title: 6ng 5hmc Jump-seq rep5


title: NT2: RA-10-2

status: Public on Mar 07 2019

type: SRA

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

country: USA

institute: University of Georgia

library_source: transcriptomic

data_processing:
Reads from RNA-seq were aligned using STAR.
Read counts for each gene were obtained using FeatureCounts
Likelihood ratio test for differential expression analysis across all time points were carried out using DESeq2
p-values were adjusted by the Benjamini-Hochberg procedure
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain the read counts and RPKM for each gene.

molecule: total RNA

organism: Homo sapiens

source_name: NT2 cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, USA) at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was then isolated using RNA Reagent (Invitrogen) and PureLink RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For induction of NT2 cells into neurons, 10 mM all-trans retinoic acid (RA) (Sigma), dissolved in DMSO, was added into the culture medium at a final concentration of 10 µM. Bone morphogenetic protein-2 (BMP-2) (GenScript) at a final concentration of 30 ng/ml was firstly used to test the muscle cell induction, and then 40 ng/ml BMP-2 was used in later experiments. As a negative control, DMSO was added into the culture medium for a final concentration of 0.1%. NT2 cells were treated with differentiation induction agents or DMSO for up to 21 days and the culture medium was changed every 2 days.

tag: cell line

tag: treatment

value: RA

tag: treatment time (d)


title: NT2: NT2-0-2

value: No treatment


title: 6ng 5hmc Jump-seq rep4

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

library_source: genomic

data_processing:
Library strategy: Jump-seq
For each 50 bp Illumina sequencing read, umi_tools were used to trim the first 8 bases which constitute a unique molecular identi-fier (UMI) and attach the UMI information to the name of each read.
The UMI sequence of each read was used later to remove PCR duplicates (reads starting at the same genomic location and sharing a same UMI sequence are likely to arise from one DNA fragment with a hydroxymethylated site, thus need to be collapsed and count-ed as one read).
After extracting UMI, cutadapt was used to retain reads with a Jump-Seq barcode “NNNNNNN” (The Jump barcode used for each library used in this study could be found in Table S4) and to trim the barcode from each of these retained reads.
We also used cutadapt to remove the bases that match the invariant adaptor sequence at the 3’end of each read.
Bowtie was used to map the reads to the mouse genome (mm9) not allowing any mismatch in the first 35 bp of each read. Only uniquely mapped reads were kept and processed with umi_tools to remove PCR duplicates based on the UMI sequence of each read.
Use a Binomial model to call peaks. Since reads are generated from 5hmC (unknown), it is more appropriate and reasonable to check the distribution of reads over C (known), rather than over every possible base. To avoid multiple counting of one read, the 5' end of every reads could be used when calling the coverage, instead of the entire length of the reads.
Genome_build: mm9
Supplementary_files_format_and_content: .txt files are tab-delimited text files of peaks called for each library; .5prime.bed files include information for the 5'prime end positions (the landing location) of reads for each library.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embryonic Stem Cells

growth_protocol: mESCs were cultured in feeder-free gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen Cat. No. 11995) supplemented with 20% FBS (GIBCO), 2 mM L-glutamine (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), 1 × nonessential amino acids (GIBCO), 1,000 units/ml LIF (Millipore Cat. No. ESG1107), 1 × pen/strep (GIBCO), 3 mM CHIR99021 (Stemgent), and 1 mM PD0325901 (Stemgent). mESCs were passaged every other day with Trispin (GIBCO) and seeded on gelatin-coated plates. Cells were kept under standard 37 ℃ and 5% CO2 conditions.

extract_protocol:
mESCs genomic DNA was purified using Quick-DNA™ Microprep Plus Kit (Zymo Research). The Tn5 reaction protocol has been described previously1. In brief, genomic DNA was fragmented and tagmented by mixing 4 µL 5 × TAPS-MgCl2-PEG 8,000 (for DNA < 1 ng) or 5 × TAPS-MgCl2-DMF, 1 µL of the assembled Tn5 and adaptor complex, genomic DNA and suitable volume of H2O up to 20 µL. Buffer used were: TAPS-MgCl2-PEG 8,000 (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2, 40% PEG 8,000) or 5 × TAPS-MgCl2-DMF (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2, 50% DMF). For 48 ng genomic DNA, 1 µL of 2-fold diluted Tn5 is sufficient; for 24 ng genomic DNA, Tn5 needs to be diluted 4 folds and for less genomic DNA, Tn5 should be diluted accordingly. For 600 pg genomic DNA or 100 cells, Tn5 should be diluted 320 folds and added 1 µL into the reaction. The reactions were incubated for 7 min at 55℃, and Tn5 was inactivated for 7 min at 55℃ after adding 1 µL proteinase K (Thermo Fisher Scientific). Typically, all the genomic DNA was converted to fragments of average size 200-300 bp. The fragmented DNA was purified by DNA Clean & Concentrator™-5 kit (Zymo Research) and eluted into H2O. T4 bacteriophage β-GT and Tet was prepared as previously described3,4. The 5-hmC labeling reactions were performed in a 20 μL solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, tagmented genomic DNA (100-500 bp), 100 μM UDP-6-N3-Glu, and 1 μM wild-type β-GT. The reactions were incubated for 1 h at 37 °C. In the case of 5mC, the strategy of coupling Tet oxidation with β-GT was used5: 5hmC base is protected by transferring a regular glucose from UDP-glucose using β-GT, followed by purifica-tion with DNA Clean & Concentrator™-5 kit (Zymo Research). After the azide-glucose transfer reaction, the DNA substrates were purified by Clean & Concentrator™-5 kit (Zymo Research) and reconstituted in H2O. The click chemistry was performed with addi-tion of 0.8 nmol dibenzocyclooctyne modified Jump P5 probe into the DNA solution, and the reaction mixture was incubated for 24 h at 37 °C.
The click products were incubated with Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher Scientific) in 1 × B & W Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) at RT for 20min (the click reactions with different barcoded Jump P5 probe could be pooled together for purification), followed by extensively washing steps: 1 × B & W Buffer 1 time, 0.15 M NaOH 1 time, 0.1 M NaOH twice, 1 × B & W Buffer with 200M Tris-HCl pH 7.5 one time, H2O three times and finally the beads were resuspended in 6 µL H2O and 2 µL of 5 × Sequenase Reaction Buffer for annealing (the loop shape Jump probe formed hairpin to initiate primer ex-tension). The reaction was heated at 95 °C and slowly ramped to 4 °C in Thermocycler. 1 µL Sequenase Version 2.0 DNA Polymer-ase (Thermo Fisher Scientific) and 1 µL dNTP (NEB) were added in the annealed solution, incubated at 37 °C for 2 h. Then 1 µL USER® Enzyme (NEB) was added to cleave at the dU linker region to release the newly synthesized strand. The 11 µL Jump prod-ucts were subjected to library construction with limited cycle amplification. Next-generation sequencing (NGS) libraries were gen-erated using NEBNext® Ultra™ II Q5® Master Mix (NEB), NEBNext® Multiplex Oligos for Illumina® (NEB) for NEB kit compat-ible Jump P7 adaptor and Jump P5 probe and Illumina Nextera DNA oligo sets for Nextera DNA kit compatible Jump P7 adaptor and Jump P5 probe.

treatment_protocol: Hyperactive Tn5 was produced following the published protocol with some details modified1,2. In brief, pTXB1-Tn5 plasmid (Catalog # 60240, Addgene) was transformed into C3013 cells (NEB). 6 L culture was grown at 37 ℃ to OD600 ~ 1. The culture was then cooled to 16 ℃ and IPTG was added to 0.1 mM. After continued growth for additional 16 h at 16 ℃, cells were harvested and lysed by French press in lysis buffer (25 mM Tris, pH = 8.0, 0.7 M NaCl, 0.1% Triton X-100). Then the lysate was centrifuged at 13,000 rpm for 30 min, followed by adding 10% PEI (Sigma) to remove E. coli DNA. The supernatant was loaded on a chitin column (NEB), followed by extensively wash by lysis buffer and 36 h cleavage with 100 mM DTT. The elution was purified by Source 15S column using Buffer A: 20 mM Tris 7.5 and Buffer B: 20 mM Tris 7.5, 200 mM NaCl. Tn5 comes out at conduction ~ 30. Collected fractions were pooled and subjected to gel filtration with gel filtration buffer (20 mM HEPES-KOH pH 7.6, 200 mM NaCl, 0.1 mM EDTA, 1 mM DTT). Finally, the 3-step purified Tn5 was concentrated to OD280 = 3.0 and stored at -80 ℃ after adding 1.1 vol 100% glycerol and 0.33 vol of 2 × Tn5 dialysis buffer (20 mM HEPES-KOH pH = 7.6, 200 mM NaCl, 0.2 mM EDTA, 2 mM DTT, 20% glycerol). For assembly, oligonucleotides (Jump-P7 adapter and Tn5 bottom adaptor) were resuspended in 1 × TE (pH = 8.0) to a final concentration of 100 µM each. Equimolar amounts of Jump-P7 adapter and Tn5 bottom adaptor were mixed, denatured at 95 ℃ for 10 min and slowly cooled down to anneal. One vol Tn5 was added 0.143 vol annealed adaptor, mixed gently but thoroughly and the Tn5-adaptor complex was incubated for 60 min at RT and stored at -80 ℃.

tag: tissue

value: Mouse Embryonic Stem Cells


title: HpSC_FL732: Hepatic stem cell

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: T7 006 Vet Research Tower

institute: Cornell University

description: small RNA

data_processing:
Small RNA-seq data was processed using the approach described in Kanke et al. (J. Integr. Bioinform, 2016)
Reads were trimmed using Cutadapt/1.1.2
Trimmed reads were mapped to the hg19 reference genome using Bowtie/1.1.0 without mismatches. These perfectly aligned reads represent miRNA loci.
Imperfectly aligned reads were re-mapped to miRNA loci using SHRiMP/2.2.2
Read counts were normalized using RPMMM (reads per million mapped to miRNAs)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files include RPMMM (reads per million mapped to miRNAs) values for each sample

source_name: Hepatic stem cell

extract_protocol:
RNA was extracted using the Norgen Total RNA Purification kit.
Libraries were prepared using TriLink CleanTag Small RNA Library Prep kit protocol per manufacturer's instructions by the the Genome Sequencing Facility of the Greehey Children’s Cancer Research Institute at the University of Texas Health Science Center at San Antonio. Single end sequencing was performed on an Illumina HiSeq2000.

value: liver

tag: cell type

value: Hepatic stem cell


title: 6ng 5hmc Jump-seq rep2


title: 6ng 5hmc Jump-seq rep1


title: 6ng 5hmc Jump-seq rep3


title: NT2: NT2-0-1


title: NT2: BMP-21-2


title: 12ng 5hmc Jump-seq rep5


title: 2.4ng 5hmc Jump-seq rep1


title: 12ng 5hmc Jump-seq rep3


title: >200 um B29 group

type: RNA

city: Rochester

first: Ching-Ho

last: Chang

address: 60 Crittenden Blvd, Apt 709

department: Biology

institute: U of Rochester

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were analyzed using R package limma v.3.34.9.
The data were normalised using normexp background correction and quantile normalization by control probes with limma in R

label: biotin

source_name: pancreatic islets

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

growth_protocol: BALB/c mice were purchased from the Jackson Laboratory. The University Committee on Animal Resources at the University of Rochester approved all mouse experiments.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit according to the protocol provided with the kit. Quality control was performed by Yale Center for Genome Analysis (YCGA; New Haven, CT).

treatment_protocol: BALB/c mice were intraperitoneally injected four times with 25 ug of serpin B13 mAb or control mAb (total dose of 100 ug) every other day at 2 weeks old and sacrificed two weeks after the last injection (5 weeks old).

tag: strain

value: BALB/c

tag: age

value: 5 weeks old

value: pancreatic islets

value: serpin B13 mAb (clone:B29)


title: 12ng 5hmc Jump-seq rep4


title: HpSC_FL725: Hepatic stem cell

description: small RNA


title: HpSC_FL648: Hepatic stem cell

description: small RNA


title: NT2: BMP-10-2


title: FLC15_AWTJ: Fibrolamellar carcinoma

description: small RNA

source_name: Fibrolamellar carcinoma

extract_protocol:
RNA was extracted from mouse livers using the Norgen Total RNA Purification kit.
Libraries were prepared using TriLink CleanTag Small RNA Library Prep kit protocol per manufacturer's instructions by the the Genome Sequencing Facility of the Greehey Children’s Cancer Research Institute at the University of Texas Health Science Center at San Antonio. Single end sequencing was performed on an Illumina HiSeq2000.

tag: tumor type

value: Metastasis


title: HB_FL744: Hepatoblast

description: small RNA

source_name: Hepatoblast

value: Hepatoblast


title: 12ng 5hmc Jump-seq rep2


title: NT2: RA-5-2


title: 24ng 5hmc Jump-seq rep5


title: 12ng 5hmc Jump-seq rep1


title: HpSC_FL734: Hepatic stem cell

description: small RNA


title: 24ng 5hmc Jump-seq rep4


title: HB_FL739: Hepatoblast

description: small RNA


title: NT2: BMP-21-1


title: NT2: BMP-10-1


title: NT2: BMP-5-2


title: HB_FL734: Hepatoblast

description: small RNA


title: 24ng 5hmc Jump-seq rep2


title: 24ng 5hmc Jump-seq rep1


title: 24ng 5hmc Jump-seq rep3


title: 48ng hmC Jump-seq rep10


title: 48ng hmC Jump-seq rep9


title: 48ng hmC Jump-seq rep8


title: FLHCC_490: Fibrolamellar carcinoma patient-derived xenograft

description: small RNA


title: JC4256_ZR75-1_estrogen_rep3_FOXA1

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
estrogen
zr75-1_foxa1_ab23738_estrogen_peaks.narrowPeak.gz

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.0.10.20131216 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-3 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

growth_protocol: MCF-7 and ZR75-1 cells were obtained from ATCC. MCF-7 were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated foetal bovine serum (FBS), 2 mM L-glutamine, 50U/ml penicillin and 50μg/ml. ZR75-1 were grown in RPMI supplemented with 10% heat-inactivated foetal bovine serum (FBS), 2 mM L-glutamine, 50U/ml penicillin and 50μg/ml. To generate the samples for these experiments, MCF-7 and ZR75-1 cells were seeded at a density of 2,000,000 cells, in 15 cm2 plates and stripped for three days using either DMEM or RPMI media, respectively. The media was supplemented with 5% Charcoal Stripped FBS (Gibco, 12676-029), 50 U/ml penicillin, 50 μg/ml streptomycin and 2 mM L-glutamine. Stripped media was changed every 24 hours.  Cells were then treated either with ethanol or with 10nM Estrogen for 45 minutes, followed by fixation and chromatin collection as previously described (Schmidt et al., 2009).   Both cell lines were regularly genotyped using STR profilling (Promega GenePrint 10 system). Cell lines were regularly tested for mycoplasma infection.

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275951
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

treatment_protocol: Hormone deprived cells were treated either with ethanol or with estrogen (10nM) prior to ChIP-sequencing analysis

value: breast cancer cell line

tag: chip antibody

value: anti-FOXA1 (ab23738) Abcam

value: hormone-deprived cells treated with estrogen


title: FLHCC_491: Fibrolamellar carcinoma patient-derived xenograft

description: small RNA


title: BTSC_AL736: Biliary tree stem cell

description: small RNA

source_name: Biliary tree stem cell

value: Biliary tree stem cell


title: JC4258_ZR75-1_estrogen_input

description: input for estrogen

value: none (input)


title: 48ng hmC Jump-seq rep7


title: BTSC_751: Biliary tree stem cell

description: small RNA


title: JC4255_ZR75-1_estrogen_rep2_FOXA1


title: JC4253_ZR75-1_vehicle_rep3_FOXA1

description:
vehicle
zr75-1_foxa1_ab23738_vehicle_peaks.narrowPeak.gz

value: hormone-deprived cells treated with vehicle


title: NT2: BMP-5-1


title: 48ng hmC Jump-seq rep4


title: FLHCC_493: Fibrolamellar carcinoma patient-derived xenograft

description: small RNA


title: 48ng hmC Jump-seq rep5


title: JC4252_ZR75-1_vehicle_rep2_FOXA1


title: 48ng hmC Jump-seq rep3


title: AHEP_AL4094: Adult hepatocyte

description: small RNA

source_name: Adult hepatocyte

value: Adult hepatocyte


title: JC4251_ZR75-1_vehicle_rep1_FOXA1


title: 48ng hmC Jump-seq rep2


title: FLC13_QQEI: Fibrolamellar carcinoma

description: small RNA


title: JC4250_ZR75-1_estrogen_rep3_FOXA1

description:
estrogen
zr75-1_foxa1_ab5089_estrogen_peaks.narrowPeak.gz

value: anti-FOXA1 (ab5089) Abcam


title: JC4249_ZR75-1_estrogen_rep2_FOXA1


title: with LPS and AG, 2

city: Guangzhou

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

country: China

institute: Guangzhou University of Chinese Medicine

description: Sample 5

data_processing:
Illumina HiSeq X Ten system for next-generation sequencing by OE Biotech. Co., Ltd. (Shanghai, China)
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Genome_build: mm9
Supplementary_files_format_and_content: mRNA_counts.xls include raw read for each Sample ...

growth_protocol: Cells were cultured in 1640 medium containing 10% foetal bovine serum (FBS), 100 unit/mL penicillin, and 100 g/mL streptomycin. The cells were maintained at 37°C under 5% CO2 (v/v) in a humidified incubator

extract_protocol:
Total mRNA was extracted from cells using an RNA extraction kit (Qiagen K.K., Tokyo, Japan). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA.Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophage (RAW264.7) with vector, with 0.5 mg/mL LPS alone or combined 1 μM arctigenin treatment.

value: macropahge

tag: agent

value: with LPS and AG


title: 48ng hmC Jump-seq rep6

value: Mouse Embryonic Stem Cells


title: BTSC_2176: Biliary tree stem cell

description: small RNA

value: liver


title: FLC12_CTTF: Fibrolamellar carcinoma

description: small RNA

value: Recurrent


title: AHEP_AL4104: Adult hepatocyte

description: small RNA


title: FLC09_TZOG_Normal: non-malignant liver

description: small RNA

value: Normal (non-malignant)


title: small RNA-Seq, mESC, huntingtin-null Hdhex4/5/ex4/5

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description:
small RNA sequencing from mESC in a huntingtin-null Hdhex4/5/ex4/5 mouse model
smallRNAseq_ESC_KO

data_processing:
RNA-Seq: 50 bp paired-end reads were were aligned to the mouse genome (GRCm38.p4) with Tophat (version 2.0.14, default settings), using the Gencode M6 transcript annotation as transcriptome guide. All programs were used with default settings unless otherwise specified. Mapped reads were assembled into transcripts guided by reference annotation (Gencode M6) with Cufflinks (version 438 2.2.1). Expression levels were quantified by HTSeq (Version 0.6.1, --mode intersection-nonempty) using Gencode M6 annotation. Normalization was performed using the TMM method implemented in edgeR. Differential expression was calculated using edgeR.     small RNA-Seq: 50 bp single-end reads were trimmed against Illumina’s TruSeq Small RNA 3’ (TGGAATTCTCGGGTGCCAAGG) and 5’ (GUUCAGAGUUCUACAGUCCGACGAUC) adapters using cutadapt(v. 1.3) with parameters –e 0.1 –O 5 –m 15. Next, trimmed sequence reads with length of 16-25bp were mapped to 1915 known mature miRNA sequences from miRBase (release 21) database, using BWA aln (v. 0.7.5a-r418) with parameter –n 1. Uniquely mapped reads were identified by selecting alignments with non-zero mapping quality and “XT:A:U” tag using samtools (v 0.1.18). Normalization was performed using the TMM method. Differential expression was calculated using edgeR.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-7) and sample-specific counts of aligned reads for RNA-Seq.   smallRNAseq_counts.txt: tab-delimited text file including miRNA annotations (columns 1-7) and sample-specific counts of aligned reads for small RNA-Seq.

source_name: ESC

growth_protocol: ESCs were maintained on feeder layers of γ-irradiated mouse embryonic fibroblasts or on gelatin-coated plates (1% gelatin solution). ES cell media contained Knock-Out D-MEM, 15% FBS, 50 I.U/ml of penicillin, 50 mg/ml of treptomycin, 0.2 mM Gluta-Max, 0.1 mM non-essential aminoacids, 0.1 mM 2-mercaptoethanol and 1000 U/ml of leukemia inhibitory factor (LIF).

extract_protocol:
RNA-Seq: RNA was extracted from cell lines by using TRIzol reagent (Life technologies), following manufacturer’s instructions. All RNA samples were subjected to DNAse I treatment (Ambion).
RNA-Seq: RNA sequencing was performed following the protocol described by the Broad Institute (Cambridge, MA). Briefly, poly-A-plus mRNA, was retro-transcribed to cDNA using a strand specific dUTP method, random hexamers and amplified by PCR using bar-coded DNA adaptors from Illumina. HiSeq2000 platform and 50bp pair-end (PE) was used for sequencing.    Small RNA-Seq: library preparation was obtained using the Illumina TruSeq Small RNA protocol (Illumina) according to manufacturer instructions and libraries were sequenced using single-end (SE), 50bp reads on HiSeq2000 platform.

treatment_protocol: ESCs were deprived of feeder cells for 4 passages, then 3 million cells were used for formation of embryoid bodies (EBs).

tag: sequencing method

value: small RNA-Seq

tag: cell

value: ESC

tag: genotype

value: huntingtin-null Hdhex4/5/ex4/5


title: small RNA-Seq, mESC, WT

description:
small RNA sequencing from mESC in a wild type mouse model
smallRNAseq_ESC_WT

value: Wild type


title: JC4248_ZR75-1_estrogen_rep1_FOXA1

value: breast cancer cell line


title: with LPS, 2

description: Sample 3

value: with LPS


title: small RNA-Seq, differentiated cells, WT

description:
small RNA sequencing from differentiated cells in a wild type mouse model
smallRNAseq_diff_WT

source_name: differentiated EB

value: differentiated EB


title: with LPS and AG, 1

description: Sample 4


title: JC4247_ZR75-1_vehicle_rep3_FOXA1

description:
vehicle
zr75-1_foxa1_ab5089_vehicle_peaks.narrowPeak.gz


title: JC4246_ZR75-1_vehicle_rep2_FOXA1


title: with LPS, 1

description: Sample 2


title: FLC09_MUOD: Fibrolamellar carcinoma

description: small RNA

value: Primary


title: FLC07_LFOC: Fibrolamellar carcinoma

description: small RNA


title: small RNA-Seq, differentiated cells, huntingtin-null Hdhex4/5/ex4/5

description:
small RNA sequencing from differentiated cells in a huntingtin-null Hdhex4/5/ex4/5 mouse model
smallRNAseq_diff_KO


title: FLC04_CDHM: Fibrolamellar carcinoma

description: small RNA

value: Metastasis


title: FLC01_LNBS: Fibrolamellar carcinoma

description: small RNA


title: JC4245_ZR75-1_vehicle_rep1_FOXA1

value: hormone-deprived cells treated with vehicle


title: JC4243_MCF-7_vehicle_input

description: input for vehicle

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275950
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

value: none (input)


title: JC4244_MCF-7_estrogen_input

description: input for estrogen

value: hormone-deprived cells treated with estrogen


title: JC4257_ZR75-1_vehicle_input

description: input for vehicle


title: FLC06_GMKX: Fibrolamellar carcinoma

description: small RNA


title: with vector

description: Sample 1

value: macropahge

value: with vector


title: JC4242_MCF-7_estrogen_rep3_FOXA1

description:
estrogen
mcf7_foxa1_ab23738_estrogen_peaks.narrowPeak.gz

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275949
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

value: anti-FOXA1 (ab23738) Abcam


title: 48ng hmC Jump-seq rep11

value: Mouse Embryonic Stem Cells


title: RNA-Seq, mESC, WT

description:
total RNA sequencing from mESC in a wild type mouse model
RNAseq_ESC_WT

value: RNA-Seq


title: 48ng hmC Jump-seq rep1


title: RNA-Seq, differentiated cells, huntingtin-null Hdhex4/5/ex4/5

description:
total RNA sequencing from differentiated cells in a huntingtin-null Hdhex4/5/ex4/5 mouse model
RNAseq_diff_KO


title: RNA-Seq, differentiated cells, WT

description:
total RNA sequencing from differentiated cells in a wild type mouse model
RNAseq_diff_WT


title: GIFN3 B

city: Stanford

first: Juan

middle: Luis

last: Mendoza

state: CA

address: 279 Campus Dr., Beckman Room B173

department: Molecular and Cellular Physiology

institute: Stanford University

data_processing:
Ion Torrent Suite version 5.10.0 (Thermo Fisher).
Arguments: BaseCaller –barcode-filter-minreads 10 –phasing-residual-filter=2.0 –max-phasing-levels 2 –num-unfiltered 1000 –barcode-filter-postpone
The ampliSeqRNA plugin in Torrent Suite 5.10.0 is used with the Ion AmpliSeqTranscriptome Human Gene Expression Kit. The plugin generates statistics, downloadable data files, and interactive visualizations that represent targeted RNA transcripts. Use the ampliSeqRNA plugin on runs that are aligned to the human transcriptome references (hg19_AmpliSeq_Transcriptome_V1.2) and appropriate target regions (hg19_AmpliSeq_Transcriptome_v1.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files relative abundance for each gene

source_name: lung

extract_protocol:
RNA was extracted using the RNAeasy micro kit (QIAGEN) and protocols.
Libraries were prepared for sequencing using standard Thermo protocols
Ampliseq human transcriptome kit (Thermo)

treatment_protocol: A549 were plated in 6-well format, treated with protein at 62.nM concentration for 48 hours.

value: lung

value: A549 cancer cell line


title: GIFN4 B


title: IFNG WT B

value: IFNG WT


title: RNA-Seq, mESC, huntingtin-null Hdhex4/5/ex4/5

description:
total RNA sequencing from mESC in a huntingtin-null Hdhex4/5/ex4/5 mouse model
RNAseq_ESC_KO

value: ESC

value: huntingtin-null Hdhex4/5/ex4/5


title: JC4254_ZR75-1_estrogen_rep1_FOXA1

value: breast cancer cell line


title: JC4241_MCF-7_estrogen_rep2_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275948
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: JC4240_MCF-7_estrogen_rep1_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275947
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: GIFN4 A


title: JC4239_MCF-7_vehicle_rep3_FOXA1

description:
vehicle
mcf7_foxa1_ab23738_vehicle_peaks.narrowPeak.gz

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275946
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: GIFN3 A


title: GIFN2 B


title: GIFN2 A


title: JC4238_MCF-7_vehicle_rep2_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275945
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: JC4237_MCF-7_vehicle_rep1_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275944
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: mfNPC-2_P2

city: Dresden

first: Lydia

last: Reinhardt

address: Fetscherstraße 105

country: Germany

institute: CRTD

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in Illumina GenomeStudio

source_name: Cell culture

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: completely confluent human pluripotent stem cells were differentiated as a monolayer on matrigel using double-SMAD inhibition by SB-431542, Dorsomorphin and Purmorphamine and matured for 30 days with spliting when too confluent.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

value: midbrain floorplate neural progenitor cells (mfNPC)

tag: passage


title: B6J_111905-38

city: Kobe

first: Pei-Chieng

last: Cha

state: Hyogo

address: 7-5-1 Kusunoki-chou, Chuo-ku

department: Division of Neurology/Molecular Brain Science

country: Japan

institute: Kobe University Graduate School of Medicine

description:
Mouse with inconsistent cognition, sample 13
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.

hyb_protocol: The hippocampal RNAs were then hybridized onto the Affymetrix Mouse Genome 430 2.0 Array, comprising of over 39,000 transcripts, following manufacturer's instructions. Hybridization, washing, and staining of the GeneChip® probe arrays were performed by using Affymetrix Fluidics Station 450.

scan_protocol: Scanning was conducted following manufacturer's instructions by using GCS 3000 Scanner.

data_processing: Raw signal intensities for each probe set in the .CEL files were analyzed by using the Partek Genomic Suite software (v6.5) (Partek Inc.). Analysis was conducted following the default setting with a pre-background adjustment of probe intensities for the GC contents followed by the robust multi-chip average (RMA) background correction, quantile normalization and mean probe set summarization. Expression values were transformed into log2 prior to statistical analysis. One-way analysis of variance (ANOVA) was employed to detect genes that expressed differentially between mice with high and low cognition. The resulting list of differentially expressed genes was filtered to include only genes that demonstrated 1.3-fold or greater up- or down-regulation with an FDR value of smaller than 0.30.

label: Biotin

source_name: Hippocampus

label_protocol: Labeling has been performed as per manufacturer's instruction.

extract_protocol: One month after all the tests have been completed, mice were sacrificed and RNAs were extracted from hippocampi of mice.

treatment_protocol: Male inbred mice of C57BL/6J Strain (10 week-old) were subjected to a comprehensive behavioral test battery consisting of general health and neurological screening, open field test, new social interaction test (Crawley’s version), Barnes circular maze test (BM), 8-arm radial maze test (RM), T-maze test (TM), light/dark transition test, elevated plus-maze test, hotplate, social interaction test (novel environment), tail suspension, rotarod, prepulse inhibition, Porsolt forced swimming test, cued and contextual fear conditioning (FZ), gait analysis and passive avoidance (PA) (tests were listed following the sequence the tests were being conducted). Five of the aforementioned tests, namely BM, RM, TM, FZ, and PA, measured memory and cognitive performance of mice. BM, RM, and TM tests were conducted when mice aged 10-11, 12-14, and 15-19 week-olds, respectively; whereas FZ and PA, which leave stronger impacts on mice, were conducted at later stage when mice were 33 and 37-38 week-olds, respectively. The raw data including those of other behavioral tests, which are not measuring cognitive performance of mice and therefore not described in this paper, are disclosed in mouse phenotype database (http://www.mouse-phenotype.org/) as “B6J” strain. General cognitive ability of the 39 mice with complete data on the 11 parameters of the five behavioral tests aforementioned was determined. Detailed procedures were described in our paper. Mice that were consistently ranked as having high, medium, and low cognition by both ranking systems were identified and were subjected to subsequent gene expression profiling analysis.  All behavioral testing procedures have been approved by Animal Care and Use Committee of Kyoto University Graduate School of Medicine, where the tests have been performed.

value: 10 week-old

tag: gender

value: Male


title: JC4236_MCF-7_estrogen_rep3_FOXA1

description:
estrogen
mcf7_foxa1_ab5089_estrogen_peaks.narrowPeak.gz

value: anti-FOXA1 (ab5089) Abcam


title: Untreated B

value: Untreated


title: mfNPC-1_P12


title: Untreated A


title: smNPC_P10

value: small molecule neural precursor cells (smNPC)


title: GFP- cells at 22-24 hpf

city: Beijing

first: Bo

last: Gong

address: Qinghua Yuan street No.1

department: School of Life Science

institute: Tsinghua University

description: No

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to zv9 whole genome using SOAPaligner/soap2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from mortazavi et al., nature method, 2008.
Genome_build: zv9
Supplementary_files_format_and_content: files include RPKM values for each Sample

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were cultured in the holfretor water.

extract_protocol:
Zebrafish embryos were lysed into single cell suspension for cell sorting. Then RNA from GFP+ and GFP- cells were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: zebrafish background

value: GFP- cells from Tg(fli1a:EGFP)y1

value: non-endothelial cells


title: B6J_111905-41

description:
Mouse with incomplete data, sample 2
Mouse with incomplete behavioral data.


title: B6J_111905-40

description:
Mouse with incomplete data, sample 1
Mouse with incomplete behavioral data.


title: mfNPC-1_P2


title: B6J_111905-37

description:
Mouse with inconsistent cognition, sample 12
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: GFP+ cells at 22-24 hpf

description: No

value: GFP+ cells from Tg(fli1a:EGFP)y1

value: endothelial cells


title: mfNPC-2_P12


title: B6J_111905-39

description:
Mouse with inconsistent cognition, sample 14
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: B6J_111905-36

description:
Mouse with inconsistent cognition, sample 11
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: IFNG WT A

tag: cell line


title: B6J_111905-35

description:
Mouse with inconsistent cognition, sample 10
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: JC4235_MCF-7_estrogen_rep2_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275943
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

tag: treatment

value: hormone-deprived cells treated with estrogen


title: B6J_111905-34

description:
Mouse with inconsistent cognition, sample 9
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: JC4233_MCF-7_vehicle_rep3_FOXA1

description:
vehicle
mcf7_foxa1_ab5089_vehicle_peaks.narrowPeak.gz

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275941
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

value: hormone-deprived cells treated with vehicle


title: JC4234_MCF-7_estrogen_rep1_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275942
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: TAC_rg108_RRBS_3

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
RRBS-seq reads were aligned to the mouse reference genome, rn5, using Bismark (Krueger and Andrews, 2011) with default parameters.
Methylation calling and differential methylation analysis were performed using Methylkit.
Genome_build: rn5
Supplementary_files_format_and_content: COV file format: <chr><start><end><beta><total Methylated Reads><total Unmethylated Reads>

organism: Rattus norvegicus

source_name: TAC_rg108_RRBS_cardiomyocyte nuclei

extract_protocol:
DNA was extracted using Phenol:Chloroform, followed by ethanol precipitation, and dissolved in 150 mL TE buffer (10 mM Tris-Cl pH 8.0, 0.5 mM EDTA).
RRBS-seq was performed as described (Gu et al., 2011). 50 ng of purified DNA was digested with MspI (Fast digest MspI, Thermo Scientific FD0544) for 30 min at 37°C followed by heat inactivation at 65°C for 5 min. Library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (New England BioLabs, E7370L) and ligated with methylated adapters for Illumina at a dilution of 1:10 (New England BioLabs, E7535L). The adapter ligated DNA was subjected to bisulfite conversion with EpiTect fast bisulfite conversion kit (Qiagen, 59824) using the following cycling conditions: 2 cycles of (95°C; 5min, 60°C; 10min, 95°C; 5min, 60°C; 10min) and hold at 20°C. Bisulfite converted DNA was PCR amplified for 14-16 cycles using 2.5 U of Pfu Turbo Cx Hotstart DNA polymerase (Agilent Technologies, 600410) and size selected for fragments between 200 bp to 500 bp with Ampure Xp magnetic beads (Agencourt, A63880). The purified DNA was subjected to single end sequencing using the Illumina Hiseq 2500.

value: Wistar

tag: subjected to

value: clip-based TAC surgery

tag: treated daily with

value: cardiomyocyte


title: JC4232_MCF-7_vehicle_rep2_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275940
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939

tag: cell type


title: JC4231_MCF-7_vehicle_rep1_FOXA1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275939
phenol chloroform isoamyl DNA extraction
ChIPseq, Schmidt et al, 2009. PMID: 19275939


title: DSS+DPG treated replicate 2

city: Rome

first: Roberta

last: Vitali

state: Italy

address: Via Anguillarese 301

institute: ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development

description: DSS induced colitis+DPG

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/pcr/arrayanalysis For the normalization it uses the average of five housekeeping genes: Actb, B2m, Gapdh, Gusb, Hsp90ab1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)] The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. Matrix normalized worksheet reports normalized signal (against housekeeping genes). The Qiagen website https://dataanalysis.qiagen.com/pcr/arrayanalysis) only provides the tested samples but not for the control group. Fold Change worksheet reports test/control ratios.

label: SYBR green

source_name: DSS+DPG treated replicate 2

label_protocol: PCR assays were performed using the RT² Profiler™ PCR Array Mouse Wound Healing  (PAMM-121Z; Qiagen, DE) following the Manufacturer’s instructions. Reverse transcription was performed from 1 microgram of total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Bio-Rad CFX96) with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds.

extract_protocol: Total RNA was isolated from mouse colonic tissues using the RNeasy Microarray tissue kit (Qiagen)

tag: strain

tag: Sex

value: female

value: DSS+DPG treated


title: DSS+DPG treated replicate 3

description: DSS induced colitis+DPG

source_name: DSS+DPG treated replicate 3


title: DSS+DPG treated replicate 1

description: DSS induced colitis+DPG

source_name: DSS+DPG treated replicate 1


title: TAC_rg108_RRBS_2


title: TAC_RRBS_3

source_name: TAC_RRBS_cardiomyocyte nuclei

value: solvent


title: TAC_RRBS_2


title: Sham_rg108_RRBS_4

source_name: Sham_rg108_RRBS_cardiomyocyte nuclei

value: Sham


title: TAC_RRBS_4


title: Sham_rg108_RRBS_3


title: B6J_111905-31

description:
Mouse with inconsistent cognition, sample 6
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.

tag: age

value: 10 week-old

value: Male


title: B6J_111905-33

description:
Mouse with inconsistent cognition, sample 8
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: DSS treated replicate 3

description: DSS induced colitis

source_name: DSS treated replicate 3

value: DSS treated


title: B6J_111905-29

description:
Mouse with inconsistent cognition, sample 4
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: B6J_111905-28

description:
Mouse with inconsistent cognition, sample 3
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: B6J_111905-30

description:
Mouse with inconsistent cognition, sample 5
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: B6J_111905-27

description:
Mouse with inconsistent cognition, sample 2
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: DSS treated replicate 2

description: DSS induced colitis

source_name: DSS treated replicate 2


title: DSS treated replicate 1

description: DSS induced colitis

source_name: DSS treated replicate 1


title: B6J_111905-26

description:
Mouse with inconsistent cognition, sample 1
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.


title: Sham_RRBS_4

source_name: Sham_RRBS_cardiomyocyte nuclei


title: Untreated replicate 3

description: control

source_name: Untreated replicate 3

value: Untreated


title: EastIndiaNyshiD401

type: genomic

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Nyishi

tag: region

value: Asia

tag: tissue

value: blood


title: EastIndiaNaga146

value: Naga


title: Untreated replicate 2

description: control

source_name: Untreated replicate 2


title: EastIndiaNyshiD399


title: Sham_RRBS_2


title: B6J_111905-25

description:
Mouse with high cognition, sample 5
Mouse that was consistently ranked as having high cognition by the two ranking systems in our study.


title: B6J_111905-23

description:
Mouse with high cognition, sample 3
Mouse that was consistently ranked as having high cognition by the two ranking systems in our study.


title: Untreated replicate 1

description: control

source_name: Untreated replicate 1


title: TAC_rg108_RRBS_1


title: TAC_RRBS_1


title: Sham_rg108_RRBS_2


title: Sham_rg108_RRBS_1


title: B6J_111905-24

description:
Mouse with high cognition, sample 4
Mouse that was consistently ranked as having high cognition by the two ranking systems in our study.


title: B6J_111905-21

description:
Mouse with high cognition, sample 1
Mouse that was consistently ranked as having high cognition by the two ranking systems in our study.


title: RNAseq_RNaseR_seedling

city: Nanjing

first: Fang

last: Yuan

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

data_processing:
The raw data sets were trimmed adapter sequences and removed low-quality bases by Trim Galore version 0.4.3.
dDRIP_seq: Clean reads were aligned to the rice reference genome (MSU 7.0) with Bowtie1. We distinguished the strand specific reads using flags of SAM files. The direction of the nascent RNA strand associated with R-loops is concordant with the direction of R2 reads (R2 of the pair-end reads) aligned to the genome. We then extracted unique mappable wR-loops reads by flags of R2 reads equal to 163, and cR-loops reads by flags of R2 reads equal to 147.
dDRIP-seq: Unique mappable reads corresponding to w/c R-loops were used for R-loop peak calling using MACS2(Zhang et al. 2008). The parameter was set with macs2 callpeak --keep-dup 1 -g 3.8e+8 -B --extsize 200 -q 0.01 --nomodel --SPMR
NBS-seq:  Low-quality reads and adapters were removed from the raw data by using Trim Galore. The clean data were mapped to the rice reference genome (MSU7.0) by using Bismark (Krueger and Andrews 2011). Uniquely mappable reads were used for calculating the methylated cytosines using the bismark methylation_extractor program.
RNAseq_RNaseR: Clean reads were strand-specific aligned to the rice genome (MSU 7.0) by  tophat2 with parameter --library-type fr-firststrand.
Genome_build: MSU7.0
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: CX_report.txt files were generated using Bismark
Supplementary_files_format_and_content: align_summary.txt files were generated using tophat2
Supplementary_files_format_and_content: junctions.bed files were generated using tophat2

organism: Oryza sativa

source_name: seedlings

growth_protocol: rice cultivar “Nipponbare” seeds were grown in a greenhouse with temperature ranging from 30-34°Cwith a 12h/12h light-dark cycle for two weeks. Two-week-old rice seedlings were collected and ground into a fine powder in liquid nitrogen, which were used for nuclei isolation and genomic DNA preparation in the downstream assays.For calli induction, the same “Nipponbare” seeds were sterilized and cultured in rice calli induction medium (NB basal medium plus vitamin, glutamine, proline, casein hydrolysate, sucrose, and phytogel as well as 3 mg/L 2,4-D at pH 5.8) in growth chamber at 28°C–29°C with dark conditions. Three-week-old calli were collected and ground into a fine powder in liquid nitrogen, which were used for for nuclei isolation and genomic DNA preparation using the same method as for the seedling tissue above.

extract_protocol:
Briefly,the purified nuclei were used for extraction of high quality genomic DNA using three rounds of phenol, phenol:chloroform, and chloroform extraction coupling with ethanol precipitation. The purified genomic DNA was fragmented into main sizes between 200-500bp using sonication. The 5μg sonicated DNA with or without RNase H treatment was purified using Qiaquick PCR purification kit and incubated with 30μl of well characterized S9.6 antibody bound Dynalbeads overnight at 4°C in IP buffer (10mM NaPO4, 140mM NaCl,0.05%Triton X-100). After washing with IP buffer three times, Dynalbeads was eluted with elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 0.5% SDS) two times with 250μl at 65°C for 15 mins each. Antibody bound DNA was finally purified using phenol-chloroform extraction and pelleted with ethanol. Air-dried DNA was resuspended in 20 μl of 10 mM Tris-HCl (pH 8.0).
dDRIP-seq:Directional DRIP-seq libraries were prepared using DRIPed DNA above followed the published protocol with minor modifications(Wang et al. 2011). The library preparation directly started from the second strand synthesis step by skipping preparation of mRNA fragments and the first cDNA synthesis steps. The dUTP incorporated second-strand DNA was synthesized using DNA polymerase I. The remaining steps were exactly following the published protocol mentioned above. The final DRIP-seq library was QCed and sequenced using Illumina Hiseq2500 platform.
NBS-seq:The non-denatured sonicated genomic DNA, the same as the one used in dDRIP experiment, was used for bisulfite treatment using EZ DNA methylation-gold kit purchased from ZYMO research. The bisulfite reaction and purification f bisulfite treated DNA was exactly followed the manual. The final purified DNA was used for BS-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina purchased from NEB (Cat#: E7645S)
RNAseq_RNaseR: Total RNAs were prepared using Trizol (Cat.# 15596026, ThermoFisher Scientific) followed by DNase I treatment and removal of majority of mRNAs with oligo(T)-conjugated magnetic beads purchased from Promega (Z5310). Approximately 80 μg RNAs were treated with RNase R (Cat.# RNR07250, Lucigen) one times followed by adding “A” base and treating with RNase R one more time. Finally, about 1μg RNAs were used for directional RNA-seq library preparation according to published procedures. The final RNase R-treated RNA-seq library was QCed and sequenced using Illumina X-ten platform.

tag: cultivar

value: Nipponbare

value: seedlings

tag: replicate

value: biological replicate1

value: three weeks

tag: growth temperature


title: NBS-seq_calli

data_processing:
The raw data sets were trimmed adapter sequences and removed low-quality bases by Trim Galore version 0.4.3.
dDRIP_seq: Clean reads were aligned to the rice reference genome (MSU 7.0) with Bowtie1. We distinguished the strand specific reads using flags of SAM files. The direction of the nascent RNA strand associated with R-loops is concordant with the direction of R2 reads (R2 of the pair-end reads) aligned to the genome. We then extracted unique mappable wR-loops reads by flags of R2 reads equal to 163, and cR-loops reads by flags of R2 reads equal to 147.
dDRIP-seq: Unique mappable reads corresponding to w/c R-loops were used for R-loop peak calling using MACS2(Zhang et al. 2008). The parameter was set with macs2 callpeak --keep-dup 1 -g 3.8e+8 -B --extsize 200 -q 0.01 --nomodel --SPMR
NBS-seq:  Low-quality reads and adapters were removed from the raw data by using Trim Galore. The clean data were mapped to the rice reference genome (MSU7.0) by using Bismark (Krueger and Andrews 2011). Uniquely mappable reads were used for calculating the methylated cytosines using the bismark methylation_extractor program.
Genome_build: MSU7.0
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: CX_report.txt files were generated using Bismark

source_name: calli

growth_protocol: rice cultivar “Nipponbare” seeds were grown in a greenhouse with temperature ranging from 30-34℃with a 12h/12h light-dark cycle for two weeks. Two-week-old rice seedlings were collected and ground into a fine powder in liquid nitrogen, which were used for nuclei isolation and genomic DNA preparation in the downstream assays.For calli induction, the same “Nipponbare” seeds were sterilized and cultured in rice calli induction medium (NB basal medium plus vitamin, glutamine, proline, casein hydrolysate, sucrose, and phytogel as well as 3 mg/L 2,4-D at pH 5.8) in growth chamber at 28°C–29°C with dark conditions. Three-week-old calli were collected and ground into a fine powder in liquid nitrogen, which were used for for nuclei isolation and genomic DNA preparation using the same method as for the seedling tissue above.

extract_protocol:
Briefly,the purified nuclei were used for extraction of high quality genomic DNA using three rounds of phenol, phenol:chloroform, and chloroform extraction coupling with ethanol precipitation. The purified genomic DNA was fragmented into main sizes between 200-500bp using sonication. The 5μg sonicated DNA with or without RNase H treatment was purified using Qiaquick PCR purification kit and incubated with 30μl of well characterized S9.6 antibody bound Dynalbeads overnight at 4℃ in IP buffer (10mM NaPO4, 140mM NaCl,0.05%Triton X-100). After washing with IP buffer three times, Dynalbeads was eluted with elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 0.5% SDS) two times with 250μl at 65℃ for 15 mins each. Antibody bound DNA was finally purified using phenol-chloroform extraction and pelleted with ethanol. Air-dried DNA was resuspended in 20 μl of 10 mM Tris-HCl (pH 8.0).
dDRIP-seq: Directional DRIP-seq libraries were prepared using DRIPed DNA above followed the published protocol with minor modifications(Wang et al. 2011). The library preparation directly started from the second strand synthesis step by skipping preparation of mRNA fragments and the first cDNA synthesis steps. The dUTP incorporated second-strand DNA was synthesized using DNA polymerase I. The remaining steps were exactly following the published protocol mentioned above. The final DRIP-seq library was QCed and sequenced using Illumina Hiseq2500 platform.
NBS-seq: The non-denatured sonicated genomic DNA, the same as the one used in dDRIP experiment, was used for bisulfite treatment using EZ DNA methylation-gold kit purchased from ZYMO research. The bisulfite reaction and purification f bisulfite treated DNA was exactly followed the manual. The final purified DNA was used for BS-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina purchased from NEB (Cat#: E7645S)

value: calli


title: B6J_111905-32

description:
Mouse with inconsistent cognition, sample 7
Mouse that was inconsistently ranked as having high, medium, or low cognition by the two ranking systems in our study.

source_name: Hippocampus

tag: gender


title: EastIndiaNyshiD397


title: B6J_111905-22

description:
Mouse with high cognition, sample 2
Mouse that was consistently ranked as having high cognition by the two ranking systems in our study.


title: Sham_RRBS_1

value: Wistar

value: cardiomyocyte


title: B6J_111905-20

description:
Mouse with medium cognition, sample 12
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: TAC_rg108_RRBS_4

source_name: TAC_rg108_RRBS_cardiomyocyte nuclei

value: clip-based TAC surgery


title: EastIndiaNyshiD148


title: dDRIP-seq_calli_RNaseH+

data_processing:
Library strategy: dDRIP-seq
The raw data sets were trimmed adapter sequences and removed low-quality bases by Trim Galore version 0.4.3.
dDRIP_seq: Clean reads were aligned to the rice reference genome (MSU 7.0) with Bowtie1. We distinguished the strand specific reads using flags of SAM files. The direction of the nascent RNA strand associated with R-loops is concordant with the direction of R2 reads (R2 of the pair-end reads) aligned to the genome. We then extracted unique mappable wR-loops reads by flags of R2 reads equal to 163, and cR-loops reads by flags of R2 reads equal to 147.
dDRIP-seq: Unique mappable reads corresponding to w/c R-loops were used for R-loop peak calling using MACS2(Zhang et al. 2008). The parameter was set with macs2 callpeak --keep-dup 1 -g 3.8e+8 -B --extsize 200 -q 0.01 --nomodel --SPMR
NBS-seq:  Low-quality reads and adapters were removed from the raw data by using Trim Galore. The clean data were mapped to the rice reference genome (MSU7.0) by using Bismark (Krueger and Andrews 2011). Uniquely mappable reads were used for calculating the methylated cytosines using the bismark methylation_extractor program.
Genome_build: MSU7.0
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: CX_report.txt files were generated using Bismark

tag: antibody


title: Tr_1: transcriptome of T. fuciformis mycelia which interacted with A. stygium

city: wuhan

first: Dongmei

state: hubei

address: shi zi shan NO1 hubei

department: college of food science and technology

institute: Huazhong Agricultural University

data_processing:
Trinity: Version: v2.0.6 was used to perform de novo assembly with clean reads
Tgicl: Version: v2.0.6 was used to remove abundance from transcripts and get Unigenes
TransDecoder: Version: v3.0.1 Parameters: default
MISA: Version: v1.0 Parameters: 1-12,2-6,3-5,4-5,5-4,6-4 100 150 was used to detect SSR in Unigenes
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Tremella fuciformis

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

value: one week after interaction with A. stygium

tag: genotype

value: wild type


title: B6J_111905-19

description:
Mouse with medium cognition, sample 11
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.

value: 10 week-old

value: Male


title: dDRIP-seq_seedllings_RNaseH+_rep2

value: biological replicate2

value: two weeks


title: B6J_111905-18

description:
Mouse with medium cognition, sample 10
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: dDRIP-seq_seedllings_RNaseH+_rep1


title: dDRIP-seq_calli_rep2


title: B6J_111905-17

description:
Mouse with medium cognition, sample 9
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: HV-122

city: Ribeirão Preto

first: Eduardo M.

last: Rocha

state: SP

address: Av. Bandeirantes, 3900 - Vila Monte Alegre

department: Ophthalmology

country: Brazil

institute: University of São Paulo

description: healthy volunteer

hyb_protocol: Only cRNA with a total yield of >1.65 μg and a specific avidity of > 9.0 pmoles Cy3/μg cRNA was used in the hybridization step. Gene expression analysis involved the use of 4 × 44K microarrays (Agilent) containing ~41K human oligo probes. Microarrays were hybridized according to the manufacturer’s recommendations for One-Color Microarray-Based Gene Expression Analysis.

scan_protocol: According to the manufacturer’s recommendations for One-Color Microarray-Based Gene Expression Analysis.

data_processing: Quality control criteria were established based on the results of previously published experiments. Microarrays that met ≥ 9 of 12 quality control criteria were deemed suitable for statistical analysis.

source_name: minor salivary gland

label_protocol: Total RNA from both patient and healthy volunteer samples was amplified and labeled with a low RNA input linear amplification kit (Agilent). A total of 500 ng of RNA was labeled with Cy3-CTP, and the quality and yield of complementary RNA (cRNA) were then analyzed using a NanoDrop ND-1000 UV-VIS Spectrophotometer (version 3.2.1).

extract_protocol: MSGs were obtained from study participants and stored in RNAlater (Qiagen) until RNA extraction. Samples were homogenized with a Bullet-Blender (Next Advance) or an Omni TH (Omni International). Total RNA was extracted with an RNeasy Mini kit according to the instructions of the manufacturer (Qiagen). The quality of RNA was measured using a 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ribosomal RNA ratio of 1.7 and an RNA integrity number of ≥ 6.5 were used for the arrays.

treatment_protocol: No treatment

value: Female


title: B6J_111905-16

description:
Mouse with medium cognition, sample 8
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: HV-102

description: healthy volunteer


title: dDRIP-seq_seedllings_rep2


title: Tr_0: transcriptome of T. fuciformis mycelia

source_name: T. fuciformis mycelia


title: HV-88

description: healthy volunteer


title: B6J_111905-13

description:
Mouse with medium cognition, sample 5
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: B6J_111905-14

description:
Mouse with medium cognition, sample 6
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: B6J_111905-15

description:
Mouse with medium cognition, sample 7
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: HV-86

description: healthy volunteer


title: ST_37

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).

value: Santhal

value: Asia

value: blood


title: SHZ_23


title: The sixth sample of warmed plots

city: Biejing

first: Jingmin

last: Cheng

address: NO. 30 Shuangqing Road, Haidian District

department: School of Environment

hyb_protocol: For hybridization, DNA was resuspended in hybridization solution containing a sample tracking control, formamide, SSC, SDS, a Cy3-labelled alignment oligonucleotide, a Cy5-labelled alignment oligonucleotide and a Cy5-labelled common oligonucleotide reference standard target. After denaturing, the mixtures were deposited onto the glass microarray and hybridized at 42  °C for 16 h.

scan_protocol: Then the arrays were washed and dried, and scanned by an MS 200Microarray Scanner (NimbleGen) at 532nm and 635 nm.

data_processing: NimbleScan software version 2.5 (NimbleGen) was used to grid and process the images to transform them into signal intensity. The raw signals from NimbleScan were submitted to the Microarray Data Manager on our website (http://ieg.ou.edu/microarray), cleaned, normalized and analysed using the data analysis pipeline.

organism: soil metagenome

source_name: Soil Fungi

label_protocol: One microgram of DNA from each sample was mixed with random primers and denatured before dNTP, fluorescent dye Cy-3 dUTP and DNA polymerase were added for labelling at 37  C for 6 h, followed by heating at 95  C for 3 min.

extract_protocol: Soil DNA was extracted following the instructions of the PowerMax Soil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA). DNA quality was assessed via NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA), based on UV spectrometry absorbance ratios at wavelengths of 260 nm/280 nm and 260 nm/230 nm. DNA concentration was measured by PicoGreen using the FLUOstar OPTIMA fluorescence plate reader (BMG Labtech, Jena, Germany) before microarray labeling.

tag: group

value: warmed plots


title: dDRIP-seq_calli_rep1

value: Nipponbare

value: biological replicate1

value: three weeks


title: The fifth sample of warmed plots


title: HV-85

description: healthy volunteer


title: B6J_111905-11

description:
Mouse with medium cognition, sample 3
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: SH_6


title: SS_26


title: SM_1


title: B6J_111905-10

description:
Mouse with medium cognition, sample 2
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: SS_27


title: The fourth sample of warmed plots


title: The third sample of warmed plots


title: S_4


title: B6J_111905-12

description:
Mouse with medium cognition, sample 4
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: HV-81

description: healthy volunteer


title: Laos9

value: Lao


title: pSS-144

description: primary Sjögren’s syndrome


title: Laos8


title: The second sample of warmed plots


title: S_1


title: pSS-141

description: primary Sjögren’s syndrome


title: B6J_111905-08

description:
Mouse with low cognition, sample 8
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: pSS-139

description: primary Sjögren’s syndrome


title: The sixth sample of control plots

value: control plots


title: B6J_111905-09

description:
Mouse with medium cognition, sample 1
Mouse that was consistently ranked as having medium cognition by the two ranking systems in our study.


title: The first sample of warmed plots


title: pSS-106

description: primary Sjögren’s syndrome


title: SMR_25


title: Laos7


title: B6J_111905-07

description:
Mouse with low cognition, sample 7
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: SHZ_36


title: pSS-105

description: primary Sjögren’s syndrome


title: B6J_111905-05

description:
Mouse with low cognition, sample 5
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: pSS-101

description: primary Sjögren’s syndrome


title: B6J_111905-06

description:
Mouse with low cognition, sample 6
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: Laos32


title: The fifth sample of control plots


title: The fourth sample of control plots


title: The third sample of control plots


title: B6J_111905-03

description:
Mouse with low cognition, sample 3
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: Laos29


title: pSS-37

description: primary Sjögren’s syndrome


title: pSS-94

description: primary Sjögren’s syndrome


title: Hy_0: transcriptome of A. stygium mycelia

organism: Annulohypoxylon stygium

source_name: A. stygium mycelia

value: mycelia

value: one week


title: Laos6


title: The second sample of control plots


title: B6J_111905-04

description:
Mouse with low cognition, sample 4
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: Hy_1: transcriptome of  A. stygium mycelia which interacted with T. fuciformis

value: one week after interaction with T. fuciformis

value: wild type


title: The first sample of control plots


title: Tr_Inter_Hy: transcriptome of dual mycelia of both T. fuciformis and A. stygium

organism:
Tremella fuciformis
Annulohypoxylon stygium

source_name: dual mycelia of both

value: one week after interaction with each other


title: Laos26a


title: B6J_111905-02

description:
Mouse with low cognition, sample 2
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.

value: 10 week-old

value: Male


title: Laos25


title: 22Rv1 shCENPA2, Replicate 3

status: Public on Mar 06 2019

city: Ann Arbor

first: Anjan

middle: Kumar

last: Saha

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description:
sample name in processed data file:
103427.L007

data_processing:
Illumina RTA2 for basecalling
TrimGalore low-quality bases and adapters
STAR to align reads to the human reference genome
Htseq to assemble aligned reads
edgeR to call differentially expressed genes (fold change > 2.0 and false-discovery rate < 0.05)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 22Rv1 Prostate Carcinoma Cell Line

extract_protocol:
The All Prep DNA/RNA Mini Kit (Qiagen) was utilized to isolate RNA from cell lysates. RNase-Free DNase (Qiagen) was used to eliminate contaminating genomic DNA.
Strand-specific libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer’s protocol.

tag: shRNA

tag: cell line

value: Prostate


title: 22Rv1 shCENPA2, Replicate 2

description:
sample name in processed data file:
103426.L008


title: 22Rv1 shCENPA1, Replicate 2

description:
sample name in processed data file:
103424.L008


title: 22Rv1 shCENPA1, Replicate 3

description:
sample name in processed data file:
103425.L007


title: 22Rv1 shCENPA1, Replicate 1

description:
sample name in processed data file:
103424.L007


title: Laos30

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).


title: B6J_111905-01

description:
Mouse with low cognition, sample 1
Mouse that was consistently ranked as having low cognition by the two ranking systems in our study.


title: 22Rv1 shCENPA2, Replicate 4

description:
sample name in processed data file:
103427.L008


title: 22Rv1 shNT, Replicate 3

description:
sample name in processed data file:
103423.L007

value: shNT


title: 22Rv1 shCENPA2, Replicate 1

description:
sample name in processed data file:
103426.L007


title: Input Replicate 2

data_processing:
Illumina RTA2 for basecalling
TrimGalore low-quality bases and adapters
Bowtie2 (version 2.2.1) to align reads to the human reference genome
PePr (version 1.1.14) to identify CENPA bound regions
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig; Scores indicates how dark the peak will be displayed in the browser (0-1000)

source_name: VCaP Prostate Carcinoma Cell Line

extract_protocol:
Native ChIP was conducted as previously described using a monoclonal antibody against CENPA (Abcam ab13939).
CENPA targeted ChIP DNA and input control DNA were prepared for parallel sequencing using the TruSeq ChIP Library Preparation kit (Illumina) according to the manufacturer’s protocol.

value: VCaP


title: 22Rv1 shNT, Replicate 1

description:
sample name in processed data file:
103422.L007


title: Laos28

value: Asia

value: blood


title: Input Replicate 3


title: Input Replicate 1


title: CENPA IP Replicate 2

value: CENPA


title: CENPA IP Replicate 1


title: CENPA IP Replicate 3


title: H3K4me3 ChIP-seq on 4w cultured HSPC with CTR virus

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description:
H3K4me3_CTR
Sonicated crosslinked chromatin

data_processing:
Alignment: Bowtie2 v2.2.5
Coverage file: Bamcoverage, Deeptools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks for each of the samples

source_name: human FL CD34+CD38-/lowCD90+GFP+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells are magnetically separated. cells are infected with MLLT3_OE lentivitus or control and cultured for 4 weeks on OP9M2

extract_protocol:
Cells are crosslinked 10' in 1%formaldehide, lysed and sonicated. The indicated mark is immunoprecipitated overnaight, and enriched by magnetical isolation. IP fraction is eluted and decrosslinked.
Ovation Ultralow v2 (Nugen)

treatment_protocol: lentivirus infection with MLLT3 overexpression or empty vector

value: 4w cultured HSPC

tag: genotype/variation

value: control

tag: chip antibody

value: Abcam ab8580


title: H3K36me3 ChIP-seq on 4w cultured HSPC with CTR virus

description:
H3K36me3_CTR
Sonicated crosslinked chromatin

tag: cell type

value: Abcam ab9050


title: MLLT3 ChIP-seq on 4w cultured HSPC with MLLT3 virus

description:
MLLT3_MLLT3OE
Sonicated crosslinked chromatin

value: MLLT3 overexpression

value: Genetex, GTX102835


title: MLLT3 ChIP-seq on 4w cultured HSPC with CTR virus

description:
MLLT3_CTR
Sonicated crosslinked chromatin


title: V5tag ChIP-seq on 4w cultured HSPC with MLLT3 virus

description:
V5tag_MLLT3OE
Sonicated crosslinked chromatin

value: Abcam, ab15828


title: H3K79me2 ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample3

description:
H3K79me2_MLLT3OE_3
Sonicated crosslinked chromatin

value: Abcam, ab3594


title: V5tag ChIP-seq on 4w cultured HSPC with CTR virus

description:
V5tag_CTR
Sonicated crosslinked chromatin


title: H3K79me2 ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample2

description:
H3K79me2_MLLT3OE_2
Sonicated crosslinked chromatin


title: H3K79me2 ChIP-seq on 4w cultured HSPC with CTR virus, sample2

description:
H3K79me2_CTR_2
Sonicated crosslinked chromatin


title: H3K79me2 ChIP-seq on 4w cultured HSPC with CTR virus, sample1

description:
H3K79me2_CTR_1
Sonicated crosslinked chromatin


title: Input for ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample3

description:
INPUT_MLLT3OE_3
Sonicated crosslinked chromatin


title: H3K79me2 ChIP-seq on 4w cultured HSPC with CTR virus, sample3

description:
H3K79me2_CTR_3
Sonicated crosslinked chromatin


title: Laos3

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).

value: Lao


title: Input for ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample1

description:
INPUT_MLLT3OE_1
Sonicated crosslinked chromatin


title: H3K79me2 ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample1

description:
H3K79me2_MLLT3OE_1
Sonicated crosslinked chromatin


title: Input for ChIP-seq on 4w cultured HSPC with CTR virus, sample2

description:
INPUT_CTR_2
Sonicated crosslinked chromatin


title: Input for ChIP-seq on 4w cultured HSPC with CTR virus, sample3

description:
INPUT_CTR_3
Sonicated crosslinked chromatin


title: Input for ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample2

description:
INPUT_MLLT3OE_2
Sonicated crosslinked chromatin


title: H3K36me3 ChIP-seq on 4w cultured HSPC with MLLT3 virus

description:
H3K36me3_MLLT3OE
Sonicated crosslinked chromatin


title: ChIP-seq for RNApolII in FL-HSPC, sample8

description:
RNApolII_FL_HSPC_1
Sonicated crosslinked chromatin

data_processing:
Alignment: Bowtie2 v2.2.5
Coverage file: Bamcoverage, Deeptools
Peak calling: macs2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks for each of the samples

source_name: human FL CD34+CD38-/lowCD90+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells and CD34- cells are magnetically separated. The indicated phenotype are facs sorted

treatment_protocol: Untreated

value: FL-HSPC

value: Biolegend 664911


title: ChIP-seq for MLLT3 in FL-Erythroblasts, sample9

description:
MLLT3_FL_Ery_1
Sonicated crosslinked chromatin

source_name: human FL CD34-CD71+CD235a+

value: FL-Erythroblasts


title: 22Rv1 shCENPA1, Replicate 4

description:
sample name in processed data file:
103425.L008

value: Prostate


title: ChIP-seq for H3K9ac in FL-HSPC, sample5

description:
H3K9ac_FL_HSPC_1
Sonicated crosslinked chromatin


title: ChIP-seq for H3K79me2 in FL-HSPC, sample7

description:
H3K79me2_FL_HSPC_1
Sonicated crosslinked chromatin


title: ChIP-seq for H3K4me3 in FL-HSPC, sample4

description:
H3K4me3_FL_HSPC_1
Sonicated crosslinked chromatin


title: Laos20

source_name: blood


title: ChIP-seq for MLLT3 in FL-HSPC, sample3

description:
MLLT3_FL_HSPC_3
Sonicated crosslinked chromatin


title: Input for ChIP-seq in Fetal liver HSPC, sample2

description:
INPUT_FL_HSPC_2
Sonicated crosslinked chromatin


title: ChIP-seq for MLLT3 in FL-HSPC, sample2

description:
MLLT3_FL_HSPC_2
Sonicated crosslinked chromatin


title: Laos22


title: ChIP-seq for MLLT3 in FL-Erythroblasts, sample10

description:
MLLT3_FL_Ery_2
Sonicated crosslinked chromatin


title: ChIP-seq for MLLT3 in FL-HSPC, sample1

description:
MLLT3_FL_HSPC_1
Sonicated crosslinked chromatin


title: Laos31

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).


title: Laos24


title: H3K4me3 ChIP-seq on 4w cultured HSPC with MLLT3 virus

description:
H3K4me3_MLLT3OE
Sonicated crosslinked chromatin


title: 22Rv1 shNT, Replicate 4

description:
sample name in processed data file:
103423.L008

value: shNT


title: mdxmTR6

city: New York

first: Christopher

middle: L

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

description:
WT_vs_Mdxmtr.deseq.counts.txt
WT_vs_Mdxmtr.deseq.txt

data_processing:
Quality assessment and fold change calculations were performed in BaseSpace (Illumina).
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10, UCSC, Santa Cruz, CA, USA) with the STAR software package.
Differential expression based on fragments per kilobase of transcript per million mapped reads was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2

source_name: Tibialis anterior muscle

extract_protocol:
RNA was isolated from TA muscles using a miRNEasy kit (Qiagen, Valencia, CA, USA). RNA quality was assessed using a TapeStation (Agilent, Santa Clara, CA, USA) and all samples had a RNA integrity number greater than 9.0. For each sample, 250ng total RNA was delivered to the University of Michigan Sequencing Core for RNA sequencing (RNAseq) analysis. Sample concentrations were normalized, and cDNA pools were created for each sample, and then subsequently tagged with a barcoded oligo adapter to allow for sample specific resolution.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mdx/mTR

value: 4 months

tag: Sex

value: Male


title: Laos17

tag: population

value: Asia

value: blood


title: mdxmTR4

tag: age


title: mdxmTR5


title: mdxmTR3


title: mdxmTR1


title: Laos23

tag: region

tag: tissue


title: mdxmTR2


title: WT4


title: WT3


title: WT5


title: WT6


title: WT1


title: Laos12


title: RNA-seq_dLGN_Math5KO_P23

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

data_processing:
Sequencing adapters in raw sequencing reads were removed by Cutadapt (v.11.2). Moreover, the bad quality of bases in either ends of reads were trimmed by a customized Perl script. After trimming, reads were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH (.bdg)

source_name: dLGN from P23 Math5-KO mouse

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Total RNA was extracted from mouse dLGN tissues using Aurum Total RNA Fatty and Fibrous Kit (BioRad) according to the manufacturer’s instructions. RNA-Seq libraries were generated from total RNA with polyA+ selection using the TruSeq Stranded mRNA Library Preparation Kit (Cat# RS-122-2101, Illumina, San Diego, CA).
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: tissue/cell type

value: brain (dLGN)

value: male


title: 22Rv1 shNT, Replicate 2

description:
sample name in processed data file:
103422.L008


title: RNA-seq_dLGN_Math5KO_P3

source_name: dLGN from P3 Math5-KO mouse

tag: gender


title: WGBS_mm_dLGN_Math5KO_P6

data_processing:
Sequecing adapters and low quality sequences were removed by Trim Galore (v0.4.1) with parameters: -q 28 --length 30. Trimmed reads were mapped to mm10 by Bismark (v0.16.3) with Bowtie2 (v2.2.9). PCR duplicates were removed by bismark deduplication script in paired end mode.
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH (.bdg)

source_name: dLGN from P6 Math5-KO mouse

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee, Virginia Polytechnic Institute and State University

extract_protocol:
Genomic DNA was extracted from mouse dLGN tissues using DNeasy mini Kit (Qiagen) according to the manufacturer’s instructions. One microgram genomic DNA per sample was used for library construction following the standard Whole Genome Bisulfite Sequencing (WGBS) method.
One microgram mouse genomic DNA was spiked with 0.02% unmethylated cl857 Sam7 Lambda DNA (Promega) and sonicated to 200-bp fragments with Covaris M2 (AB). After end repair, dA tailing, the DNA fragments were ligated with cytosine-methylated Illumina TruSeq DNA adapters using T4 DNA ligase (NEB) overnight. After purification, Adapter-ligated DNA fragments were subject to bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. The recovered libraries were sequenced on Hiseq 4000 platform (Illumina).

value: brain

value: dLGN (dorsolateral geniculate nucleus)


title: RNA-seq_dLGN_Math5KO_P14

source_name: dLGN from P14 Math5-KO mouse


title: RNA-seq_dLGN_WT_P23

source_name: dLGN from P23 WT mouse

value: WT


title: RNA-seq_dLGN_WT_P3

source_name: dLGN from P3 WT mouse


title: RNA-seq_dLGN_WT_P14

source_name: dLGN from P14 WT mouse


title: Laos21


title: WGBS_mm_dLGN_CD1_P6

source_name: dLGN from P6 WT mouse


title: WGBS_mm_dLGN_CD1_P23


title: RNA-seq_dLGN_Math5KO_P7

source_name: dLGN from P7 Math5-KO mouse


title: Laos11


title: Laos15


title: RNA-seq_dLGN_WT_P7

source_name: dLGN from P7 WT mouse


title: Laos1


title: Laos13


title: M59

city: Aberdeen

first: Imke

last: Mulder

address: Cornhill Road

institute: 4D Pharma Research Ltd

description:
M59
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip NuGO Mouse Array (NuGO_Mm1a520177). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.

source_name: Mouse ascending colon, 13-14w, B. theta

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: SPF C57BL/6 homozygous IL10KO mice were purchased from the Jackson Laboratory (USA). They were housed and bred over three generations within flexifilm isolators.

extract_protocol: Ascending colon tissue was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: Weanling mice (20 days old) were orally dosed for 13 weeks (2-3 times a week) with a viable culture (1x10^10 CFU/kg BW) of BT.

value: homozygous IL10KO mice

value: ascending colon

tag: treated with

value: B. theta


title: Laos10

value: Lao


title: WGBS_mm_dLGN_Math5KO_P23

tag: genotype


title: WT 3

first: Isabelle

last: Lombaert

address: 2800 Plymouth Rd

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.4.2a in  two-pass mode. First and second pass parameters:  --outSAMstrandField None   --outFilterType BySJout   --outFilterMultimapNmax 10   --outFilterMismatchNmax 10   --outFilterMismatchNoverLmax 0.3   --clip3pAdapterSeq -   -      --alignIntronMin 21   --alignIntronMax 0   --alignMatesGapMax 0   --alignSJoverhangMin 5   --alignSJDBoverhangMin 3.
Gene counts were generated with Subread’s  v1.4.6-p3 featureCounts utility against the Gencode GRCm38 vM4 annotation with the following parameters: -s 2 -p -t exon -g gene_name.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2 and EdgeR R packages.
Genome_build: mm10/GRCm38.p3
Supplementary_files_format_and_content: Tab delimited files include a raw counts expression matrix and results from DE analysis using the DESeq2 and EdgeR packages.

extract_protocol:
SMGs were removed, and RNA was harvested using an Ambion RNA isolation Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared using Illumina’s TruSeq stranded protocol. Briefly, polyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

tag: strain background

value: wild type

value: embryonic day 16 (E16)

value: submandibular glands (SMGs)


title: Sox10fl/fl 1


title: Sox10fl/fl 4


title: WT 2


title: WT 1


title: M14

description:
M14
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: Sca-1+CD45- rep 2

city: Adelaide

first: Peter

middle: James

last: Psaltis

state: South Australia

address: North Terrace

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

description: Biological Replicate 8

data_processing:
The log-2 of the gene expression data was normalised using the non-linear normalisation fastlo
To assess differential expression between groups of interest, the LIMMA package in R was utilised to implement the empirical Bayes method of Smyth to shrink the gene-wise sample variances towards a common value.  The false discovery rate (FDR 44), which is the expected proportion of false discoveries amongst the rejected hypotheses, was also calculated.

source_name: aortic adventitia

label_protocol: High-quality samples were labelled according to instructions for the Illumina Direct Hyb labelling method (San Diego, CA, USA).

extract_protocol: Total RNA was isolated and purified immediately using an RNeasy® Plus Mini Kit (Qiagen, Germany), as per manufacturer's instructions. The quality of all total RNA samples was assessed according to manufacturer’s instructions for the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: 12 weeks

value: aortic adventitia


title: Sca-1+CD45- rep 3

description: Biological Replicate 9


title: M44

description:
M44
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.

source_name: Mouse ascending colon, 13-14w, untreated

value: Untreated


title: Sox10fl/fl 2


title: M49

description:
M49
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: Sca-1-CD45+ rep 3

description: Biological Replicate 6


title: Sca-1+CD45- rep 1

description: Biological Replicate 7


title: M13

description:
M13
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: Input for ChIP-seq in Fetal liver HSPC, sample1

description:
INPUT_FL_HSPC_1
Sonicated crosslinked chromatin

source_name: human FL CD34+CD38-/lowCD90+

value: FL-HSPC


title: Sca-1+CD45+ rep 3

description: Biological Replicate 3


title: Sca-1-CD45+ rep 2

description: Biological Replicate 5


title: M22

description:
M22
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: M10

description:
M10
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: Input for ChIP-seq on 4w cultured HSPC with CTR virus, sample1

description:
INPUT_CTR_1
Sonicated crosslinked chromatin

source_name: human FL CD34+CD38-/lowCD90+GFP+

value: 4w cultured HSPC

value: control


title: thiostrepton_4uM_12hr, biological rep 2

city: New Taipei City

first: Yu-Lun

last: Kuo

address: 7F-3, No.99, Sec. 1, Xintai 5th Rd., Xizhi Dist.

country: Taiwan

institute: BIOTOOLS

description: gene expression after 12hours 4uM thiostrepton treatment in NPC cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix HG U133 plus 2.0 probe arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix 7G Gene Chip Scanner

data_processing: The raw fluorescence intensity data within CEL files of these datasets were preprocessed and normalized using the GCRMA package, which is based on the Robust Multichip Average (RMA) algorithm with R language from Bioconductor. The base 2 logarithm of the intensity in the samples was used as the expression value for each probe.

source_name: cell line derived from biopsy specimens of nasopharyngeal carcinoma patient and treated with 4 uM thiostrepton 12 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: The NPC cell line was maintained in DMEM with 10% FBS at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted using an illustra RNAspin Mini RNA isolation kit (GE Healthcare, Little Chalfont, UK) according to the manufacturer’s instructions.

treatment_protocol: Thiostrepton (Sigma, St. Louis, MO, USA) supplied as a crystalline solid and powder were dissolved in dimethylsulfoxide and 0.9% sodium chloride. NPC cells treated with or without 4 μM thiostrepton for 12 hours at 37°C

value: NPC

tag: passage

value: passage at p3-p10

tag: agent

value: 4uM thiostrepton


title: Sca-1+CD45+ rep 1

description: Biological Replicate 1


title: M45

description:
M45
IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: thiostrepton_4uM_12hr, biological rep 1

tag: cell line


title: thiostrepton_4uM_12hr, biological rep 3


title: DMSO, biological rep1

description: DMSO control

source_name: cell line derived from biopsy specimens of nasopharyngeal carcinoma patient

value: DMSO


title: DMSO, biological rep2

description: DMSO control


title: Sca-1+CD45+ rep 2

description: Biological Replicate 2


title: DMSO, biological rep3

description: DMSO control


title: Sox10fl/fl 3

tag: genotype/variation


title: Subject 12

city: Tucson

first: Michael

last: Hammer

state: Arizona

address: 1657 E Helen St

institute: University of Arizona

data_processing:
Basecalls performed using CASAVA
Fastqs were trimmed using Trimmomatic
Sequence reads were aligned using STAR v2.5.2b
Gene expression counts were calculated using htseq-count v0.9.1
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample

source_name: Hippocampus

extract_protocol:
RNA was isolated and initial QC assessed.
Libraries were constructed using a stranded mRNA-Seq Kit and average fragment size was assessed. After concentrations were determined with an adaptor-specific qPCR kit, equimolar samples were pooled and clustered for sequencing on the HiSeq2500 (Illumina). Sequencing was performed using Rapid-Run SBS 2x100bp chemistry (Illumina).

tag: seizures/month


title: Subject 8


title: Subject 7


title: Subject 3


title: Subject 2


title: Subject 5


title: Subject 4


title: Subject 6


title: Subject 1


title: GAC028_Fat4_ctrl

city: Stanford

first: Sabina

last: Kanton

address: 318 Campus Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

description:
2d neurons
Neurons_Dchs1_Control_1188cells.txt
GAC028_Fat4_ctrl_barcodes.tsv, GAC028_Fat4_ctrl_matrix.mtx

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers for SmartSeq2 data (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.). Cellranger (v 2.1.0) was used for basecalling for 10X data.
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.). For 10X data, demultiplexing was performed using Cellranger (v 2.1.0).
or SmartSeq2 data, reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.9. For 10X data, alignment to GRCh38 was performed using Cellranger (v 2.1.0).
For SmartSeq2 data, Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1. For 10X data, gene count matrix was computed using Cellranger (v 2.1.0)
For 10X data, barcode is found in R1 from bp 1-16 and UMI is found in bp 17-26.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: For SmartSeq2 data, data frame including sample name, gene ID, and FPKM values for each single cell. For 10X data, log transformed and normalized gene expression values as computed by Seurat (v 2.3.0) with gene IDs and cell barcode information for Dchs1 and Ctrl cells used in further analysis.

molecule: polyA RNA

source_name: iPSC Fat4_ctrl

growth_protocol: Cerebral organoids were generated according to Lancaster et al. (Nature Protocols, 2014). Neurons were differentiated according to Boyer et al. (Current Prot Stem Cell Biol, 2012, PMID:22872424).

extract_protocol:
Single cells from dissociated organoids were sorted into 96 well plates using FACS and cDNA was obtained using SmartSeq2 protocol (Picelli et al., Nature Protocols, 2014). Neurons from 2d culture were encapsulated into droplets and cDNA was generated using 10X Genomics single cell 3' v2 kit.
Libraries for SmartSeq2 data were generated using the NexteraXT kit. Libraries from 2d cultured neurons were generated using the 10X Genomics 3' Single Cell v2 kit.

treatment_protocol: Dissected regions of organoids were dissociated into single cell suspensions using Papain-based (Neural tissue dissociation kit, Miltenyi Biotec) dissociation with intermittend triturations. Cell suspensions underwent several filtering (30um, 20um) and washing steps (using HBSS). Neuronal cells in 2D culture.  were brought into single cell suspension using 1% (v/v) Accutase (Sigma) in DPBS/EDTA  (0.5 mM, Gibco, Invitrogen)

tag: Stage

value: 14 days

value: 2d neurons

tag: scrna-seq protocol

value: 10X Genomics 3' Single Cell v2


title: GAC028_Dchs1_GL

description:
2d neurons
Neurons_Dchs1_Control_1188cells.txt
GAC028_Dchs1_GL_barcodes.tsv, GAC028_Dchs1_GL_matrix.mtx

source_name: iPSC Dchs1_GL


title: H9B_Control_2

description:
dissected cerebral organoid
Data_Fat4_Dchs1_805cells.csv

source_name: iPSC Control

value: 51 days

value: Control organoid 2


title: H6B_Control_2


title: H8B_Control_2


title: H4B_Control_2


title: Subject 11


title: H12B_Control_2


title: Subject 9


title: H3B_Control_2


title: H10B_Control_2


title: G1B_Control_2


title: G4B_Control_2


title: G12B_Control_2


title: F9B_Control_2


title: G3B_Control_2


title: F8B_Control_2


title: F4B_Control_2


title: F1B_Control_2


title: F7B_Control_2


title: F5B_Control_2


title: F6B_Control_2


title: F12B_Control_2


title: F10B_Control_2


title: F11B_Control_2


title: E4B_Control_2


title: E3B_Control_2


title: E7B_Control_2


title: E9B_Control_2


title: E5B_Control_2


title: E2B_Control_2


title: G2B_Control_2


title: E10B_Control_2


title: E1B_Control_2


title: E12B_Control_2


title: G11B_Control_2


title: E11B_Control_2


title: D8B_Control_2


title: D9B_Control_2


title: D5B_Control_2


title: D4B_Control_2


title: C9B_Control_2


title: D12B_Control_2


title: C7B_Control_2


title: E6B_Control_2


title: C8B_Control_2


title: C5B_Control_2


title: C4B_Control_2


title: C1B_Control_2


title: C10B_Control_2


title: B9B_Control_2


title: B8B_Control_2


title: B3B_Control_2


title: Subject 10


title: B4B_Control_2


title: B11B_Control_2


title: B12B_Control_2


title: A7B_Control_2


title: A5B_Control_2


title: A9B_Control_2


title: D3B_Control_2


title: A6B_Control_2


title: A4B_Control_2


title: A2B_Control_2


title: D2B_Control_2


title: A3B_Control_2


title: A12B_Control_2


title: A11B_Control_2


title: A10B_Control_2


title: H8A_Control_1

value: Control organoid 1


title: H5A_Control_1


title: H12A_Control_1