first of three biological replicates used in this experiment, each from separate cultures.
som03ZWP


title: time 15 minutes; soil extract DA; biological replicate 3

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract DA. It is the third of three biological replicates used in this experiment, each from separate cultures.
som03ZX0


title: time 15 minutes; soil extract TA; biological replicate 2

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract TA. It is the second of three biological replicates used in this experiment, each from separate cultures.
som03ZWR


title: time 0; biological replicate 3

description:
This sample is Listeria monocytogenes EGD-e time 0. It is the third of three biological replicates used in this experiment, each from separate cultures.
som04LV3


title: Sample 15_LC12

description:
processed data file:
LC1-35_fpkm.txt


title: time 0; biological replicate 1

description:
This sample is Listeria monocytogenes EGD-e time 0. It is the first of three biological replicates used in this experiment, each from separate cultures.
somO4LV5


title: time 15 minutes; soil extract DA; biological replicate 2

description:
This sample is Listeria monocytogenes EGD-e time 15 minutes of incubation in soil extract DA. It is the second of three biological replicates used in this experiment, each from separate cultures.
som03ZWT


title: time 30 minutes; soil extract TA; biological replicate 1

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract TA. It is the first of three biological replicates used in this experiment, each from separate cultures.
som03ZX1


title: K562_ChIP-seq_with_CTCF_RabbitC_Abs

description: CTCF_K562_RabbitC_treat_afterfiting_all.wig.gz

value: CTCF rabbit polyclonal Millipore (07-729)


title: time 30 minutes; soil extract TA; biological replicate 3

description:
This sample is Listeria monocytogenes EGD-e time 30 minutes of incubation in soil extract TA. It is the third of three biological replicates used in this experiment, each from separate cultures.
som03ZWV


title: WBJPE171125288


title: Nalm-6 cells, UBE2R2 knockout replicate 2 day 14

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description: sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Genome_build: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library.
Supplementary_files_format_and_content: tab separated sgRNA read counts for each sample

source_name: Nalm-6 pre-B lymphoid cell line

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA sequences were recovered and fitted with Illumina adaptors by PCR as previously described (Bertomeu et al., 2017, PMID:29038160).

tag: cell type

value: pre-B lymphoid cells

value: UBE2R2 knockout

tag: time

value: day 14

tag: infection

value: pooled sgRNA library


title: K562_ChIP-seq_with_CTCF_MonoC_Abs

value: CTCF mouse monoclonal SantaCruz (SC-271514, B-5)


title: WBJPE171125287


title: Sample 13_LC10

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 14_LC11

description:
processed data file:
LC1-35_fpkm.txt


title: Nalm-6 cells, UBE2R2 knockout replicate 2 day 0

description: sgRNAs PCR-amplified from genomic DNA

value: day 0


title: Sample 11_LC8

description:
processed data file:
LC1-35_fpkm.txt


title: Nalm-6 cells, UBE2R2 knockout replicate 1 day 14

description: sgRNAs PCR-amplified from genomic DNA


title: Nalm-6 cells, UBE2R2 knockout replicate 1 day 0

description: sgRNAs PCR-amplified from genomic DNA


title: WBJPE171125283


title: WBJPE171125281


title: Sample 12_LC9

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125282


title: Nalm-6 cells, UBE2R1 and UBE2R2 double-knockout replicate 2 day 14

description: sgRNAs PCR-amplified from genomic DNA

value: UBE2R1 and UBE2R2 double-knockout


title: Sample 9_LC6

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 8_LC5

description:
processed data file:
LC1-35_fpkm.txt


title: Nalm-6 cells, UBE2R1 and UBE2R2 double-knockout replicate 2 day 0

description: sgRNAs PCR-amplified from genomic DNA


title: WBJPE171125276


title: Nalm-6 cells, UBE2R1 and UBE2R2 double-knockout replicate 1 day 14

description: sgRNAs PCR-amplified from genomic DNA


title: WBJPE171125280


title: WBJPE171125277


title: Sample 5_LC2

description:
processed data file:
LC1-35_fpkm.txt

source_name: FGSG_04692::neo; Δkmt6

value: FGSG_04692::neo; {delta}kmt6


title: Sample 6_LC3

description:
processed data file:
LC1-35_fpkm.txt

source_name: FGSG_08791::neo; Δkmt6

value: FGSG_08791::neo; {delta}kmt6


title: WBJPE171125274


title: Sample 7_LC4

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 10_LC7

description:
processed data file:
LC1-35_fpkm.txt


title: WBJPE171125275


title: Nalm-6 cells, UBE2R1 and UBE2R2 double-knockout replicate 1 day 0

description: sgRNAs PCR-amplified from genomic DNA


title: Sample 4_LC1

description:
processed data file:
LC1-35_fpkm.txt


title: Sample 3_PNNL3

description:
processed data file:
PNNL1-3_fpkm.txt


title: Nalm-6 cells, UBE2R1 knockout day 0

description: sgRNAs PCR-amplified from genomic DNA

value: UBE2R1 knockout


title: Nalm-6 cells, UBE2R1 knockout day 14

description: sgRNAs PCR-amplified from genomic DNA


title: Nalm-6 cells, GFP and AAVS1 double sgRNA infection control day 14

description: sgRNAs PCR-amplified from genomic DNA


title: WBJPE171125273


title: Sample 2_PNNL2

description:
processed data file:
PNNL1-3_fpkm.txt


title: Nalm-6 cells, GFP and AAVS1 double sgRNA infection control day 0

description: sgRNAs PCR-amplified from genomic DNA


title: WBJPE171125270


title: Sample 1_PNNL1

description:
processed data file:
PNNL1-3_fpkm.txt


title: Posterior Capsule 4D

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

data_processing:
TopHat for alignment
FeatureCounts to quantify expression
Genome_build: hg19
Supplementary_files_format_and_content: tsv format containg raw gene counts and RPKM normalize expression values

source_name: Posterior Capsule

extract_protocol:
During primary or revision TKA surgeries, tissues were collected directly from the surgery room.  RNA was extracted from frozen tissue using the miRNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Posterior Capsule

tag: tissue type

value: rTKA-A


title: WBJPE171125267


title: Posterior Capsule 20D


title: WBJPE171125264


title: Posterior Capsule 18D


title: WBJPE171125256


title: WBJPE171125268


title: Posterior Capsule 13D


title: Posterior Capsule 14F

value: rTKA-NA


title: gDNA from normal human bone marrow BM5776

type: genomic

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum  concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours.  Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode.

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

source_name: Bone marrow, normal

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

tag: group

value: normal

tag: age at diagnosis (days)


title: Posterior Capsule 1F


title: Posterior Capsule 5F


title: Posterior Capsule 3E

value: pTKA


title: WBJPE171125261

value: mice skeletal muscle

value: male


title: Posterior Capsule 1E


title: Posterior Capsule 13F


title: WBJPE171125262


title: WBJPE171125247


title: Posterior Capsule 11E


title: WBJPE171125249


title: WBJPE171125254


title: WBJPE171125255


title: gDNA from normal human bone marrow BM5756


title: WBJPE171125242


title: Posterior Capsule 10E


title: gDNA from normal human bone marrow BM5751


title: gDNA from normal human bone marrow BM4641


title: Sample 19_LC16

description:
processed data file:
LC1-35_fpkm.txt

tag: strain background

value: mycelia

tag: library construction

value: SOLiD total RNA-seq kit


title: gDNA from normal human bone marrow BM5759


title: WBJPE171125239


title: WBJPE171125240


title: WBJPE171125238


title: E-UnTD31

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequencing reads were mapped to the the human genome (hg19) and the GencodeV7 (Harrow et al., 2012) transcriptome annotation
the resulting BAM files were converted to SAM format and sorted, using SAMtools
The BEDtools function coverageBed (Quinlan and Hall, 2010) was then used to estimate gene expression as counts
The RSEQtools function MRFquantifier (Habegger et al., 2011) was used to estimate gene expression as RPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts and RPKM values for each Sample. Column headers are: Chromosome, Gene Start Coord, Gene End Coord,GeneID, N of Reads Overlapping With Gene, N of Bases In Gene With Non Zero Coverage, Gene Length, Fraction Of Gene Length With Non-zero Coverage

molecule: polyA RNA

source_name: ORG

growth_protocol: We used three human male control iPSC cell lines (07-01#1, 1123-01#3, 1120-01#7), previously generated in our laboratory (Mariani et al., 2015). Telencephalic organoids (ORG) were differentiated as described  (Mariani et al., 2015) by manually dissecting neural rosettes and culturing them free-floating. For the ‘dissociation followed by immediate re-aggregation’ (REAG) and ‘monolayer’ (MON) culture conditions, neuronal rosettes were dissociated into single cells and quickly re-aggregated in a 96 well plate (REAG), or plated onto poly-L-ornithine and laminin coated well as monolayer cultures (MON). The preparations were analyzed at TD 2, TD11 and TD 31 of terminal differentiation

extract_protocol:
Total cellular RNA was extracted from 15-20 randomly collected intact and re-aggregated organoids, and from a 9 cm2 well for the monolayer culture at TD 2, TD 11 and TD 31 and purified using PicoPure RNA isolation kit (Applied Biosciences). Poly(A)+ RNA was used as template for the preparation of cDNA libraries, which were then subject to single end RNA sequencing experiments.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: day of terminal differentiation (td)

tag: batch


title: E-DiTD31

source_name: REAG


title: E-DiTD11


title: E-MoTD11

source_name: MON


title: gDNA from normal human bone marrow BM4473


title: WBJPE171125236

tag: tissue

tag: strain


title: E-UnTD11

tag: cell line


title: gDNA from normal human bone marrow BM4508

tag: gender


title: WBJPE171125237


title: gDNA from normal human bone marrow RO02815


title: WBJPE171125235


title: gDNA from normal human bone marrow RO02722


title: WBJPE171125233


title: WBJPE171125286


title: E-DiTD2


title: WBJPE171125234


title: WBJPE171125230


title: WBJPE171125228


title: D-DiTD31


title: WBJPE171125245


title: gDNA from normal human bone marrow RO02590


title: D-MoTD31


title: WBJPE171125226


title: gDNA from normal human bone marrow RO02505B


title: D-DiTD11


title: K562_ChIP-seq_with_IGG_Abs_Control

value: wild type (wt)

tag: expressed vector

tag: treatment

value: Mouse IGG, Diagenode (C15400001-15)


title: WBJPE171125224


title: E-UnTD2


title: E-MoTD2


title: WBJPE171125289


title: WBJPE171125223


title: D-MoTD2


title: WBJPE171125222


title: WBJPE171125221


title: D-UnTD2


title: gDNA from normal human bone marrow RO02461


title: D-DiTD2


title: gDNA from normal human bone marrow RO02441


title: WBJPE171125220


title: B-DiTD31


title: WBJPE171125219


title: SH-SY5Y cells, dCT2_1

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

description: transduced SH-SY5Y

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

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

data_processing: R Studio

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from SH-SY5Y samples using Quick-gDNA MiniPrep kit (Zymo Research) according to standard instructions

value: Female

value: SH-SY5Y neuroblastoma cell line

value: transduced with dCT


title: SH-SY5Y cells, NT1_1

description: non-transduced SH-SY5Y

value: non-transduced


title: WBJPE171125215


title: SH-SY5Y cells, dCdT2_1

description: transduced SH-SY5Y

value: transduced with dCdT


title: gDNA from normal human bone marrow RO02431


title: B-MoTD11


title: D-MoTD11


title: WBJPE171125213


title: SH-SY5Y cells, dCdT1_1

description: transduced SH-SY5Y


title: B-DiTD11


title: SH-SY5Y cells, dC1_1

description: transduced SH-SY5Y

value: transduced with dC


title: B-MoTD2


title: WBJPE171125227


title: WBJPE171125211


title: WBJPE171125212


title: SH-SY5Y cells, NT2_1

description: non-transduced SH-SY5Y


title: B-DiTD2


title: WBJPE171125210


title: WBJPE171125209


title: B-UnTD11


title: B-UnTD2


title: gDNA from normal human bone marrow RO02356


title: SH-SY5Y cells, dCT1_1

description: transduced SH-SY5Y


title: A-MoTD31


title: WBJPE171125207


title: A-DiTD31


title: A-UnTD31


title: gDNA from normal human bone marrow RO02297


title: D-UnTD11


title: WBJPE171125205


title: A-UnTD11


title: WBJPE171125204


title: WBJPE171125203


title: A-DiTD11


title: gDNA from subject PASWAT

source_name: AML, pre-treatment

value: tumor


title: A-MoTD2


title: WBJPE171125201


title: WBJPE171125225


title: SH-SY5Y cells, dC2_1

description: transduced SH-SY5Y


title: WBJPE171125200


title: gDNA from subject PASGGK


title: A-DiTD2


title: A-UnTD2


title: WBJPE171125199


title: H2O2 rep3

first: Cong

last: Lin

state: Jilin

address: Renmin Street

institute: Northeast Normal University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: lung

growth_protocol: IMR90 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % (vol/vol) fetal bovine serum, and penicillin-streptomycin at 37℃, 5% CO2 and 5% O2. HEK-293T cultured at 37℃, 5% CO2.

extract_protocol:
IMR90 cells were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For H2O2-induced premature senescence, the growing IMR90 cells were seed at a cell density of 1.5x106 in 100mm dishes.On second day after seeding, the cells were incubated with the culture medium containing 150μM concentrations of H2O2 for 2 h. After H2O2 treatment,the cells were washed twice with PBS and cultured with fresh complete medium for 48h

value: human diploid fibroblast IMR-90

tag: passages

tag: age

value: 16 weeks


title: WBJPE171125198

source_name: skeleton muscle


title: WBJPE171125197


title: Ctrl rep3

tag: cell type


title: WBJPE171125202


title: H2O2 rep1


title: gDNA from subject PARJCR

value: Male


title: gDNA from subject PARUNX


title: Ctrl rep2


title: gDNA from subject PASCCS


title: Ctrl rep1


title: WBJPE171125195


title: WBJPE171125194


title: gDNA from subject PARIHK


title: gDNA from subject PASIZX


title: WBJPE171125208


title: WBJPE171125193


title: WBJPE171125192


title: USP36 siRNA

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_11 was used.
Clean read sequences were aligned with STAR version 2.6.1c.
Read counting for exonic regions was performed with subread featureCounts version 1.6.3.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

source_name: HeLa cervical carcinoma cells

growth_protocol: parental human cervix carcinoma HeLa cells were routinely grown in DMEM supplemented with 10% FBS without antibiotics

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen, Germany) following the manufacturer's instructions and 600 ng of RNA were reverse transcribed using the Transcriptor High Fidelity cDNA Synthesis Kit (Roche, Switzerland)  following the manufacturer's instructions
Sequencing libraries have been prepared with Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer's handbook.

treatment_protocol: HeLa cells were transfected with 10nM control or USP36 siRNA on three consecutive days, with media change after every 24h, and RNA was extracted 24h after the last siRNA treatment

value: parental epithelial HeLa cells

value: low passage number <8

tag: sirna treatment


title: U1_OE-2

city: Tianjin

first: Sha

last: Zhou

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

description:
2_combined
OE_2

data_processing:
Adapter and low quality reads was trimmed by TrimGalore.RNA-seq reads were mapped to hg38 genome using STAR.
Reads count were caculated by FeatureCounts.The differentially expressed gene analysis was performed by DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include count values for each Sample.

source_name: neuron_U1 OE

growth_protocol: Maintenance of Human Pluripotent Stem Cells (H1) in TeSR™-E8™ for complete instructions on culturing high-quality ES cells using feeder-free maintenance media.  STEMdiff™ Neural Induction Medium was used to generate CNS-type NPCs from human ES using monolayer culture protocols. STEMdiff™ Neuron Differentiation Kit was used to generate neuronal precursors from NPCs derived from human ES cells  using the STEMdiff™ Neural Induction Medium. The neuronal precursors  was matured using STEMdiff™ Neuron Maturation Kit to produce functional neurons.

extract_protocol:
Total RNA of cells were extracted by RNAiso plus reagent (TaKaRa) following the manufacture‘sprotocol. For genes expression analysis, total RNA was treated by DNase I (Thermosentific, EN0521) for 30~45min to remove genome DNA. DNase I was inactivated in 70~75 °C for 10min.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. mRNA were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription , then was followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. PCR is to amplify the cDNA fragments with adaptors from previous step. PCR products are purified with the SPRI beads, and dissolved in EB solution. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library . Library was validating on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: Neurons (1 × 105 cells) were transfected 10μL U1 snRNA overexpression lentivirus vector for 36h.

tag: cell line source

value: Human Pluripotent Stem Cells (H1)

value: neuron

tag: genotype/variation

value: snRNA U1 overexpression


title: control siRNA

value: control


title: U1_OE-1

description:
1_combined
OE_1


title: WBJPE171125191

city: Hangzhou

first: Yixiao

last: Liu

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

value: mice skeletal muscle

value: male


title: WBJPE171125190


title: WBJPE171125196


title: B-UnTD31


title: WT_3D7-G7-Input_R_rep1_ChIRP-seq

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

description: the probe pool were designed on the antisense strand of RUF6 ncRNAs

data_processing:
Library strategy: ChIRP-seq
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
ChIRP peaks were predicted by MACS2 (v2.1.1)  with Q-value < 0.01 and the parameter: -c.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

organism: Plasmodium falciparum

growth_protocol: Parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin.

extract_protocol:
Ring-stage (15 hr post invasion ±5 hr) synchronized 3D7-G7 and the PfRrp6-DD-1C line were used in ChIRP assay. Parasites culture (1x109 rings) were cross-linked as the ChIP arrays. After three washes with cold 1 x PBS, the parasite pellets were lysed with the swelling buffer (0.1M Tris pH 7.0, 10mM KOAc, 15mM MgOAc, 1% NP-40, 1mM DTT, protease inhibitor, and RNase inhibitor) at 4℃ for 10min with rotator. After centrifuge at 10,000 rpm for 10 min at 4 ℃, the parasites were resuspended in 150μl SDS Lysis Buffer ( 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0 ) for sonication. Chromatin was sheared into 200-500 bp fragments with Bioruptor (BioruptorTM UCD-200) of highest power for 4x4 min at 30 sec intervals. Chromatin is diluted in 2 times volume of hybridization buffer (500mM NaCl, 1%SDS, 100mM Tris 7.0, 10mM EDTA, 15% Formamide, add DTT, PMSF, P.I, and RNase inhibitor fresh). 100 pmol probes were added to each reaction, which was mixed by end to-end rotation at 37℃ for 4 hours. Streptavidin-magnetic T1 beads were washed three times in lysis buffer, blocked with 500ng/μl yeast total RNA and 1mg/ml BSA for 1 hour at 37℃, and washed three times again in lysis buffer before resuspended in its original volume. 100μl washed/blocked T1 beads were added per 100 pmol of probes, and the whole reaction was mixed for another 45min at 37℃. Beads : biotin -probes : RNA : chromatin products were captured by magnets (Invitrogen) and washed five times with 40x beads volume of wash buffer (2 x SSC, 0.5% SDS, add DTT and PMSF fresh). After last wash buffer was removed carefully with P-10 pipette, beads were resuspended in 3x original volume DNA elution buffer (50mM NaHCO3, 1%SDS, 200mM NaCl), and DNA was eluted with 100μg/ml RNase A and 0.1U/μl RNase H. RNase elution was carried out twice at 37 ℃ with end-to-end rotation. Then chromatin was reverse-crosslinked with  0.2U/μl protease K at 65℃ overnight. DNA was then extracted with equal volume of phenol : chloroform : isoamyl. Eluted DNA was subject to high-throughput sequencing.
To prepare sequencing libraries, 10 ng of input DNA, 3-5ng IPed DNA were end repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific). Libraries were amplified using an optimized KAPA protocol using KAPA HiFi HotStart ready mix (KAPA Biosystems) and the following PCR program: 98°C for 3 min followed by 14 cycles of 98°C for 20 sec, 65°C for 30 s; 68°C for 30s; finally extended 68°C for 5min. Amplified libraries were size-selected for 300-600 bp using 2% agarose gels. ChIP-seq libraries were sequenced on the HiSeq X Ten machine.

treatment_protocol: Parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments ((Lambros and Vanderberg, 1979)

tag: development stage

value: Ring

value: Pf 3D7

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: WT-2

description:
C3_combined
Control_2

value: wild type (empty vector control)


title: WT_3D7-G7_R_rep2_ChIRP-seq


title: WBJPE171125189

address: Yuhangtang road


title: WBJPE171125188


title: WT-1

description:
C2_combined
Control_1


title: WT_3D7-G7_R_rep1_ChIRP-seq


title: HFE145 HNF4α-002

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: HNF4α overexpression in HFE145

data_processing:
Reads from ChIP-seq were mapped to the hg19 reference genome using BWA, retaining reads with MAPQ>=10, removing PCR duplicates by using samtools. Peaks were predicted using MACS2 with -q 0.01 --extsize 250
RNA-seq reads were processed using the star-rsem pipeline published at https://github.com/gis-rpd/pipelines
Genome_build: hg19
Supplementary_files_format_and_content: peaks, counts, and FPKM

source_name: Normal Gastric Line

extract_protocol: ChIP-seq libraries were prepared following manufacturer protocols (New England Biolabs). RNAseq libraries were prepared using Illumina Tru-Seq RNA Sample Preparation v2 protocol, according to the manufacturer’s instructions.


title: WBJPE171125187


title: PfRrp6-DD-1C_R_rep2_ChIRP-seq


title: WBJPE171125214


title: WBJPE171125185


title: PfRrp6-DD-1C_R_rep1_ChIRP-seq


title: YCC3 shHNF4α-2

description: HNF4α knockdown in YCC3

source_name: Gastric Cancer Line


title: WBJPE171125184


title: WBJPE171125186


title: YCC3 shHNF4α-1

description: HNF4α knockdown in YCC3


title: H2O2 rep2


title: WBJPE171125182


title: gDNA from subject PASWIM

tag: group

value: tumor

tag: age at diagnosis (days)

value: Female


title: YCC3 shCtrl

description: A control for HNF4α knockdown in YCC3


title: YCC3 INPUT

description: A control library for HNF4α ChIP-seq in YCC3 cells


title: gDNA from subject PARDRM


title: WBJPE171125181

tag: tissue


title: gDNA from subject PAMYAS


title: WBJPE171125183

tag: strain


title: WBJPE171125180


title: NUGC4 INPUT

description: A control library for HNF4α ChIP-seq in NUGC4 cells

tag: cell line


title: NUGC4 HNF4α_ChIP

description: HNF4α ChIP-seq in NUGC4 cells


title: YCC3 HNF4α_ChIP

description: HNF4α ChIP-seq in YCC3 cells


title: PfRrp6-DD-1C-Input_R_rep1_ChIRP-seq


title: WBJPE171125178

tag: gender


title: WBJPE171125179


title: HFE145 GFP

description: A control for HNF4α overexpression in HFE145


title: KATO-III INPUT

description: A control library for HNF4α ChIP-seq in KATO-III cells

value: KATO-III


title: Ist1 INPUT

description: A control library for HNF4α ChIP-seq in Ist1 cells


title: gDNA from subject PATCLR

value: Male


title: KATO-III HNF4α_ChIP

description: HNF4α ChIP-seq in KATO-III cells


title: gDNA from subject PARAJX


title: YCC3 shHNF4α-Pool

description: HNF4α knockdown in YCC3


title: Ist1 HNF4α_ChIP

description: HNF4α ChIP-seq in Ist1 cells


title: WBJPE171125177


title: WBJPE171125176


title: WBJPE171125175


title: gDNA from subject PARERV


title: WBJPE171125173


title: gDNA from subject PAPXVK


title: WBJPE171125172


title: gDNA from subject PASBSB


title: IM95 HNF4α_ChIP

description: HNF4α ChIP-seq in IM95 cells


title: WBJPE171125169


title: OCUM-1 INPUT

description: A control library for HNF4α ChIP-seq in OCUM-1 cells


title: WBJPE171125167


title: OCUM-1 HNF4α_ChIP

description: HNF4α ChIP-seq in OCUM-1cells


title: gDNA from subject PASNDH


title: SNU16 INPUT

description: A control library for HNF4α ChIP-seq in SNU16 cells


title: WBJPE171125166


title: gDNA from subject PASNLR


title: WBJPE171125164


title: WBJPE171125165


title: pbmc_treated2

city: Tampa

first: Alex

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adapter sequence or low quality sequence then mapped to mm10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
DEseq2 Bioconductor package was used for differential expression analysis

source_name: peripheral blood mononuclear cells

growth_protocol: heparinized blood was processed with Histopaque-1077 to isolated PBMCs which were cultured overnight in RPMI1640 with 20% autologous plasma in 60 mm tissue culture dishes

extract_protocol:
Total RNA was extracted with Qiagen Rneasy kit according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with either 0.1% DMSO or 500 nM ganetespib for 24 hrs

value: pbmc

value: ganetispib for 24hr


title: WBJPE171125163


title: gDNA from subject PARPBF


title: pbmc_treated1


title: gDNA from subject PASTTJ


title: IM95 INPUT

description: A control library for HNF4α ChIP-seq in IM95 cells


title: gDNA from subject PASFEW


title: pbmc_control1

value: vehicle


title: WBJPE171125160


title: WBJPE171125162


title: gDNA from subject PAPZJT


title: gDNA from subject PASUHK


title: WBJPE171125161


title: WBJPE171125158


title: WBJPE171125159


title: iCrLin28 hESC-β like cells –dox rep2 mRNA

city: San Francisco

first: Cassandra

last: Belair

address: 35 Medical Center Way

department: Urology

institute: UCSF

description:
processed data file: Supp_XZlib2_kallisto_counts.txt
d27Doxm2
XZ08_S14_L002_R1_001

data_processing:
miRNA sequencing data was demultiplexed and adapter trimmed using CutAdapt v1.8
miRNA sequences aligned using Bowtie v1.1.2 parameters  -n 0 -l 18 --best
RNA sequencing data were preprocessed using Kallisto using an index generated to Gencode v24
Genome_build: Gencode Version 24 (August 2015 freeze, GRCh38) - Ensembl 83, 84
Supplementary_files_format_and_content: tab-delimited text files, counts

source_name: iCrLin28 hESC-β like cells –dox

extract_protocol:
Total RNA was extracted with micro RNeasy kit (Qiagen), treated with DNase I kit (Qiagen) and quantified with Qubit (Invitrogen). Bioanalyzer (Agilent) was employed to evaluate RNA quality.
Small RNA-seq libraries were made as previously described(Hafner et al., 2012). RNA-seq libraries were made by using Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and Nextera XT DNA Library Preparation kit (Illumina) thereafter.

value: hESC-derived beta like cells

tag: origin

value: INS-GFP MEL-1

tag: genetic manipulation

value: Lin28 guide RNA and doxycycline inducible Cas9 in hAAVS1 locus


title: iCrLin28 hESC-β like cells –dox rep3 mRNA

description:
processed data file: Supp_XZlib2_kallisto_counts.txt
d27Doxm3
XZ09_S15_L002_R1_001


title: iCrLin28 hESC-β like cells +dox rep3 mRNA

description:
processed data file: Supp_XZlib2_kallisto_counts.txt
d27Doxp3
XZ12_S18_L002_R1_001

source_name: iCrLin28 hESC-β like cells +dox


title: gDNA from subject PASWGS


title: iCrLin28 hESC-β like cells +dox 2 mRNA

description:
processed data file: Supp_XZlib2_kallisto_counts.txt
d27Doxp2
XZ11_S17_L002_R1_001


title: iCrLin28 hESC-β like cells +dox rep1 mRNA

description:
processed data file: Supp_XZlib2_kallisto_counts.txt
d27Doxp1
XZ10_S16_L002_R1_001


title: WBJPE171125157

value: mice skeletal muscle


title: WBJPE171125155

value: male


title: gDNA from subject PASWVH


title: WBJPE171125156


title: gDNA from subject PASZNB


title: SNU16 HNF4α_ChIP

description: HNF4α ChIP-seq in SNU16 cells


title: Post Tx hESC-β cells rep 3 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA24_721
trimmed-TA24_721

source_name: Post Tx hESC-β cells

value: kidney capsule matured hESC-derived beta like cells


title: pbmc_control2

tag: treatment


title: gDNA from subject PASYTG


title: D-UnTD31

tag: day of terminal differentiation (td)

tag: batch


title: WBJPE171125153


title: WBJPE171125152


title: gDNA from subject PASYTW


title: gDNA from subject PASZJC


title: gDNA from subject PASYYW


title: WBJPE171125151


title: Post Tx hESC-β cells rep2  microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA23_720
trimmed-TA23_720

tag: cell type


title: hESC-β like cells rep 2 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA08_6.10_P4_Ghigh
trimmed-TA08_6-10_P4_Ghigh

source_name: hESC-β like cells


title: Post Tx hESC-β cells rep 1 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA22_4736
trimmed-TA22_4736


title: WBJPE171125150


title: hESC-β like cells rep 1 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA04_6.2_P4_Ghigh
trimmed-TA04_6-2_P4_Ghigh


title: WBJPE171125149


title: human islets rep 3 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA17_Hip83
trimmed-TA17_Hip83

source_name: human islet

value: human pancreatic islet

value: cadaveric pancreas


title: gDNA from subject PATBPW


title: human islets rep 2 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA16_Hip82
trimmed-TA16_Hip82


title: WBJPE171125148


title: gDNA from subject PATBXU


title: WBJPE171125146


title: gDNA from subject PATCTM


title: human islets rep 1 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA15_HI7.11.14
trimmed-TA15_HI7-11-14


title: WBJPE171125154


title: Post Tx hESC-β cells rep 2 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Mouse721
XZ12_S58_L005_R1_001


title: gDNA from subject PATDLH


title: WBJPE171125147


title: WBJPE171125145


title: Post Tx hESC-β cells rep 1 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Mouse720
XZ11_S57_L005_R1_001


title: hESC-β like cells rep 3 microRNA

description:
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA12_6.17_P4_Ghigh
trimmed-TA12_6-17_P4_Glow


title: gDNA from subject PATGGI


title: gDNA from subject PATBIR


title: WBJPE171125143


title: gDNA from subject PATANY


title: hESC-β like cells rep 4 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
BL4
XZ4_S50_L005_R1_001


title: WBJPE171125142


title: hESC-β like cells rep 3 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
BL3
XZ3_S49_L005_R1_001


title: hESC-β like cells rep 1 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
BL1
XZ1_S47_L005_R1_001


title: gDNA from subject PATHIW


title: hESC-β like cells rep 2 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
BL2
XZ2_S48_L005_R1_001


title: WBJPE171125141


title: WBJPE171125140


title: human islets rep 4 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Hip90
XZ8_S54_L005_R1_001


title: gDNA from subject PATKGM


title: gDNA from subject PATKLS


title: human islets rep 3 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Hip83
XZ7_S53_L005_R1_001


title: human islets rep 2 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Hip82
XZ6_S52_L005_R1_001


title: m6A_IP_1

city: Chicago

first: Qili

last: Fei

state: Illinois

address: 929 E 57th Ave

institute: University of Chicago

data_processing:
After quality control and adapter trimming, readsd were mapped to the human genome mm9 using TopHat v2.1.0 allowing for no more than two mismatches.
For m6A-seq data analysis, the m6A-enriched regions in each m6A-IP sample were identified by MACS2 v2.1.0 with corresponding input library as control.
Genome_build: mm9
Supplementary_files_format_and_content: peaks

extract_protocol:
Total RNA was purified from whole brains with the TRIzol reagent. Polyadenylated RNA was purified from total RNA using the Dynabeads mRNA DIRECT kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: antibody

value: m6A antibody


title: m6A_IP_2


title: WBJPE171125144


title: gDNA from subject PASRSS

value: tumor


title: gDNA from subject PATKUG


title: m6A_input_3


title: gDNA from subject PATCWP

value: Female


title: WBJPE171125138


title: gDNA from subject PATELT


title: WBJPE171125137


title: m6A_input_2


title: WBJPE171125136


title: gDNA from subject PAPWFN


title: WBJPE171125135


title: gDNA from subject PASVWK


title: m6A_input_1


title: m6A_IP_3


title: pNSC_3D_ab42+IL4_R3

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

data_processing:
The FastQ files were aligned to human genome (GRCh38/hg19) using gsnap (2016-09-23) with default options. The read counts for each gene were calculated using featureCounts (V1.5.3) and GTF file from ensemble genome browser (Homo_sapiens.GRCh38.90.gtf).
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: The processed data file contains read counts calculated by featureCounts. The first 6 columns contain information about the gene (Geneid, Chr, Start, End, Strand, Length), and the remaining columns countain read counts of each gene in each sample. The colnames have not been changed and contain Raw Files names with additional suffix ".gz.sam"

source_name: 3D cell culture

growth_protocol: Primary human neural stem cells (human cortical astrocytes) from fetus, gestation week 21, obtained from ScienCell Reaserch Laboratory (SRL) (Cat#1800) at passage one and delivered frozen. The HCCs are seeded on conventional T75 flasks or 24-well plates and cultured using Astrocyte medium (SRL, Cat No. 1801) supplemented with 5% of fetal bovine serum (SRL, Cat. No.0010), 1% of astrocyte growth supplement (SRL,Cat. No. 1852) and 1% of penicillin/streptomycin solution (SRL, Cat. No. 0503) in an incubator with an atmosphere of 5% CO2/95% air and 37 °C. Induced human neural stem cells (HIP, BC1 line, Amsbio, Cat No. GSC-4311) were thawed and cultured for expansion using Geltrex precoating of flasks according to manufacturer’s instructions. The medium used for expansion and further culturing was the “expansion medium” formulation according to the manufacturer’s instructions. NeuralX™ NSC Medium; 2% GS22™ Neural Supplement 10; 1X Non-Essential Amino Acids, 2mM L-alanine/L-glutamine; 20 ng/ml FGF2 were used. The gels were cultured and incubated in 5% CO2/95% air at 37 °C.

extract_protocol:
For cells from 3D gels, we used Norgen Total RNA Isolation Kit. RNA isolation performed according to the protocol suggest by the company except; 3 gels lysed in 1ml RL buffer with 10 µL beta-mercaptoethanol. Centrifuged at 10000g for 5 min at RT and supernatant (~930 µL) transfered to a new eppendorf. 580 µL %96-99 ethanol added and mixed throughly. After passing through samples on columns, washings and DNase I treatment done accroding to the protocol suggests and RNA eluted in50 µL  nuclease free water. Samples ran on Agilent Bioanalyser for RNA quality, samples with RNA integrity >= 9.0 used for library preparation.
Total RNA with an integrity number of ≥ 8 was used. mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

treatment_protocol: For 3D cultures, Abeta42 is mixed with heparin solution at the time the gels are prepared. Cultures are performed for three weeks with frequent media changes. DMSO, KYNA and IL4 were present in the culture medium throughout the culture at the following concentrations: IL4 (10 nM), KYNA (10 uM), DMSO (0.1%). Cultures are performed for three weeks with frequent media changes.

tag: cells

value: Human Cortical Astrocytes from human fetal cortex


title: pNSC_3D_ab42+IL4_R2


title: WBJPE171125139


title: WBJPE171125134


title: pNSC_3D_ab42+IL4_R1


title: gDNA from subject PARAEG

value: Male


title: gDNA from subject PARAPD


title: WBJPE171125133


title: WBJPE171125132


title: human islets rep 1 mRNA

description:
processed data file: Figure2_XZLib1_kallisto_counts.txt
Hip7_11_14
XZ5_S51_L005_R1_001


title: gDNA from subject PARIAP


title: mut CH12

first: Elena

last: Pugacheva

institute: NIH

description: mutant

data_processing:
Hi-C reads (paired end, 50 bases) were aligned against the mm9 genome using BWA-mem.
PCR duplicate reads were removed using Picard MarkDuplicates.
We used juicebox to create hic file with -q 30 -f options and to visualize Hi-C data.
The aggregate analysis of chromatin loops was performed using Aggregate Peak Analysis (APA) with default parameters and 10 kb resolution.
Genome_build: mm9
Supplementary_files_format_and_content: hic files for visualizion of Hi-C data.

source_name: Mouse B lymphoma cell

growth_protocol: CH12F3 (CH12) B lymphoma cell line was maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol.

extract_protocol:
In situ Hi-C experiments were performed using the MboI restriction enzyme. The crosslinked pellets (1.5 million cells) were incubated and washed with 200 μL of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 33 μL Protease Inhibitor (Sigma, P8340)) on ice, and then incubated in 50 μL of 0.5% SDS for 10 min at 62°C. After heating, 170 μL of 1.47% Triton X-100 was added and incubated for 15 min at 37˚C. To digest chromatin 100 U MboI and 25 μL of 10X NEBuffer2 were added followed by overnight incubation at 37˚C. The digested ends were filled and labeled with biotin by adding 37.5 μL of 0.4 mM biotin-14-dATP (Life Tech), 1.5 μL of 10 mM dCTP, 10 mM dTTP, 10 mM dGTP, and 8 μL of 5 U/μL Klenow (New England Biolabs) and incubating at 23°C for 60 minutes with shaking at 500 rpm on a thermomixer. Then the samples were mixed with 1x T4 DNA ligase buffer (New England Biolabs), 0.83% Triton X-100, 0.1 mg/mL BSA, 2000 U T4 DNA Ligase (New England Biolabs, M0202), and incubated for at 23°C for 4 hours to ligate the ends. After the ligation reaction, samples were resuspended in 550 μL 10 mM Tris-HCl, pH 8.0. To reverse the crosslinks, 50 μL of 20 mg/mL Proteinase K (New England Biolabs) and 57 μL of 10% SDS were mixed with the samples, and incubated at 55°C for 30 minutes, and then 67 μL of 5 M NaCl were added followed by overnight incubation at 68°C. After cooling at room temperature, 0.8X Ampure (Beckman-Coulter) purification was performed, and the samples were sonicated to a mean fragment length of 400 bp using Covaris M220. Two rounds of Ampure (Beckman-Coulter) beads purification was performed for size selection.
Biotin-labeled DNA was purified using Dynabeads MyOne T1 Streptavidin beads (Invitrogen). The beads were washed with 400 μL of 1x Tween Wash Buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), and resuspended in 300 μL of 2x Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl). The beads were added to samples and incubated for 15 minutes at room temperature. Then the beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Then the beads were equilibrated once in 100 uL 1x NEB T4 DNA ligase buffer (New England Biolabs) followed by removal of the supernatant using a magnetic rack. To repair the fragmented ends, the beads were resuspended in 100 μL of the following: 88 μL 1X NEB T4 DNA ligase buffer (New England Biolabs, B0202), 2 μL of 25 mM dNTP mix, 5 μL of 10 U/μL T4 PNK (New England Biolabs), 4 μL of 3 U/μL NEB T4 DNA Polymerase (New England Biolabs), 1 μL of 5 U/μL Klenow (New England Biolabs). The beads were incubated for 30 minutes at room temperature. The beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. To add a dA-tail, the beads were resuspended in 100 μL of the following: 90 μL of 1X NEBuffer2, 5 μL of 10 mM dATP, and 5 μL of 5 U/μL Klenow (exo-) (New England Biolabs). The beads were incubated for 30 minutes at 37˚C. The beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Following the washes, the beads were equilibrated once in 100 μL 1x NEB Quick Ligation Reaction Buffer (New England Biolabs) and the supernatants were removed using a magnetic rack. The beads were then resuspended in 50 μL 1x NEB Quick Ligation Reaction Buffer. To ligate adapters, 2 μL of NEB DNA Quick Ligase (New England Biolabs) and 3 μL of Illumina Indexed adapter were added to the beads and incubated for 15 minutes at room temperature. The supernatant was removed and the beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Then the beads were resuspended once in 100 μL 10 mM Tris-HCl, pH 8.0, followed by removal of the supernatant and resuspension again in 50 μL 10 mM Tris-HCl, pH 8.0. After deciding an optimal PCR cycle number using KAPA DNA Quantification kit (Kapa Biosystems), 6 cycles of PCR amplification were performed with the following reaction mixture: 10 μL Phusion HF Buffer (New England Biolabs), 3.125 μL 10 μM TruSeq Primer 1, 3.125 μL 10 μM TruSeq Primer 2, 1 μL 10 mM dNTPs, 0.5 μL Fusion HotStartII, 20.75 μL ddH20, 11.5 μL Bead-bound Hi-C library. PCR products were subjected to a final purification using AMPure beads (Beckman-Coulter) and were eluted in 30 μL 10 mM Tris-HCl, pH 8.0. Libraries were sequenced on the Illumina HiSeq 4000 platform.

tag: expressed vector

value: homozygous deletion of ZF9-11 in CTCF gene


title: mut CH12+FL-CTCF

description: mutant

value: Full-length ORF of CTCF inserted into pMy-MouseCTCFbiotag-T2A-mOrange

tag: genotype


title: WBJPE171125130


title: wt CH12

description: wt

value: wildtype


title: WBJPE171125131


title: pNSC_3D_KYNA_R3


title: gDNA from subject PATLMH


title: gDNA from subject PASKAS


title: pNSC_3D_IL4_R1


title: pNSC_3D_KYNA_R1


title: WBJPE171125129


title: WBJPE171125128


title: WBJPE171125127


title: SH 1

city: Albuquerque

first: Nikolaos

last: Mellios

state: NM

address: 915 Camino De Salud NE

department: Neuroscience

institute: University of New Mexico

data_processing:
Image analysis and base calling were performed using solexa platform v1.8, Sequence quality was examined using FastQC software.
Adapter trimming and filtering by cutadapt software. Reads were then aligned to mouse genome using HiSat 2 Software.
Transcript abundance for each for each sample was estimated using StringTie, and the FPKM value for gene and transcript levels were caluclated using R package Ballgown.
Genome_build: GRCm28
Supplementary_files_format_and_content: FPKM

source_name: Orbital Frontal Cortex

extract_protocol:
OFC was removed from mouse and flash frozen in liquid nitrogen. RNA was extracted by Qiagen miRNeasy kit according to manufacturer supplied protocol. 1ug of Total RNA was used for library construction.
Libraries were constructed using Kapa Stranded RNA-seq Library Kit

treatment_protocol: SH group mice were treated with OFC injection of lentiviral packaged shRNA targeting circHomer1a splice junction

value: Brain

tag: age

value: 12 weeks


title: SH 2


title: Control 3


title: gDNA from subject PATAML

tag: group


title: pNSC_3D_DMSO_R3


title: pNSC_3D_IL4_R3


title: WBJPE171125126

state: 浙江


title: pNSC_3D_DMSO_R2


title: pNSC_3D_IL4_R2


title: mut CH12+(N-terminus+11ZFs of CTCF)

city: Bethesda

description: mutant

value: ORF of N-terminus and 11ZFs of CTCF inserted into pMy-MouseCTCFbiotag-T2A-mOrange


title: WBJPE171125125

value: mice skeletal muscle


title: gDNA from subject PASVUI

tag: age at diagnosis (days)


title: WBJPE171125124

tag: tissue

value: male


title: Control 1

tag: strain


title: SH 3


title: pNSC_3D_KYNA_R2


title: pNSC_3D_DMSO_R1


title: WBJPE171125123


title: pNSC_3D_ab42_R2 2


title: gDNA from subject PARKJZ


title: 14_Lung_Treg [scRNA-seq]

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

data_processing:
Fastq files were processed using Cell Ranger version 2.0.1 based on 10xGenomics provided mm10 reference genome (refdata-cellranger-mm10-1.2.0). Cell Ranger was run per sample (using cellranger count). For downstream analysis the R package Seurat (version 2.3.0) together with R (version 3.4.2) was used. Cells with less than 500 or more than 2500 transcripts were discarded as well as cells exceeding a 5% threshold of mitochondrial transcripts. The data was log normalized (using NormalizeData) and scaled (using ScaleData) which includes regressing for mitochondrial DNA content and the number of UMIs using a negative binomial distribution. Highly variable genes (HVGs) were identified (using FindVariableGenes) with default parameter settings. TSNE (using RunTSNE) was used for dimensionality reduction and visualization.   To reconstruct a developmental trajectory, Monocle (version 2.6.3) was used. Steps included size factor estimation (using estimateSizeFactors), estimation of dispersions (using estimateDispersions), applying a minimal expression threshold of 0.1 (using detectGenes), HVGs were set to be used (using setOrderingFilter) and reducing dimensionality to two components (using setOrderingFilterreduceDimension(method = ‘DDRTree’) ). For visualization purpose, cells were binned in hexagons and expression was calculated as a mean based on the gene of interest.   Pearson correlation was calculated on HVGs of precursor tisTregST2 cells. 30 most correlated and anti-correlated genes to Batf were clustered using pheatmap and R (version 3.4.2) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx, h5

source_name: Lung

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol: Samples for scRNA-seq were loaded on the Chromium Single cell Controller (10x Genomics #120212) using the Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics #120237). cDNA was amplified using 14 cycles of PCR. Library was constructed using 13 cycles of PCR. Products were purified using Ampure XP beads and quality was controlled using Agilent Tapestation.

treatment_protocol: T cells were isolated and pre-enriched as described in the associated publication. Afterwards, they were stained with live/dead dye and surface antibodies as described. Cells were then sorted on an BDTM FACSAriaTM IIu, III, or FACSAriaTM FUSION cell sorter using 70 µm or 85 µm nozzle size and 4-way-purity sort mode into 1.5 ml tubes filled with FACS buffer. Sample and post-sort quality control were recorded where applicable and are displayed in the source data file linked to this manuscript. For scRNA-seq, we sorted 15000 spleen CD25+Klrg1-Nfil3(GFP)- Treg, 15000 spleen CD25+Klrg1-Nfil3(GFP)+ Treg, 15,000 spleen CD25+Klrg1+Nfil3(GFP)+ Treg, 10000 spleen CD44+CD25+Foxp3(GFP)+ Treg, 7500 VAT CD44+CD25+Foxp3(GFP)+ Treg, 3000 skin CD44+CD25+Foxp3(GFP)+ Treg, 1500 blood CD44+CD25+Foxp3(GFP)+ Treg, 10000 inguinal lymph-node CD44+CD25+Foxp3(GFP)+ Treg, 10000 bone marrow CD44+CD25+Foxp3(GFP)+ Treg, 10000 lung CD44+CD25+Foxp3(GFP)+ Treg, and 1000 liver CD44+CD25+Foxp3(GFP)+ Treg. Samples were pooled from several Foxp3(GFP) or Foxp3(YFP) or Nfil3(GFP) reporter mice.

value: CD44+Foxp3(GFP)+ memory Treg

value: Lung

tag: tag


title: 16_Liver_Treg [scRNA-seq]

source_name: Liver

value: Liver


title: WBJPE171125121

tag: gender


title: gDNA from subject PARKHV

source_name: AML, pre-treatment


title: WBJPE171125122

source_name: skeleton muscle


title: pNSC_3D_Ctrl_R3 2


title: WBJPE171125120


title: Control 2


title: 10_LN_Treg [scRNA-seq]

source_name: Inguinal LN

value: Inguinal LN


title: gDNA from subject PATASP


title: 8_Blood_Treg [scRNA-seq]

source_name: Blood

value: Blood


title: gDNA from subject PARBZJ

value: tumor


title: pNSC_3D_Ctrl_R2 2


title: 12_BM_Treg [scRNA-seq]

source_name: Bone marrow

value: Bone marrow


title: pNSC_3D_ab42_R3 2

value: Human Cortical Astrocytes from human fetal cortex


title: gDNA from subject PATCHL

value: Female


title: WBJPE171125117


title: 6_Skin_Treg [scRNA-seq]

source_name: Skin

value: Skin


title: WBJPE171125115


title: pNSC_3D_Ctrl_R1 2


title: iNSC_3D_ab42_R2

description: Papadimitriou_2017_featureCounts_table.s2.tab

data_processing:
The FastQ files were aligned to human genome (GRCh38/hg19) using gsnap (2016-0923) with default options. The read counts for each gene were calculated using featureCounts (V1.5.3) and GTF file from ensemble genome browser (Homo_sapiens.GRCh38.90.gtf).
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: The processed data file contains read counts calculated by featureCounts. The first 6 columns contain information about the gene (Geneid, Chr, Start, End, Strand, Length), and the remaining columns countain read counts of each gene in each sample. The colnames have not been changed and contain Raw Files names with additional suffix ".gz.sam"

extract_protocol:
For 2D cells; Human fetal cortical cells were grown in monolayer. Firstly we rinsed cell monolayer with ice cold PBS once. WE add 500 ul of TRIZOL reagent to lyse cells directly in a 24 well culture dish and scrape with a cell scraper. Pass the cell lysate several times through a pipette and then we vortex thoroughly. Add 0.2 ml of chloroform per 1 ml of TRIZOL. Vortex samples for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at 12,000 x g for 15 minutes at room temperature. Transfer upper aqueous phase into fresh RNAse-free tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at 12,000 x g for 10 minutes at 4oC. Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the samples by vortexing and centrifuge at 7,500 x g for 5 minutes at 4oC. Repeat above washing procedure once. Remove all leftover ethanol. Air-dry or vacuum dry RNA pellet for 5-10 minutes. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. For cells from 3D gels, we used Norgen Total RNA Isolation Kit. RNA isolation performed according to the protocol suggest by the company except; 3 gels lysed in 1ml RL buffer with 10 µL beta-mercaptoethanol. Centrifuged at 10000g for 5 min at RT and supernatant (~930 µL) transfered to a new eppendorf. 580 µL %96-99 ethanol added and mixed throughly. After passing through samples on columns, washings and DNase I treatment done accroding to the protocol suggests and RNA eluted in50 µL  nuclease free water. Samples ran on Agilent Bioanalyser for RNA quality, samples with RNA integrity >= 9.0 used for library preparation.
Total RNA with an integrity number of ≥ 8 was used. mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

treatment_protocol: 2D cultures were treated with 2 uM Abeta42 in the culture medium for 2 days between 2 and 4 days of culture. The medium is removed and cells are washed with cell culture medium twice. Amyloid plaques remain in the culture attached to the cells throughout the cultures. New medium is added and cultures were continued. For 3D cultures, Abeta42 is mixed with heparin solution at the time the gels are prepared. Cultures are performed for three weeks with frequent media changes.

value: induced pluripotent stem cells

tag: culture medium

value: 2 uM Abeta42


title: gDNA from subject PARMGH

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

value: Male


title: WBJPE171125113


title: gDNA from subject PATFGK


title: 4_Fat_Treg [scRNA-seq]

source_name: Fat

value: Fat


title: pNSC_3D_ab42_R1 2


title: iNSC_3D_ab42_R1


title: WBJPE171125111


title: 2_Spleen_Treg [scRNA-seq]

source_name: Spleen

value: Spleen


title: gDNA from subject PARWCG


title: KLRG1_GFP_ Replicate 4 [scRNA-seq]

source_name: Spl Klrg1negNfil3neg Treg

value: Klrg1-negative Nfil3(GFP)-negative


title: gDNA from subject PATMDJ


title: WBJPE171125108

value: mice skeletal muscle

value: male


title: iNSC_3D_Ctrl_R2

value: control


title: gDNA from subject PATLFJ


title: iNSC_3D_Ctrl_R3


title: WBJPE171125106


title: gDNA from subject PASWTG


title: KLRG1_GFP_ Replicate 3 [scRNA-seq]


title: pNSC_3D_ab42_R3


title: gDNA from subject PARYXV


title: KLRG1_GFP_ Replicate 1 [scRNA-seq]


title: WBJPE171125101


title: KLRG1_GFP_plus_2 Replicate 4 [scRNA-seq]

source_name: Spl Klrg1negNfil3pos Treg

value: Klrg1-negative Nfil3(GFP)-positive


title: iNSC_3D_Ctrl_R1


title: pNSC_3D_ab42_R2


title: pNSC_3D_ab42_R1


title: KLRG1_GFP_plus_2 Replicate 3 [scRNA-seq]


title: WBJPE171125099


title: WBJPE171125100


title: pNSC_3D_Ctrl_R3


title: KLRG1_GFP_plus_2 Replicate 2 [scRNA-seq]


title: WBJPE171125087


title: pNSC_3D_Ctrl_R2


title: WBJPE171125107


title: KLRG1_GFP_ Replicate 2 [scRNA-seq]


title: WBJPE171125084


title: KLRG1_GFP_plus_2 Replicate 1 [scRNA-seq]


title: KLRG1_GFP_plus Replicate 4 [scRNA-seq]


title: gDNA from normal human bone marrow RO02214

source_name: Bone marrow, normal

value: normal