title: FLAG ChIP-seq (induced)

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the Drosophila  dm3  genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings using ChIP sample as treatment file and input as control.
Genome_build: dm3
Supplementary_files_format_and_content: coverage Wiggle files were generated with Macs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)

source_name: S2 cells

growth_protocol: S2 wildtyp cells, clones and clone pools were raised and cultured in Schneider’s Medium (Invitrogen; supplemented with 10% fetal bovine serum (FBS), 1% penicillin/ streptomycin and glutamine).

extract_protocol:
S2 wildtyp cells were seaded 2x 10^7 cells/ 20 ml flask. Inducible cells were induced with 100mM CuSO4 24 h after seading cells. After 48 h they were harvested and counted. The ChIP was performed as described previously (Bartkuhn et al. 2009) with minor modifications in sonication. The cells were fixed by 1 % formaldehyde. Fixation was stopped by the use of 0,125M Glycin. After washing cells with 1x PBS, lysis buffer (1% SDS, 10mM EDTA, 50mM Tris/HCl pH 8, supplemented with Roche proteinase inhibitor cocktail) was added to the cells and the DNA was fragmented with the Bioruptor sonicator (Diagenode). Cells were incubated for 2x 10 cycles (30 sec sonication, 30 sec pause) within the ice cooled sonicater. The resulting fragments ranged from 200 – 500 bp. Chromatin samples were diluted 1:10 by dilution buffer (0,01% SDS, 1,1% Triton X-100, 1,2% EDTA, 16,7mM Tris/HCl pH 8, 167mM NaCl in ddH2O), with addition of glycerol for stability of the chromatin. 10 % input samples were separated from prepared chromatin and were stored at -20°C. Pre-clearing of Chromatin was performed with protein A/G agarose beads (Millipore) for 45 min at 4°C. IP with specific antibodies for CP190, dCTCF, FLAG and Histone H3 was performed at 4°C. Mouse IgG was used as IP control. After 4 h beads were added and the solution was further incubated at 4°C o. n. The beads were than washed by different salt buffers with increasing salt concentration, low salt buffer (0,1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris/HCl pH 8, 150mM NaCl in ddH2O), high salt buffer (0,1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris/HCl pH 8, 500mM NaCl in ddH2O) and LiCl buffer (0,25% LiCl, 1% NP40, 1mM EDTA, 10mM Tris/HCl pH 8, 1% DOC in ddH2O), as well as 2x TE buffer (10mM Tris/HCl pH 8, 1mM EDTA). Clean up of DNA was performed with 100 µl Chelex 100 agarose beads (BioRad) to gain higher DNA amount for sequencing of ChIP-DNA. Proteinase K digestion was done with 10 µg/ml of the enzyme during Chelex DNA extraction. DNA from 10 % Input samples were also extracted by Chelex method (Nelson et al. 2006).
Sequencing libraries were prepared with the NEBNext ChIP-Seq Library Prep Reagent (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: For induction of recombinant proteins cells were treated with 100mM CuSO4 24 h after seading cells. Cells were harvested and counted after 48 h.

tag: cell line

value: S2 cells

tag: stably transfected with

tag: treated with

value: 100mM CuSO4 24 h after seading cells

tag: chip-antibody


title: Input (control)

status: Public on Aug 07 2017

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster


title: Input (induced)


title: quadAvrRpt2.Mock.0min.rep1

city: St Paul

first: Fumiaki

last: Katagiri

state: Minnesota

address: 1500 Gortner Ave

department: Dept of Plant and Microbial Biology

country: USA

institute: Univ of Minnesota

library_source: transcriptomic

data_processing:
bcl2fastq version 2.17.1.14 was used for demultiplexing and fastq file creation.
The 5-base UMI and 3-base "GGG" were trimmed from the beginning of the read. In addition, polyA from the end of the read were also trimmed.
The trimmed reads were mapped onto the Arabidopsis TAIR10 gene model using STAR version 2.4.2a.
The STAR parameters used different from the defaults were: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0
The uniquely mapped reads were counted for each gene with no distinction among the transcript variants.
Per gene, the total read count and the UMI-based read count were weighted-averaged and rounded to an integer value, which we call the read count per gene.
Since this was 3SEQ data, no correction of the read count for the transcript length was made.
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: It is a csv file of the read count per gene for each sample. The gene names (in the AGI code) are shown as the row names, and the sample titles are shown as the column names.
Supplementary_files_format_and_content: The genes that had at least one read count across the samples are included in the processed data file.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Adult leaves

growth_protocol: Four-week old plants grown at 22C with 75%RH and a 12-hr light/12-hr dark cycle were used.

extract_protocol:
Total RNA was extracted from the frozen pulverized leaf tissue using Trizol.
Smart-3SEQ, which is a modified 3SEQ method, was used (Foley et al., manuscript in preparation). The first 5 bases of the sequence read is Unique Molecular Identifier (UMI), which helps determining PCR duplicates.
RNA-tag-SEQ: The following "GGG" was used for reverse transcriptase template switching. Thus, total 8 bases from the beginning of the read need to be trimmed for an actual mRNA sequence.

treatment_protocol:
Two leaves per plant selected from leaf numbers 7-9 were infiltrated with one of four treatment solutions: (1) Mock (0.1% ethanol); (2) 1 uM flg22; (3) 10 uM estradiol(Ed), 0.1% ethanol; (4) 1 uM flg22, 10 uM Ed, 0.1% ethanol.
Plants were given treatment 3 to 4 hours after the subjective dawn. The infiltrated leaves from two plants were harvested, pooled, and flash-frozen the indicated minutes after treatment.

tag: ecotype

tag: genotype

value: dde2 ein2 pad4 sid2 Ed-AvrRpt2

tag: tissue

value: Adult leaves

tag: treatment

value: Mock

tag: minutes


title: FLAG ChIP-seq (control)


title: CTCF ChIP-seq (induced)

value: Anti-dCTCF (N3)


title: CTCF ChIP-seq (control)


title: CP190 ChIP-seq (induced)


title: Astrocytes, T. gondii-infected

city: Göttingen

first: Carsten

last: Lueder

address: Kreuzbergring 57

institute: Institut für Medizinische Mikrobiologie

description: pools from 4 biological replicates

data_processing:
Reads were mapped to reference genomes using CLC bio (Qiagen, Aarhus, Denmark).
Reads aligned to exons were transformed into relative expression values by calculating RPKM values for each gene.
Differentially expressed genes were identified using a moderated Chi2 test as described by Tran et al., 2014 using the MarVis filtering and visualization software (Kaever et al., 2009). P-values were adjusted for multiple testing using Holm-Bonferroni familywise error rate (FWER) correction as described by Holm, 1979. Identification of T. godii DEGs was confined to genes with at least 5 total reads aligned.
Log-transformed RPKM values of DEGs were used for hierarchical cluster analysis based on linear correlation (distance corresponds to 1 – Pearson coefficient) and average linkage method. Clustering and visualization of normalized gene expression profiles based on one-dimensional self-organizing maps was performed using the MarVis-Suite software (Kaever et al., 2015) and default settings.
Genome_build: mm9 (for *mm9_RNA-Seq.xlsx data files)
Genome_build: Toxoplasma gondii ME49 ToxoDB 7.0 (for *Toxo_RNA-Seq_CL.xlsx data)
Supplementary_files_format_and_content: Excel files containing RPKM values

organism: Mus musculus

source_name: New-born mouse brain

extract_protocol:
Total RNA was isolated using the GenElute Mammalian Total RNA Miniprep Isolation Kit (Sigma-Aldrich). For each sample, high-quality RNA from 4 biological replicates were pooled. cDNA libraries of each mRNA pool were prepared using the mRNA-Seq Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue/cell line

value: New-born mouse brain

tag: cell type

value: Astrocyte

tag: infection

value: Toxoplasma gondii, strain NTE

tag: infection time

value: 24 hours


title: Fibroblasts, T. gondii-infected

description: pools from 4 biological replicates

source_name: NIH/3T3 fibroblasts

value: NIH/Swiss

value: NIH/3T3 fibroblasts

value: Fibroblast


title: Fibroblasts, non-infected

description: pools from 4 biological replicates

value: not applicable


title: Astrocytes, non-infected

description: pools from 4 biological replicates


title: CP190 ChIP-seq (control)


title: SkMCs, T. gondii-infected

description: pools from 4 biological replicates

source_name: Mature C2C12 myotubes

value: Mature C2C12 myotubes

value: Skeletal muscle cell (myotube)


title: SkMCs, non-infected

description: pools from 4 biological replicates


title: FMC5

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Reads were mapped to the mm10 murine genome and USCS transcriptome annotation (obtained from Illumina iGenomes) using Tophat 2 and uniquely mapped reads associated with each gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited table of uniquely aligned read counts for each gene in the annotation.

molecule: polyA RNA

source_name: Nf1(flox/-), GFAP-Cre mouse

growth_protocol: Optic glioma stem cells (o-GSCs) were isolated from optic glioma mouse models. For NVP-BKM120 treatments, cells were cultured in neural stem cell medium without EGF and bFGF for 1 hour, followed by treatment with DMSO (vehicle) or 0.2 μM NVP-BKM120 for 5 hours at 37°C, and cells harvested for RNA isolation or western blotting.

extract_protocol:
Tissue samples or cell lines were homogenized in Trizol and total RNA was extracted using Trizol and isopropanol precipitation. Poly(A)+ mRNA was then isolated from each total RNA sample using streptavidin-coated superparamagnetic beads (Dynabeads, Life Technologies) coated in biotinylated LNA-oligo(dT) (Exiqon).
Purified poly(A)+ mRNA from each sample was reverse transcribed and Illumina sequencing libraries were enriched usign the SMARTer Stranded RNA-Seq kit (Clontech). The resulting libraries were sequenced on an Illumina HiSeq 2500 or NextSeq 500 with single-end 100-base or 75-base reads, respectively.
template-switching RNA-Seq with random primers

treatment_protocol: 50 mg/kg/day minocycline (Sigma-Aldrich; PBS, vehicle) was delivered by intraperitoneal (i.p.) injection 5 days/week for two weeks. 5 mg/kg/day rapamycin (Selleckchem; 5.2% Tween 80/5.2% polyethylene glycol 400 as vehicle) was administered by i.p. injection 5 days/week for two weeks. 20 mg/kg/day NVP-BKM120 (Selleckchem; N-methyl-2-pyrrolidone/ polyethylene glycol 300 (10/90v/v) as vehicle) was delivered by oral gavage 5 days/week for two weeks [40]. 60 mg/kg/day carboplatin (Sigma-Aldrich; PBS as vehicle) was administered by i.p. injection every other day for 1 week.

value: optic glioma tissue


title: FMC3


title: FMC4


title: FMC1


title: FMC2


title: FF4

source_name: Nf1(flox/flox) mouse

value: optic nerve


title: FF2


title: D-H3K4me3

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Paired sequences were aligned to hg19 using nvBowtie and a NVIDIA Tesla K40c
Bedgraphs were generated using bedtools genomecov
Bedgraphs were normalized to the average number of mapped reads (samtools view -q 1) for all samples within each experiment (A, B, or C)
Bedgraphs were converted to bigwig using kentUtils
Subsequent metagene and heatmap profiles were generated using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs contain depth-adjusted ChIP-Seq pileups
Supplementary_files_format_and_content: E-1kNELFpeaks-Enhancers-NoRefSeqTSSWithin1kb.bed: Regions used to generate enhancer metagene profiles
Supplementary_files_format_and_content: E-EPDnew-Promoters-noTSSwithin1kb.bed: Regions used to generate promoter metagene and heatmap profiles

organism: Homo sapiens

source_name: Suspension HeLa cells

growth_protocol: Adherent HeLa cells were grown at 37°C and 5% CO2 to 80% confluency in T150 flasks in 30 ml DMEM supplemented with 10% FBS; suspension HeLa cells were grown to 5 × 10^5 cells/ml in spinner flasks at 37°C and 5% CO2 in SMEM supplemented with 2 mM L-glutamine and 10% FBS.

extract_protocol:
Cells were crosslinked at RT by adding 16% paraformaldehyde (Electron Microscopy Sciences 130218) to a final concentration of 1% in 37°C media for 10 or 15 min. Crosslinking was quenched with Tris pH 7.6 to a final concentration of 1.33 M. ChIP protocols vary between experiments and are detailed in the STAR Methods
NEXTflex Rapid DNA-Seq Kit (Bioo Scientific 5144-04)

treatment_protocol: Flavopiridol, H2O2, DMSO, and/or PJ34 were added to media as indicated

value: Suspension HeLa cells

tag: antibody

value: H3K4me3 (Abcam ab8580)


title: FF1


title: C-PolII-Flavo-PJ34-0-H2O2

source_name: Adherent HeLa cells

value: Adherent HeLa cells

value: 40 min 1 µM flavopiridol, then 20 min 20 µM PJ34

value: Pol II (N-20) (SCBT sc-899)


title: FF3


title: D-Input


title: D-H3K4me1

value: H3K4me1 (Abcam ab8895)


title: C-PolII-Flavo-PJ34-10min-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 20 µM PJ34, then 10 min 300 µM H2O2


title: C-PolII-Flavo-0-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 0.05% DMSO


title: C-PolII-Flavo-10min-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 0.05% DMSO, then 10 min 300 µM H2O2


title: Input

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Retroviral transduction of WT FoxP3

data_processing:
Short reads (50bp, single end) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4
Reads with multiple alignments were removed with samtools (v1.1) and de-duplicated with picard (v1.130)
To identify peaks from ChIP-seq reads, we used the HOMER package makeTagDirectory followed by the findPeaks command with the ‘histone’ parameter. Peaks displaying 4-fold enrichment and poison P-value of 1x10-4 against background IgG ChIP were considered significant and were used for further analysis.
To visualize individual ChIP-seq data on Integrative Genomics Viewer (IGV), we converted bam output files from picard into normalized bigwig format using the bamCoverage function in deepTools (v1.6) with options – fragmentLength 200 –normalizeUsingRPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Spleen

extract_protocol:
Cells were transduced with retrovirus coding WT or each mutant FoxP3 and sorted for viable Thy1.1hi after 72 hr of transduction.
Chromatin IPed with specific Abs was eluted from the Protein-G beads, treated with 1µg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample.

value: WT

value: CD4+FoxP3- Tconv

tag: antibodies/vendor/catalog#

tag: transduction

value: WT FoxP3


title: EV_rep_1

description: Retroviral transduction of Empty vector

value: anti-V5 (Invitrogen, #R960) and anti-6XHIS (Abcam, #ab9108)

value: Empty vector


title: C-NELF-Flavo-PJ34-0-H2O2


title: C-NELF-Flavo-10min-H2O2


title: M354_rep_2

description: Retroviral transduction of M354


title: M390_rep_1

description: Retroviral transduction of M390


title: M390_rep_2

description: Retroviral transduction of M390


title: C-NELF-Flavo-0-H2O2


title: C-DSIF-Flavo-PJ34-0-H2O2


title: M354_rep_1

description: Retroviral transduction of M354


title: M176_rep_1

description: Retroviral transduction of M176


title: C-DSIF-Flavo-10min-H2O2


title: 10ug/ml DAN/NBL1 protein added, rep 3

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
200-1000 cells harvested per sample
DAN_10ug_ml_3

data_processing:
Fastq files were mapped to the chicken genome galGal4 from UCSC using Tophat (2.0.13) with options -x 1 -g 1.
Ensembl 80 annotations were used to define gene coordinates.
Quality of the samples was assessed using FastQC (0.10.1). The R (3.2.2) environment was used for the statistical analysis of the data.
RPKM values and differentially expressed genes were found using edgeR (3.12.0).
Genome_build: galGal4
Supplementary_files_format_and_content: counts.txt has counts on unioned exons of genes calculated via bedtools coverage (2.24.0) for each gene. rpkms.txt has rpkms generated by edgeR (3.12.0) for each gene.

organism: Gallus gallus

source_name: in vitro migratory neural crest

growth_protocol: Fertilized leghorn chicken (Centurion Poultry, Lexington, GA, USA) were incubated at 38°C in a humidified incubator until the desired stages of development (Hamburger and Hamilton (HH), 1951). Cranial neural tubes (r3-r5) were isolated as previously described (McLennan et al., 2010). Briefly, embryos at HH St 8 were removed from eggs and washed in Ringer’s solution. Then, using a tungsten needle and forceps, transverse cuts were made at the axial levels of the r2/r3 and r5/r6 boundaries. The cranial sections were also cut down the midline before being placed in 1 mg/ml Dispase for 7 minutes on ice. The sections were then manually moved to fresh Ham’s F-12 Nutrient Mix (11765047, Thermo Fisher) and agitated to separate neural tubes from ectoderm and other tissues. After a few washes in Ham’s F-12 Nutrient Mix, the isolated neural tubes are ready for plating onto glass bottomed dishes (P06G-1.5-20-F, MatTek Corporation, Ashland, MA, USA) coated with fibronectin (F1141, Sigma-Aldrich) and Poly-d-lysine (P7886, Sigma-Aldrich) or stripe assays. To coat glass bottom dishes, Ringer’s solution with 20 ug/ml of fibronectin and 20 ug/ml of Poly-d-lysine was added to each dish and allowed to sit for at least 30 minutes at room temperature. The liquid was then removed and dishes were allowed to air dry for 30 minutes before use. When the neural tubes were ready for plating, coated dishes were rinsed with Ringers and neural tubes were immediately plated with as little liquid as possible. Neural tubes were allowed to adhere for 5-10 minutes at 37°C (depending on amount of liquid transferred with them) before being covered with Ham’s F-12 Nutrient Mix.

extract_protocol:
Neural tube cultures were prepared and plated as described above. DAN was added to the media at 0, 1 and 10 ug/ml. After overnight incubation, neural tubes and any ectoderm were removed from in vitro cultures using a tungsten needle and pipette. Media was then removed from neural tube cultures and the adherent neural crest cells were gently rinsed once with 0.1% DEPC PBS. Three biological replicates were harvested for each of the three conditions (untreated, 1 ug/ml and 10 ug/ml).
cDNA was synthesized using SMART-seq v4 Ultra Low Input RNA kit (634888, Clontech) with subsequent library preparation by Nextera XT DNA Sample Prep (FC-131-1096, Illumina) and Index kits (FC-131-1002, Illumina). cDNA samples and libraries were both confirmed on a Bioanalyzer 2100 prior to RNAseq.
Libraries were sequenced as 76 base, high output, paired reads on an Illumina NextSeq. Each sample generated in excess of 20 million fastq counts.

value: 10ug DAN


title: M176_rep_2

description: Retroviral transduction of M176


title: EV_rep_2

description: Retroviral transduction of Empty vector


title: 10ug/ml DAN/NBL1 protein added, rep 2

description:
200-1000 cells harvested per sample
DAN_10ug_ml_2

treatment_protocol: Neural tube cultures were prepared and plated as described above. DAN was added to the media at 0, 1 and 10 ug/ml.


title: WT_rep_2

description: Retroviral transduction of WT FoxP3


title: C-DSIF-Flavo-0-H2O2


title: WT_rep_1

description: Retroviral transduction of WT FoxP3


title: 1ug/ml DAN/NBL1 protein added, rep 3

description:
200-1000 cells harvested per sample
DAN_1ug_ml_3

value: 1ug DAN


title: C-Input-Flavo-PJ34-10min-H2O2


title: Neurons, T. gondii-infected

description: pools from 4 biological replicates

source_name: Embryonic mouse cortices

value: Embryonic mouse cortices

value: Cortical neuron

value: Toxoplasma gondii, strain NTE

value: 24 hours


title: Neurons, non-infected

description: pools from 4 biological replicates

value: not applicable


title: C-Input-Flavo-10min-H2O2

value: Adherent HeLa cells


title: 1ug/ml DAN/NBL1 protein added, rep 2

description:
200-1000 cells harvested per sample
DAN_1ug_ml_2


title: KOCL5

city: Richmond

first: Mario

last: de la Fuente Revenga

address: 1220 E Broad St.

department: Physiology and Biophysics

institute: School of Medicine, Virginia Commonwealth University

data_processing:
The data from the two lanes are merged
aligned with the STAR v2.5.1b software
gene annotation: Gencode M8 (Ensembl 83)
gene expression determined with featureCounts v1.5.0-p145 software
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: tab delimited text file includes the gene counts for all 12 samples.

source_name: Prefrontal cortex

extract_protocol:
RNA was purified from bilateral frontal cortex tissue samples using RNeasy mini kit (Qiagen). Total RNA (5 mg) was used for mRNA library construction
mRNA library construction following instructions of Illumina RNA sample kit.

tag: strain/background

value: HDAC2(loxP,loxP), CamKIIa-Cre(+,-)

tag: Sex

value: Male

value: Clozapine (10mg/Kg)


title: C-NELF-Flavo-PJ34-10min-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 20 µM PJ34, then 10 min 300 µM H2O2


title: 1ug/ml DAN/NBL1 protein added, rep 1

description:
200-1000 cells harvested per sample
DAN_1ug_ml_1


title: C-DSIF-Flavo-PJ34-10min-H2O2


title: KOCL4


title: C-Input-Flavo-0-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 0.05% DMSO


title: 0ug/ml DAN/NBL1 protein added, rep 3

description:
200-1000 cells harvested per sample
DAN_0ug_ml_3

value: Untreated


title: B-PolII-Flavo-35min-H2O2

value: 1 h 1 µM flavopiridol, then 35 min 300 µM H2O2

value: Pol II (N-20) (SCBT sc-899)


title: B-PolII-Flavo-0-H2O2

value: 1 h 1 µM flavopiridol


title: B-NELF-Flavo-35min-H2O2


title: KOS4

value: Vehicle


title: B-NELF-Flavo-0-H2O2


title: KOS2


title: B-Input-Flavo-35min-H2O2


title: 10ug/ml DAN/NBL1 protein added, rep 1

description:
200-1000 cells harvested per sample
DAN_10ug_ml_1

value: 10ug DAN


title: WTCL3

value: Wild-type


title: C-Input-Flavo-PJ34-0-H2O2

value: 40 min 1 µM flavopiridol, then 20 min 20 µM PJ34


title: WTCL5


title: A-PolII-Flavo-100min-H2O2

value: 1 h 1 µM flavopiridol, then 100 min 300 µM H2O2


title: A-PolII-Flavo-30min-H2O2

value: 1 h 1 µM flavopiridol, then 30 min 300 µM H2O2


title: B-Input-Flavo-0-H2O2


title: WTCL2


title: WTS4


title: Tassel-RRBS-CviQI

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
[BS-seq] reads were aligned to the AGPv3 genome using BS Seeker2
[BS-seq] If multiple alignments mapped to the same location only one is kept.
[RNA-seq] alignment using Tophat 2.0.4, AGPv3 as library junction
[RNA-seq] Abundance counting using cuffdiff
[RNA-seq] Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff
[RNA-seq] Calculate p-values with edgeR
Genome_build: AGPv3
Supplementary_files_format_and_content: [.CGmap] BS-seq processed data file is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
Supplementary_files_format_and_content: [.txt] RNA-seq processed data file includes RPKM values for each sample

organism: Zea mays

source_name: B73 Tassel primordium

growth_protocol: For shoot sample, seeds were grown in the incubator in the dark on wet paper towels. After 4-5 days, coleoptile-stage shoots were excised and stored at -80°C. For tassel, plants were grown in the field until the V6 stage. Tassel primordia (~0.5 cm) were excised and stored at -80.

extract_protocol:
Tissue samples were ground with mortar and pestle in liquid Nitrogen, and nuclei were washed and separated from organelles by centrifuging through 30% OptiPrep (Axis-Shield PoC, Oslo, Norway, cat #1114542). Nuclei were lysed with 2% SDS and genomic DNA was isolated from organic phase using phenol/chloroform/isoamyl alcohol. After RNase digestion, genomic DNA was precipitated with sodium acetate and ethanol.
genomic DNA was digested with CviQI and size-selected. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the Qiagen EpiTect Fast bisulfite conversion kit was utilized for bisulfite treatment. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna Hiseq 2000 sequencer).

value: 0.5-cm tassel primordium

tag: inbred line

tag: enzyme

value: CviQI


title: WTS3


title: A-PolII-Flavo-10min-H2O2

value: Adherent HeLa cells

value: 1 h 1 µM flavopiridol, then 10 min 300 µM H2O2


title: A-PolII-Flavo-3min-H2O2

value: 1 h 1 µM flavopiridol, then 3 min 300 µM H2O2


title: WTS1

value: Male


title: A-PolII-Flavo-0-H2O2


title: KOS5

value: HDAC2(loxP,loxP), CamKIIa-Cre(+,-)


title: 0ug/ml DAN/NBL1 protein added, rep 2

description:
200-1000 cells harvested per sample
DAN_0ug_ml_2

value: Untreated


title: KOCL3

value: Clozapine (10mg/Kg)


title: Shoot-RRBS-CviQI

source_name: B73 shoots

value: Coleoptile-stage shoots


title: A-PolII-Control-100min-H2O2

value: Pol II (N-20) (SCBT sc-899)


title: untransfected_1

city: London

first: Emily

last: Saunderson

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

description: RNA-seq_primary_myoepithelial_cells_3A3L_delta_untransfected_raw_reads.txt

data_processing:
Sequencing reads were mapped to GRCh37.EBVB95-8wt.ERCC using bwa
Data were processed using SeqMonk and the RNA-seq quality controls and analysis pipeline to generate Reads Per Kilobase of exon per Megabase of library size (RPKM). All isoforms were kept separate nad the number of reads falling in the exons of this transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: GRCh37.EBVB95-8wt.ERCC
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: Primary breast myoepithelial cell

extract_protocol:
RNA was extracted as above, before mRNA was isolated from 1.5 µg of total RNA using mRNA DIRECT (Thermo Fisher Scientific) and fragmented with RNA fragmentation reagent (Thermo Fisher Scientific). First strand cDNA synthesis was performed with SuperScript III First-Strand Synthesis System and 3 μg/μl random hexamers (Thermo Fisher Scientific) followed by second strand synthesis with DNA polymerase I and RNase H.
After purification, the double stranded cDNA was ligated to in house designed adapters (based on TruSeq Indexed adapters (Illumina)) using NEBNext Ultra II (NEB) followed by 15 cycles of amplification and library purification.

value: Breast

value: Myoepithelial

tag: transfection

value: untransfected


title: A-PolII-Control-30min-H2O2

value: 30 min 300 µM H2O2


title: 232614.Thpok_LRF_plus

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

data_processing:
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (v. 2.4.0h) on 2-pass mode with mouse gencode (release 4) gtf
Genes were subsequently counted using Rsubread and further analyzed for gene expression changes using limma-voom with quantile normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Genes were subsequently counted using Rsubread and further analyzed for gene expression changes using limma-voom with quantile normalization.

source_name: T regulatory cells

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)

tag: strain background

tag: genotype/variation

value: LRFffThpokff Foxp3 Cre-YFP/X

value: Spleen and Lymph node

tag: phenotype


title: Tassel-RRBS-MseI

extract_protocol:
Tissue samples were ground with mortar and pestle in liquid Nitrogen, and nuclei were washed and separated from organelles by centrifuging through 30% OptiPrep (Axis-Shield PoC, Oslo, Norway, cat #1114542). Nuclei were lysed with 2% SDS and genomic DNA was isolated from organic phase using phenol/chloroform/isoamyl alcohol. After RNase digestion, genomic DNA was precipitated with sodium acetate and ethanol.
genomic DNA was digested with MseI and size-selected. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the Qiagen EpiTect Fast bisulfite conversion kit was utilized for bisulfite treatment. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna Hiseq 2000 sequencer).

tag: tissue

value: 0.5-cm tassel primordium

value: MseI


title: A-PolII-Control-10min-H2O2

value: Adherent HeLa cells

tag: treatment

value: 10 min 300 µM H2O2


title: 432614.Thpok_LRF_plus


title: Shoot-RRBS-MseI


title: 142114.Thpok_LRF_plus


title: 232614.Thpok_LRF_min

value: YFP+MHCII-


title: 432614.Thpok_LRF_min


title: Wnt9a2

city: West Lafayette

first: Donna

middle: M

last: Fekete

state: IN

address: 915 West State St

department: Biological Sciences

institute: Purdue University

data_processing:
Tophat2 was used to align reads to the Galgal4 Ensembl Gallus Gallus genome database version 83.4.
DeSeq, and EdgeR were used to calculate the number of reads per transcript. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes (false discovery rate of 5%)
Genome_build: Galgal4 Ensembl Gallus Gallus genome database version 83.4
Supplementary_files_format_and_content: FeketeGeneCounts_forRanalysis.txt
Supplementary_files_format_and_content: abundance measurements
Supplementary_files_format_and_content: Fekete_DESeq2_DEresults_annot.txt
Supplementary_files_format_and_content: DESeq analysis
Supplementary_files_format_and_content: Fekete_edgeR_DEresults_annot.txt
Supplementary_files_format_and_content: edge R analysis
Supplementary_files_format_and_content: fpkmValues.txt
Supplementary_files_format_and_content: Fragments per kb per million reads

source_name: basilar papilla

growth_protocol: Embryos were incubated at approximately 37 °C for 6 days.

extract_protocol:
Basilar papillas were removed in HBSS and placed in QIAzol lysis reagent. Total RNA was extracted using the QIAGEN miRNeasy kit with an on-column DNase digest. The quality and quantity of the RNA was checked using an Agilent Bioanalyzer.
An Illumina TruSeq Stranded kit was used to construct a cDNA library

treatment_protocol: On embryonic day 3, right otocysts were infected with RCAS(A) parent retrovirus (control group) or RCAS(A)-Wnt9a virus (experimental group).

value: RCAS(A)-Wnt9a virus

tag: age

value: Embryonic day 6

value: basliar papilla


title: A-PolII-Control-3min-H2O2

value: 3 min 300 µM H2O2


title: A-PolII-Control-0-H2O2


title: Wnt9a1


title: RCASA4

value: RCAS(A) parent virus (control)


title: 142114.Thpok_LRF_min


title: A-Input-Control-0-H2O2


title: 8800.Ctrl

value: WT Foxp3 Cre-YFP/X


title: RCASA3


title: Late-maturation stage whole seed

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected. The entire embryo is yellow including the axis and cotyledons.

data_processing:
Original unprocessed and unfiltered data file from the Illumina sequencing pipeline. Each lane of sequencing is attached as an individual compressed file. The sequence data are in the QSEQ format
Raw sequence reads were initially filtered using the Illumina purity filter parameter. Then, the remaining reads were mapped to a reference containing soybean ribosomal RNA (rRNA) sequences using Bowtie [Langmead et al., Genome Research, (2009)]. The final filtered reads have passed the Illumina purity filter and are devoid of rRNA sequences. These sequences were used to map against the soybean reference genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net). Only uniquely mapped reads (i.e. reads that map to one position within the genome) were used for subsequent analysis.
Read counts to Glycine max gene models (v1.1) models were computed using BedTools. Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008)
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including normalized RPKM count of each sampled gene

organism: Glycine max

source_name: Soybean seeds containing late-maturation-stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., 2010). Whole seeds containing globular stage, heart stage, cotyledon stage, early-, mid-, and late-maturation stage embryos were collected.  Dry seeds weighed approximately 200 mg. Seedlings were isolated from seeds imbibed for six days. Vegetative tissues (trifoliate leaves, roots, stems) were isolated from a mature plant 3-4 months old. Floral buds consists of unopened buds with no signs of dehisced anthers.

extract_protocol:
Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to the manufacturerâs instructions. Isolated total RNA was treated with RNase-free DNase I (Ambion, Austin, TX) and was subjected to two rounds of poly-A+ RNA selection using oligo-d(T)25 magnetic beads (Dynabeads, Invitrogen, Carlsbad, CA).
Sequencing libraries were prepared using 100 nanograms of twice-selected polyA+ RNA following the Illumina mRNA-Seq Protocol (Part #1004898 Rev. D). Briefly, polyA+ RNA was fragmented and used as template for random-primed cDNA synthesis. Double-stranded cDNAs were treated with T4 and Klenow DNA Polymerases and T4 PNK to generate blunt-end cDNAs. An 'A' base was added to the 3â ends of the phosphorylated blunt-end cDNAs, followed by the ligation of Illumina adapters. Adapter-ligated cDNAs were size selected on an agarose gel for the desired size of ~ 200 bp. Purified cDNAs were amplified by PCR for 15 cycles. Quantification of cDNA libraries was carried out using a Nanodrop ND-3300 Fluoro-spectrophotometer (Thermo Scientific, Waltham, MA). Amplified cDNA size was determined by agarose gel electrophoresis. Single-end 76-bp reads were generated for each library by the UCLA Genome Sequencing Center (http://gsc.ucla.edu/) using an Illumina Genome Analyzer IIx and HiSeq 2000.

tag: cultivar

value: Williams 82

value: whole seeds

tag: developmental stage

value: late-maturation-stage embryos


title: Mid-maturation stage whole seed

description: Whole seeds with 1.1 - 1.3 cm in length and fresh weight between 150 - 250 mg were collected. Tip of the embryonic axis is yellow while the rest of the embryonic axis is green.

source_name: Soybean seeds containing mid-maturation-stage embryos

value: mid-maturation-stage embryos


title: 8619.Ctrl


title: RCASA2


title: OK Illumina RNASeq

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Sequence reads were trimmed using Cutadapt v 1.8.3 (adapter and qual 30)
60 million RNASeq reads were randomly selected
Selected reads were assembled with de novo Trinity v 2.1.1 at minimum kmer coverage 3
Assembled contigs were aligned with protein sequences in Swiss-Prot db, using BLASTx v2.2.31, for annotation. Alignments were filtered for hits to proteins from mammals, e-value < 1e-4,  70% Identity and 40% covered bases of database protein
Expression values of filtered genes and transcripts were calculated using RSEM v 1.2.21
Selected 60 million reads were aligned to reference using Tophat v 2.1.0
Mapped reads were assembled using Cufflinks and Cuffmerge v 2.2.1
Sequences of Cuffmerge were assembled transcripts extracted using gffread tool of Cufflinks software suite
Expression values of assembled genes and transcripts were calculated using RSEM v 1.2.21
Expression values of de novo assembled genes and cuffmerge assembled genes were consolidated into a single tab delimited text file
Genome_build: monDom5
Supplementary_files_format_and_content: fasta files contain fasta sequences assembled transcripts; bedgraph file contains coverage from tophat alignment of randomly selected 60 million reads to ncbi monDom5; gtf file contains annotation information of all cuffmerge assembled transcripts; tab-delimited text file contains TPM values of genes from both de novo assembly approach and alignment approach such that "-" represent no transcript for the gene was assembled in that approach, list of assembled transcript ids of genes from de novo assembly and alignment, average length of assembled transcripts from de novo assembly and alignment, %Identity from BLASTx output, %covered bases of database protein sequence from BLASTx output, and species name of database protein from BLASTx output

organism: Didelphis virginiana

source_name: OK (ATCC CRL-1840)

growth_protocol: Cells were cultured in DMEM/F12 medium with 10% FBS (Atlanta Biologicals) and 5 mM GlutaMAX (Gibco). 4x105 cells were plated on 12-mm Transwells with 0.4 µm pore polycarbonate membrane inserts (Corning) in a 12-well plate, with 0.5 mL apical medium and 1.0 mL basolateral medium.

extract_protocol:
Cells were collected using Accutase (Sigma) and RNA was extracted using the ambion PureLink RNA mini kit (ThermoFisher) according to the manufacturer’s protocol. Ribosomal RNA sequences were removed before library construction.
Library preparation was performed using the TruSEQ Stranded Total RNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions. RNA was fragmented for 8 minutes and reverse transcription performed. Double stranded cDNA was subjected to 3’ adenylation and ligation of sequencing adapters. Sequencing was carried out on a NextSeq 500 (Illumina) for 2 x 75 bp paired end reads. Loading concentration was 1.6 pM.

tag: cell line

value: OK

tag: cell type

value: Proximal tubule epithelial

tag: passages

value: Kidney Proximal Tubule


title: cKO-1

status: Public on Aug 06 2017

city: HangZhou

first: JUN

last: DAI

state: ZheJiang

address: #866 Yu Hang Tang Rd

department: School of Medicine

country: China

institute: Zhe Jiang University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to Human GRCh37  genome using Mapsplice v2.1.6 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: knee joint cartilage

growth_protocol: Cells were cultured in F12 medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).The RNA with RIN >8.0 is right for rRNA depletion. rRNA was depleted by GeneRead rRNA Depletion Kit(QIAGEN)
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Cells were treated with 4-hydroxytamoxifen (4OH-TM) (1 μM) for 48 hours.

tag: strain

value: chondrocyte

tag: genotype


title: Control


title: cKO-2


title: 124.Ctrl

value: Spleen and Lymph node


title: Wnt9a3


title: Runx123_GFP.P1.D09

status: Public on Aug 04 2017

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

description:
single cell
source_type: tissue

data_processing:
Demultiplexed reads were aligned using STAR(Dobin et al., 2013) to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCounts(Liao Y, Smyth GK and Shi W 2014).
Genome_build: GRCz10
Supplementary_files_format_and_content: text file with raw counts

organism: Danio rerio

source_name: whole kidney marrow

extract_protocol:
Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence-activated cell sorting into 96-well plates containing 5 ul TCL buffer (QIAGEN) + 1% BME (Bio-Rad). Plates were snap frozen and stored in -80°C before reverse transcription and library construction.
Whole-transcriptome amplification and library construction were performed on single cells using a modified Smart-seq2 protocol adapted by Venteicher et al. (PMID 28360267). Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit (75 cycles) (Illumina) on a NextSeq 500 platform (Illumina).

value: kidney marrow


title: Runx123_GFP.P1.D05

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D07

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D12

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D04

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D11

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D02

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D01

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C11

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C12

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D03

description:
single cell
source_type: tissue


title: Central pedicel

status: Public on Aug 05 2017

city: Seoul

first: Seong

last: Heo

address: Sinlim-dong 151-921

department: Department of Plant Science

country: South Korea

institute: Seoul National University

description: Sample 1

data_processing:
The raw reads were trimmed using the Mothur software (version 1.33.3) to remove the primers and adaptors used for library preparation.
The trimmed reads were assembled using Newbler (version 2.3, Roche) with default parameters.
Mapping was performed on the CLC Genomics Workbench (version 6.5, CLCbio) following the manufacturer’s instructions.
To identify DEGs, the expression profile obtained from CLC Genomics Workbench was imported into a Bioconductor package, the NOISeq software.
Genome_build: MalDomGD1.0
Supplementary_files_format_and_content: Mdeg.txt represents DEG list of NOISeq software.  DEGs.xls represents annotated DEGs.  C vs. L.xlsx represents expression analysis.

organism: Malus domestica

source_name: pedicel tissue

extract_protocol:
mRNA was isolated from 50 μg of total RNA using a FastTrack MAG Micro mRNA Isolation Kit (Life Technologies, http://www.lifetechnologies.com/) following the manufacturer’s protocol.
Following the quantification of the isolated mRNA using Agilent RNA 6000 Nano LabChip, 200 ng of mRNA were used to generate cDNA libraries with cDNA Rapid Library Preparation Kit (Life Technologies). The cDNA libraries were used for emulsion PCR as described by the manufacturer. Following assessment of cDNA quality using an Agilent 2100 BioAnalyzer, pyrosequencing was performed on a Roche 454 GS-FLX sequencer.

value: Saika

value: Central pedicel


title: Runx123_GFP.P1.C10

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C07

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C06

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C09

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C05

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C04

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C03

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C02

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.C01

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B12

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B10

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B05

description:
single cell
source_type: tissue


title: Lateral pedicel

description: Sample 2

value: Lateral pedicel


title: Runx123_GFP.P1.B03

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B02

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B08

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B04

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.D10

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A06

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A11

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A07

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A09

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A08

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A05

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A04

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A03

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D10

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A02

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D09

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D12

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D08

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.A01

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D06

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D07

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D05

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D03

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D02

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C12

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D01

description:
single cell
source_type: tissue


title: Runx123_GFP.P1.B01

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C11

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C10

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C09

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C07

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C06

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C08

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C04

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C05

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D11

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C03

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C02

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B12

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B11

description:
single cell
source_type: tissue


title: rag2_GFP.P2.C01

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B06

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B07

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B08

description:
single cell
source_type: tissue


title: rag2_GFP.P2.D04

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B04

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B05

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B03

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B02

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B01

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A11

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A10

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A09

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A08

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A06

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A07

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A05

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A04

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A03

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A02

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A01

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H09

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H11

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B10

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H08

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H10

description:
single cell
source_type: tissue


title: rag2_GFP.P2.B09

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H07

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H06

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G11

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H01

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H04

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G12

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H03

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G10

description:
single cell
source_type: tissue


title: rag2_GFP.P2.A12

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G06

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G04

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G07

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G03

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G02

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.H12

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F10

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F11

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G01

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F12

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F07

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F06

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F02

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G09

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F03

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E09

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E11

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E10

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E07

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E08

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.G08

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E06

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E03

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E04

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E01

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.H11

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F09

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E02

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.H08

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.H05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F04

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F08

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F05

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.H02

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.G05

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.F01

description:
single cell
source_type: tissue


title: mpx_EGFP.P4.E12

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F03

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F04

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.G12

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F12

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F01

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.E11

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.F02

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.E10

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.D10

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.E07

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.D05

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.D04

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.C01

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.C03

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.B12

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.B04

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.B03

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.B09

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.A08

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.A09

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.A06

description:
single cell
source_type: tissue


title: lck_GFP.P2.H12

description:
single cell
source_type: tissue


title: lck_GFP.P2.H07

description:
single cell
source_type: tissue


title: lck_GFP.P2.H05

description:
single cell
source_type: tissue


title: lck_GFP.P2.H06

description:
single cell
source_type: tissue


title: lck_GFP.P2.H03

description:
single cell
source_type: tissue


title: lck_GFP.P2.H08

description:
single cell
source_type: tissue


title: lck_GFP.P2.H01

description:
single cell
source_type: tissue


title: lck_GFP.P2.H02

description:
single cell
source_type: tissue


title: lck_GFP.P2.G12

description:
single cell
source_type: tissue


title: lck_GFP.P2.H04

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.E05

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.C08

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.D02

description:
single cell
source_type: tissue


title: lck_GFP.P2.G11

description:
single cell
source_type: tissue


title: lck_GFP.P2.G05

description:
single cell
source_type: tissue


title: lck_GFP.P2.G07

description:
single cell
source_type: tissue


title: lck_GFP.P2.G08

description:
single cell
source_type: tissue


title: lck_GFP_rag1.P5.B11

description:
single cell
source_type: tissue


title: lck_GFP.P2.G04

description:
single cell
source_type: tissue


title: lck_GFP.P2.G03

description:
single cell
source_type: tissue


title: lck_GFP.P2.G02

description:
single cell
source_type: tissue


title: lck_GFP.P2.F10

description:
single cell
source_type: tissue


title: lck_GFP.P2.F09

description:
single cell
source_type: tissue


title: lck_GFP.P2.G01

description:
single cell
source_type: tissue


title: lck_GFP.P2.F08

description:
single cell
source_type: tissue


title: lck_GFP.P2.F07

description:
single cell
source_type: tissue


title: lck_GFP.P2.F05

description:
single cell
source_type: tissue


title: lck_GFP.P2.F06

description:
single cell
source_type: tissue


title: lck_GFP.P2.F04

description:
single cell
source_type: tissue


title: lck_GFP.P2.F02

description:
single cell
source_type: tissue


title: lck_GFP.P2.F01

description:
single cell
source_type: tissue


title: lck_GFP.P2.E09

description:
single cell
source_type: tissue


title: lck_GFP.P2.E08

description:
single cell
source_type: tissue


title: lck_GFP.P2.G09

description:
single cell
source_type: tissue


title: lck_GFP.P2.F03

description:
single cell
source_type: tissue


title: lck_GFP.P2.E03

description:
single cell
source_type: tissue


title: lck_GFP.P2.E10

description:
single cell
source_type: tissue


title: lck_GFP.P2.E07

description:
single cell
source_type: tissue


title: lck_GFP.P2.G06

description:
single cell
source_type: tissue


title: lck_GFP.P2.E04

description:
single cell
source_type: tissue


title: lck_GFP.P2.E02

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D06

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D05

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D09

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D07

description:
single cell
source_type: tissue


title: lck_GFP.P2.E01

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D10

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D04

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D08

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D03

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D01

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C12

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.D02

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C09

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C10

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C07

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C06

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C11

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C04

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C08

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C01

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B08

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B11

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C03

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C05

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B05

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B07

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.C02

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B12

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B04

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A08

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A09

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A10

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B03

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B01

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.B02

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A07

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A11

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A03

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A01

description:
single cell
source_type: tissue


title: inDrop sequencing of multiple samples_2

description:
inDrop sequencing (technical replicate 2) of 6 animals including WT (animal #3), prkdc(D3612fs) (animal #3), il2rga(Y91fs) (animal #1 and #2), and prkdc(D3612fs) il2rga(Y91fs) double mutants (animal #1 and #2).
source_type: tissue

data_processing:
Reads were processed using the indrops pipeline(https://github.com/indrops/indrops). Briefly, reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie.
Please see file "inDrop_GEO_supplementary.xlsx " available on the series record for information on de-multiplexing and barcodes for individual samples and cells.
Genome_build: GRCz10
Supplementary_files_format_and_content: text file with read counts.

source_name: Whole kidney marrow

extract_protocol:
RNA from individual cells were reverse-transcribed, barcoded, and unique transcripts are imprinted with UMI, all within the droplet. RNA from 1,500 cells of each animal were pooled and subsequently processed together. cDNA products were pre-amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit (75 cycles) (Illumina) on a NextSeq 500 platform (Illumina).
Zebrafish cells are isolated from the kidney marrow into single-cell suspensions, and treated with 15% Optiprep (Sigma). Single cells are microfluidically sorted into droplets containing reverse-transcription and barcoding reagents.  This method is outlined in Klein et al. (PMID 26000487) and Zilionis et al. (PMID 27929523).

tag: indrop version

value: inDrop V3 protocol

value: multiple genotypes


title: cd41_GFPlow.P3.B09

description:
single cell
source_type: tissue


title: cd41_GFPlow.P3.A04

description:
single cell
source_type: tissue


title: inDrop sequencing of multiple samples_1

description:
inDrop sequencing (technical replicate 1) of 6 animals including WT (animal #3), prkdc(D3612fs) (animal #3), il2rga(Y91fs) (animal #1 and #2), and prkdc(D3612fs) il2rga(Y91fs) double mutants (animal #1 and #2).
source_type: tissue


title: cd41_GFPlow.P3.A02

description:
single cell
source_type: tissue


title: inDrop sequencing of prkdc(D3612fs) homozygous mutant zebrafish sample (animal #2)

description: source_type: tissue

value: inDrop V2 protocol


title: Normal 3

city: Wuhan

first: Yawei

last: Li

state: Hubei

address: Jiefang road

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: circRNA_expression.xls header = zhaohanqiaoN

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk and Perl version 5.8.8
Sequenced reads were aligned to the hg38 genome assembly using BWA version 0.7.10 with parameters: -t 8 -k 19
CircRNA predicted and junction reads measurements were analysed using CIRI version 1.2 with parameters: -P --high-strigency
Differential expression were analysed  using edgeR function package in R program version 3.10.0
Genome_build: ensembl hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized SRPBM values and raw fragment counts for each Sample

source_name: normal bladder tissue

extract_protocol:
The total RNA samples of three pairs of bladder cancer and normal bladder tissues were treated with the RiboZero rRNA Removal Kit and  RNase R for deleting rRNA and linear RNA, according to the manufacturer’s instructions.
The rRNA depleted and RNase R digested RNA samples were fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced by HiSeq2000 (Illumina).

tag: age(years)

tag: gender

value: male


title: Normal 2

description: circRNA_expression.xls header = zhangyuanpingN


title: Cancer 3

description: circRNA_expression.xls header = zhaohanqiaoT

source_name: bladder cancer tissue

tag: tumor stage


title: inDrop sequencing of WT sample (animal #1)

description: source_type: tissue

value: wildtype


title: inDrop sequencing of WT sample (animal #2)

description: source_type: tissue


title: E11.5 Mouse NT Input2

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
All samples were ran on a Illumina Hi-Seq 2500 and basecalls were performed using CASAVA
Sequence reads for each sample were mapped to the mm10 genome assemblies as relevant with Bowtie (v2.2.6)
Duplicate reads were removed, and the remaining unique reads were normalized to 10 million reads
Peak calling was performed by HOMER (v4.7) using an FDR cutoff of 0.001, a cumulative Poisson p-value of <0.0001, and required a 4-fold enrichment of normalized sequenced reads in the treatment sample over the control/input sample
Genome_build: mm10

source_name: Neural tube

growth_protocol: No growth performed

extract_protocol:
For full ChIP protocol see Meredith 2013 MCB 33:3166-3179. For extraction, nuclei were liberated from neural tube tissue by dounce homogenization in PBS and then fixed in 1% formaldehyde for 10 minutes at room temperature. Fixation was terminated by adding glycine to a final concentration of 0.125M. Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30s:30s on:off cycles. 100 μg chromatin was immunoprecipitated with 5 μg rabbit anti-PRDM13 antibody (Johnson Lab generated,  PA6659, rabbit anti-mouse PRDM13) followed by anti-mouse Dyna beads (Invitrogen).
Libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol

treatment_protocol: No treatment performed

tag: antibody

value: none (input)


title: E11.5 Mouse NT PRDM13 GFP ChIP

description: NT_PRDM13 GFP_ChIP

value: Life Technologies (A6455, rabbit anti-GFP)


title: E11.5 Mouse Tel PRDM13-Ab2 (FL) ChIP

description: Tel-PRDM13 Ab2(FL)-ChIP

source_name: Telencephalon

value: ICR

value: Johnson lab generated rabbit polyclonal antibodies (PRDM13-Ab2 (FL) TX970, rabbit anti-mouse PRDM13)


title: inDrop sequencing of prkdc(D3612fs) homozygous mutant zebrafish sample (animal #1)

description: source_type: tissue


title: cd41_GFPlow.P3.A12

description:
single cell
source_type: tissue


title: Cancer 2

description: circRNA_expression.xls header = zhangyuanpingT


title: Cancer 1

description: circRNA_expression.xls header = gaozhengyanT

value: female


title: ILB_9578_Illumina

city: Philadelphia

first: Nicholas

last: Lahens

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
[processed data files:]
Illumina.GSNAP.gene_quant.txt
Illumina.STAR.gene_quant.txt
Illumina.STAR_PLUS_BOWTIE2.gene_quant.txt

data_processing:
We aligned fastq files from both platforms using STAR v2.5.1b, GSNAP release 2015-12-31 (v8), or a combination of STAR and Bowtie2 v2.2.9. For the STAR + Bowtie2 combination, we first aligned reads to the genome using STAR and extracted all unmapped reads from the resulting BAM files. Next, we used Bowtie2 to align all of these unmapped reads to the reference genome. Lastly, we used custom perl scripts to merge the Bowtie2 alignments with the STAR alignment, replacing entries for the unaligned reads with the mapping information from Bowtie2.
To normalize the data within a given platform/aligner combination, we used the Pipeline Of RNA-Seq Transformations (PORT - v0.8.1-beta). Briefly, PORT filters out potential confounding factors like reads mapping to rRNA sequences and mitochondrial DNA. Next, PORT determines the input dataset with the fewest number of gene-mapping reads and re-samples all datasets to have the same number of reads, thus accounting for batch effects and differences in sequencing depth between samples.
In addition to normalization, we also used PORT to quantify the normalized, gene-level read counts for each of our datasets. For quantification, we used the gene models from the Ensembl v67 annotation.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

source_name: Liver

growth_protocol: Twelve-week old male C57/B6J mice were acquiered from Jackson Labs.

extract_protocol:
Mice were sacrificed and liver samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the liver tissue using TRIzol and Qiagen Rneasy Mini Kit, according to manufacturers’ protocols.
Ion Torrent: Total RNA was poly-A selected using Ambion’s (ThermoFisher) Dynabeads mRNA Direct Micro Purification kit. About 100 ng poly-A RNA was used to prepare strand-specific barcoded RNA library with the Ion Total RNA-Seq kit v2.0 following manufacturer’s protocol. The library quality was checked by running on the BioAnalyzer and the concentration was determined from the analysis profile. Ten barcoded libraries were pooled together on an equimolar basis and run using three PIv3 chips on an Ion Torrent Proton using HiQ chemistry.

Illumina: 200 ng total RNA from each liver sample was prepared for Illumina sequencing according to the manufacturer’s protocol using the TruSeq Stranded mRNA Sample Preparation Kit.  Following preparation, library quality was assessed using a Bioanalyzer. Libraries from all samples were pooled together and sequenced using an Illumina HiSeq 2500 (125 bp paired-end reads).

treatment_protocol: Four hours prior to tissue collection, mice were treated with either 20 µg/Kg of IL-1B or saline.

value: 12 weeks

value: Liver

tag: Sex

value: IL-1 Beta


title: ILB_9577_Illumina


title: UNT_9580_Illumina

value: saline


title: cd41_GFPlow.P3.A06

description:
single cell
source_type: tissue

value: kidney marrow


title: UNT_9576_Illumina


title: UNT_9575_Illumina


title: ILB_9579_Illumina


title: ILB_9582_Illumina


title: UNT_9574_Illumina


title: Normal 1

description: circRNA_expression.xls header = gaozhengyanN


title: E11.5 Mouse NT Prdm13 Het replicate 1

data_processing:
Mouse samples were run on a Illumina Hi-Seq 2500 and basecalls were performed using CASAVA
Mouse sequence reads were aligned to the mm10 genome assembly using TopHat v2.1.0 (Trapnell et al. 2009). All Default settings were used except: -G option and --no-novel-juncs.
RPKM values were estimated using EdgeR (v. 3.6.8)
Genome_build: mm10

extract_protocol:
Total RNA was extracted and purified with the Zymo Mini RNA Isolation Kit. 1µg of total RNA was used for mRNA (polyA) isolation.
The  sequencing library preparation used the Illumina Tru-Seq sample prep kit.

treatment_protocol: GFP+ cells were isolated by FACS from dissociated cells from embryonic mouse neural tubes

tag: developmetal stage

value: Prdm13 Heterozygous mutant


title: E11.5 Mouse NT Prdm13 Homo replicate 1

value: Prdm13 Homozygous mutant


title: E11.5 Mouse NT Prdm13 Homo replicate 2


title: E11.5 Mouse NT Prdm13 Het replicate 2


title: E11.5 Mouse NT PRDM13-Ab1 (ZF) ChIP

description: NT_PRDM13 Ab1(ZF)_ChIP

value: Johnson lab generated rabbit polyclonal antibodies (PRDM13-Ab1 (ZF) PA6659, rabbit anti-mouse PRDM13)


title: E11.5 Mouse NT PRDM13-Ab2 (FL) ChIP

description: NT_PRDM13 Ab2(FL)_ChIP


title: UNT_9584_Illumina

tag: tissue


title: ILB_9583_Illumina

tag: treatment


title: mrna-BAT2

city: Durham

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

institute: Duke University

description: Each replicate is pooled from 3 mice

data_processing:
Adapter trimming with Cutadapt 1.8.3
Build transcriptome with Tophat 2.0.9
Select most abundant transcript with python script
To most abundant transcript dataset, allowing no mismatches and one map per read, using bowtie 1.0.0
Calculate RPKM within coding sequence
Genome_build: Refseq 70
Supplementary_files_format_and_content: Spreadsheet indicating RPKM for translation and RNA-seq

source_name: 6 week old

growth_protocol: adipose tissue depots were digested in 0.2% collagenase at 37°C for 25–30 min. Digested tissues were filtered through a 100-mm membrane, and SVF cells were collected by centrifugation at 1,500 rpm for 5 min. After centrifugation, the mature adipocytes floating on top were collected for genotyping analysis. The freshly iso- lated SVF cells were seeded and cultured in DMEM con- taining 10% newborn calf serum and 0.5% penicillin/ streptomycin at 37°C with 5% CO2. On confluence, the cells were induced to differentiate for 2 days with DMEM containing 10% FBS, 850 nmol/L insulin, 0.5 mmol/L dexamethasone (Sigma-Aldrich), 250 mmol/L of 3-isobutyl- methylxanthine (Sigma-Aldrich) and 1 mmol/L rosiglita- zone (Sigma-Aldrich) in DMEM. The induction medium was replaced with DMEM containing 10% FBS and 160 nmol/L insulin for 2 days. Then cells were incubated in DMEM with 10% FBS

extract_protocol:
Total RNA from primary cells or mouse tissues were extracted with miRNeasy Mini Kit (Qiagen).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: interscapular brown fat


title: mrna-iSUB2D5-1

source_name: primary stromal vascular fraction cell culture

value: subcutaneous white fat


title: mrna-EP12

description: Each replicate is pooled from 3 mice

value: epididymal white fat


title: mrna-SUB2D0-1


title: mrna-iSUB2D5-2


title: mrna-BAT1D0-1


title: mrna-BAT1


title: mrna-BAT1D5-2


title: mrna-BAT1D5-1


title: mrna-BAT1D0-2


title: SUB2-D5b


title: mrna-SUB2D0-2

description: Each replicate is pooled from 3 mice


title: SUB2-D0a

description: Each replicate is pooled from 3 mice


title: SUB2-D0b


title: BAT1-D5b


title: SUB2-D5a


title: EPI-WT2

description: Each replicate is pooled from 3 mice


title: EPI-WT1

description: Each replicate is pooled from 3 mice


title: BAT1-D5a


title: BAT1-D0b


title: E11.5 Mouse NT Input1


title: mrna-EPI1


title: BAT1-D0a


title: BAT-WT2

description: Each replicate is pooled from 3 mice


title: BAT-WT1

description: Each replicate is pooled from 3 mice


title: RNAseq_timecourse_miNs_day20_B

city: Saint Louis

first: Matthew

middle: James

last: McCoy

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

description: Induced with miR-9/9*-124 for 20 days.

data_processing:
Data processing was performed by Cofactor Genomics (http://cofactorgenomics.com , Saint Louis, Missouri, USA).
Base-calling was performed with bcl2fastq.
Raw sequence data in FASTQ format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content (sortmeRNA, http://bioinfo.lifl.fr/RNA/sortmerna/).
NovoAlign (Novocraft, http://novocraft.com) was used to align reads to a set of transcript sequences. NovoAlign parameters were set to allow multiple alignments to the transcriptome set to allow for isoforms. Alignments to the genome were performed using STAR (https://github.com/alexdobin/STAR). Only unique alignments to the genome were allowed.
The genome alignment loci from all samples were combined and clustered to generate genomic loci (“patches”) with contiguous read coverage. Patches overlapping reference genome annotation loci were labelled as such. For each transcript or patch, the RPKM expression value was calculated for each sample. For each replicate group, the mean and coefficient of variation for each transcript or patch were calculated across the expression values for the samples in that group. These means were considered to be the expression values for the replicate group. P-values were calculated between the means of each pair of replicate groups using a Welch’s t-test corrected for FDR by the method of Benjamini-Hochberg.
BAM files were converted to bigWig with RPKM normalization by bamCoverage (deepTools).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: Human adult fibroblasts

growth_protocol: Adult Human Fibroblasts (22 year old female; GM02171, NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research) were maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 15% fetal bovine serum (Life Technologies), 0.01% β-mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution and 1% penicillin/streptomycin solution (all from Invitrogen) and never passaged more than 15 times.

extract_protocol:
RNeasy Micro Kit (Qiagen, Cat # 74004) was used with cell pellets collected by trypsin.
Total RNA was processed for library construction by Cofactor Genomics (http://cofactorgenomics.com , St. Louis, MO) according to the following procedure: Briefly, total RNA was reverse-transcribed using an Oligo(dT) primer, and limited cDNA amplification was performed using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Takara Bio USA, Inc., Mountain View, CA ). The resulting full-length cDNA was fragmented and tagged, followed by limited PCR enrichment to generate the final cDNA sequencing library (Nextera® XT DNA Library Prep, Illumina, San Diego, CA). Libraries were sequenced as single-end 75 base pair reads on an Illumina NextSeq500 following the manufacturer's instructions.

treatment_protocol: To initiate direct conversion, 1.8x10^6 cells were seeded onto Costar 6 well cell culture vessels (Corning; 300,000 cells/well). The following day, each plate was transduced with the following reprogramming cocktail: 750 uL of concentrated lentivirus containing the reverse tetracycline-controlled transactivator (rtTA; Addgene, 66810) and 500 μL of virus containing pT-BCL-9/9*- 124 or pT-BCL-9/9*-124 and 500 μl of each individual TF driven by the EF1α promoter, and polybrene (8 μg/mL; Sigma-Aldrich) all diluted up to 18 mL (3 mL per well) then spinfected at 37°C for 30 minutes at 1,000xG using a swinging bucket rotor. The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with doxycycline (Dox; Sigma Aldrich, 1 μg/mL). After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (Puromycin, 3 μg/ml; Blasticidin 5 μg/ml; Geneticin, 400 ug/mL; all from Invitrogen). Five days post-transduction cells were replated on to poly- ornithine/laminin/fibrobnectin (PLF) coated glass coverslips. Before PLF coating, glass coverslips were acid treated according to (Richner et al., 2015). For each well of a 6 well plate, cells were first washed 2x with 1 mL sterile PBS, then 320 μL of 0.25% Trypsin (Gibco) was added to each well then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes) 1 ml of MEF media supplemented with 1 μg/mL Dox was added to each well. One by one, each well was gently triturated three times to remove remaining attached cells then transferred to a sterile 1.5 mL eppendorf tube. Cells were then spun at 200xG for 5 minutes at 37°C. The supernatant was aspirated and cells were gently resuspended in 300 μL MEF media supplemented with Dox. Cells were then drop-plated onto either 18 mm (150 μL per/c.s.; placed in 12 well plate) or 12mm (60 μL per c.s.; placed in 24 well plate) coverslips. Cells were left to settle for 15 minutes in an incubator then each well was flooded with MEF media supplemented with 1 μg/mL Dox. The following day media was then changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, NT-3, CNTF, GDNF (all 10 ng/ml, Peprotech), and Retinoic Acid (1 uM; Sigma-Aldrich) and antibiotics for each vector. Dox was replenished every two days and half the media was changed every 4 days. Drug selection was halted 14 days into conversion. A diagram of the reprogramming protocol is available in Figure S1.

value: Adult fibroblasts

tag: timepoint

value: PID 20


title: RNAseq_timecourse_miNs_day10_B

description: Induced with miR-9/9*-124 for 10 days.

value: PID 10


title: RNAseq_timecourse_miNs_day6_B

description: Induced with miR-9/9*-124 for 6 days.

value: PID 6


title: RNAseq_timecourse_miNs_day20_A

description: Induced with miR-9/9*-124 for 20 days.


title: RNAseq_timecourse_miNs_day10_A

description: Induced with miR-9/9*-124 for 10 days.


title: RNAseq_timecourse_miNs_day6_A

description: Induced with miR-9/9*-124 for 6 days.


title: RNAseq_timecourse_miNs_day3_B

description: Induced with miR-9/9*-124 for 3 days.

value: PID 3


title: RNAseq_timecourse_fib_B

description: Starting fibroblasts.

value: No treatment

value: PID 0


title: RNAseq_timecourse_fib_A

description: Starting fibroblasts.


title: mre_NS_d30

description: Induced with miR-NS for 30 days.

data_processing:
Base-calls were performed using CASAVA.
Raw sequencing reads were aligned to the human hg19 genome assembly using bwa v0.6.2-r126.
The aligned reads were further processed using homemade Perl scripts. These include removing duplicated reads and bed sorting.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: Neonatal fibroblasts

growth_protocol: Human neonatal fibroblasts (PCS-201-010, ATCC) were obtained from commercial sources and maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 0.01% β-mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution and 1% penicillin/streptomycin solution (all from Invitrogen) and never passaged more than 15 times.

extract_protocol:
DNA was isolated from cell pellets via phenol/chloroform extraction.
MRE-seq was performed as in Maunakea et al. 2010, with modifications as detailed below. Five parallel restriction enzyme digestions (HpaII, Bsh1236I, SsiI (AciI) and Hin6I (Fermentas), and HpyCH4IV (NEB)) were performed, each using 1 µg of DNA per digest for each of the samples. Five units of enzyme were initially incubated with DNA for 3 h and then an additional five units of enzyme were added to the digestion for a total of 6 h of digestion time. DNA was purified by phenol/chloroform/isoamyl alcohol extraction, followed by chloroform extraction using phase lock gels. Digested DNA from the different reactions was combined and precipitated with one-tenth volume of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ethanol. The purified DNA was size selected and purified (50-300 bp) by gel electrophoresis and Qiagen MinElute extraction. Library construction was performed as per the Illumina Genomic DNA Sample Prep Kit protocol with the following modifications. During the end-repair reaction, T4 DNA polymerase and T4 PNK were excluded and 1 µl of 1:5 diluted Klenow DNA polymerase was used. For the adapter ligation reaction, 1 µl of 1:10 diluted PE adapter oligo mix was used. Ten microliters from the 30 µl of purified adapter ligated DNA was used for the PCR enrichment reaction with PCR PE Primers 1.0 and 2.0. PCR products were size selected and purified (170- 420 bp) by gel electrophoresis and Qiagen QIAquick extraction. DNA libraries were checked for quality by Nanodrop (Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent). Reads were aligned to hg19 using BWA and pre-processed using methylQA. MRE reads were normalized to account for differing enzyme efficiencies and methylation values were determined by counting reads with CpGs at fragment ends (Maunakea et al., 2010). Detailed library construction protocols for MRE-seq are publicly available at the NIH Roadmap Epigenomics project website (http://www.roadmapepigenomics.org/protocols/type/experimental/).

treatment_protocol: Human neonatal fibroblasts (1.8x10^6) were seeded onto 10 cm plates (Corning). The following day, each plate was transduced with 10 ml of unconcentrated lentivirus containing a doxycycline inducible miR-9/9*-124 vector (Victor et al., 2014) or a non-specific microRNA control vector (miR-NS) and polybrene (8 μg/mL; Sigma-Aldrich). The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with Dox. After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (see Table 1). Seven days post-transduction, cells were first washed 2x with 3 mL sterile PBS, then 1 ml of 0.25% Trypsin (Gibco) was added to each plate then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes), 4 ml of MEF media supplemented with 1 μg/mL Dox was added to each plate. Cells were transferred to Primaria modified 10 cm plates (Corning) and 5 ml fresh fibroblast media supplemented with 1 μg/mL Dox was added to a final volume of 10 ml. The following day media was changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, and NT-3 (all 10 ng/ml, Peprotech), Retinoic Acid (1 uM; Sigma-Aldrich), and 4% FBS. Dox was replenished every two days and half the media was changed every 4 days.

value: Neonatal fibroblasts

value: miR-NS


title: mre_9124_d20

description: Induced with miR-9/9*-124 for 20 days.


title: mre_9124_d30

description: Induced with miR-9/9*-124 for 30 days.


title: mre_NS_d10

description: Induced with miR-NS for 10 days.


title: mre_NS_d20

description: Induced with miR-NS for 20 days.


title: medip_9124_d20

description: Induced with miR-9/9*-124 for 20 days

extract_protocol:
DNA was isolated from cell pellets via phenol/chloroform extraction.
MeDIP-seq was performed as in Maunakea et al. 2010. Five micrograms of genomic DNA was sonicated to a fragment size of ~100-400 bp using the Bioruptor sonicator (Diagenode). End-repair, addition of 3’-A bases and PE adapter ligation with 2 µg of sonicated DNA was performed according to the Illumina Genomic DNA Sample Prep Kit protocol. Adapter- ligated DNA fragments were size selected to 166-366 bp and purified by gel electrophoresis. DNA was heat denatured and then immunoprecipitated with 5-methylcytidine antibody (Eurogentec; 1 µg of antibody per 1 µg of DNA) in 500 µl of immunoprecipitation buffer (10 µM sodium phosphate, pH 7.0, 140 mM sodium chloride and 0.05% Triton X-100) overnight at 4 °C. Antibody/DNA complexes were isolated by addition of 1 µl of rabbit anti-mouse IgG secondary antibody (2.4 mg ml-1, Jackson Immunoresearch) and 100 µl protein A/G agarose beads (Pierce Biotechnology) for 2 h at 4 °C. Beads were washed nine times with immunoprecipitation buffer and then DNA was eluted in TE buffer with 0.25% SDS and 0.25 mg ml-1 of proteinase K for 2 h at 50 °C. DNA was then purified with the Qiagen QIAquick kit and eluted in 30 µl EB buffer. Ten microliters of DNA was used for a PCR-enrichment reaction with PCR PE Primers 1.0 and 2.0. PCR products were size selected (220-420 bp) and purified by gel electrophoresis. Methylated DNA enrichment was confirmed by PCR on known methylated (SNRPN and MAGEA1 promoters) and unmethylated (a CpG-less sequence on chromosome 15 and glyceraldehyde 3- phosphate dehydrogenase promoter) sequences. DNA libraries were checked for quality by Nanodrop (Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent). Reads were aligned to hg19 using BWA and pre-processed using methylQA (an unpublished C program; available at http://methylqa.sourceforge.net/). Detailed library construction protocols for MeDIP-seq are publicly available at the NIH Roadmap Epigenomics project website (http://www.roadmapepigenomics.org/protocols/type/experimental/).


title: medip_9124_d10

description: Induced with miR-9/9*-124 for 10 days


title: medip_9124_d30

description: Induced with miR-9/9*-124 for 30 days


title: medip_NS_d10

description: Induced with miR-NS for 10 days


title: mre_9124_d10

description: Induced with miR-9/9*-124 for 10 days.


title: ATACKD_shBRG1_B

description: Induced with miR-9/9*-124 and shBRG1 for 20 days.

data_processing:
ATAC-seq reads were trimmed for Nextera adapter sequences using TrimGalore.
Trimmed ATAC reads were aligned to the hg19 genome assembly using bowtie2.
Duplicate reads were discarded with Picard and uniquely mapped reads were used.
Peaks in each sample were called using Homer findPeaks. Peaks called from all the samples were combined together.
Raw reads mapped on the combined peaks were counted using HTSeq-count.
Differential peaks were identified using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

growth_protocol: Human 22 yr adult fibroblasts (NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research, GM02171) were maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 0.01% β- mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution and 1% penicillin/streptomycin solution (all from Invitrogen) and never passaged more than 15 times.

extract_protocol:
DNA fragments were collected by column-based purification after tagmentation.
ATAC-seq was performed as previously described (Buenrostro et al., 2013). Briefly, 50,000 cells were collected for ATAC-seq library preparation at Ctrl day 10, miNs day 10, miNs day 20, shBRG1 Day20 and shEGFP day 20. Transposition reaction was carried out with Nextera Tn5 Transposase for 30 min at 37 °C. Library fragments were amplified for optimal amplification condition. Final libraries were purified using AMPure XP beads (Ampure) and sequenced with 50 bp paired-end reads on Illumina HiSeq 2500 or 75 bp paired-end reads on Illumina NextSeq 500.

treatment_protocol: 1.8x10^6 cells were seeded onto Costar 6 well cell culture vessels (Corning; 300,000 cells/well). The following day, each plate was transduced with 10 ml of unconcentrated lentivirus containing a doxycycline inducible miR-9/9*-124 vector (Victor et al., 2014) or a non-specific microRNA control vector (miR-NS) and polybrene (8 μg/mL ; Sigma-Aldrich). The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with Dox. After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (see Table 1). Seven days post-transduction, cells were first washed 2x with 3 mL sterile PBS, then 1 ml of 0.25% Trypsin (Gibco) was added to each plate then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes), 4 ml of MEF media supplemented with 1 μg/mL Dox was added to each plate. Cells were transferred to Primaria modified 10 cm plates (Corning) and 5 ml fresh fibroblast media supplemented with 1 μg/mL Dox was added to a final volume of 10 ml. The following day media was changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, and NT-3 (all 10 ng/ml, Peprotech), Retinoic Acid (1 uM; Sigma-Aldrich), and 4% FBS. Dox was replenished every two days and half the media was changed every 4 days.

value: adult fibroblasts

value: miR-9/9*-124 and shBRG1


title: ATACKD_shBRG1_A


title: medip_NS_d20

description: Induced with miR-NS for 20 days


title: ATACKD_shEGFP_B

description: Induced with miR-9/9*-124 and shEGFP for 20 days.

value: miR-9/9*-124 and EGFP


title: RNAseq_timecourse_miNs_day3_A

description: Induced with miR-9/9*-124 for 3 days.


title: ATACKD_shEGFP_A


title: melXmel_cyc14C_sl24

city: Stanford

first: Peter

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the melanogaster genome with interspecific polymorphisms masked with Ns using STAR v.2.4.2a, with arguments --clip5pNbases 6 --outSAMattributes MD NH
Absolute expression was called using cufflinks v.2.2.1 with arguments --multi-read-correct --frag-bias-correct, and using the --mask-file argument to exclude a set of ribosomal, tRNA, microRNA, and histone features.
Allele-specific expression was called using ASEr commit cfe619c69a (https://github.com/TheFraserLab/ASEr/commit/cfe619c69a31f4600670859a82aae4378381b648)
Genome_build: FlyBase r5.57
Supplementary_files_format_and_content: Tab-delimited text files containing absolute expression (.fpkms) and allele-specific (.ase) expression data for each sample.
ase_summary.tsv (Tab-separated file with complete matrix of allele-specific expression values)
expr_summary.tsv (Tab-separated file with complete matrix of absolute expression values)

growth_protocol: 25C incubator. 2 hour lay, age to appropriate stage in incubator.

extract_protocol:
TRIzol Extraction with 1ug of glycogen
SMART-seq2 with minor modifications (see Combs & Eisen, 2015)

treatment_protocol: Methanol fixation of embryos

tag: strain(s)

value: embryonic blastoderm cycle 14C


title: medip_NS_d30

description: Induced with miR-NS for 30 days


title: melXmel_cyc14C_sl23

tag: developmental stage


title: melXmel_cyc14C_sl25


title: melXmel_cyc14C_sl27


title: melXmel_cyc14C_sl22


title: melXmel_cyc14C_sl21


title: melXmel_cyc14C_sl17


title: melXmel_cyc14C_sl16


title: melXmel_cyc14C_sl18


title: melXmel_cyc14C_sl15


title: melXmel_cyc14C_sl26


title: RNAseq_miNs_D30_B

description:
Induced with miR-9/9*-124 for 10 days.
mRNA

data_processing:
RNA-seq reads were aligned to GRCh37 whole genome using STAR aligner.
Reads were counted by Htseq-count. For differential expression analysis between, edgeR and limma were used.
BAM files were converted to bigWig normalized to RPKM using bamCoverage (deepTools).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

growth_protocol: Human 22 yr adult fibroblasts (NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research, GM02171) were maintained in fibroblast media comprised of Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 0.01% β-mercaptoethanol (Life Technologies), 1% non-essential amino acids, 1% sodium pyruvate, 1% GlutaMAX, 1% 1M HEPES buffer solution and 1% penicillin/streptomycin solution (all from Invitrogen) and never passaged more than 15 times.

extract_protocol:
Total RNA from Day 30 miNs and starting human adult fibroblasts were extracted by column-based method (RNeasy plus micro kit, Qiagen).
mRNA was isolated by using SMARTer Ultra Low RNA Kit (Clontech) for Illumina sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1.8x10^6 cells were seeded onto Costar 6 well cell culture vessels (Corning; 300,000 cells/well). The following day, each plate was transduced with 10 ml of unconcentrated lentivirus containing a doxycycline inducible miR-9/9*-124 vector (Victor et al., 2014) or a non-specific microRNA control vector (miR-NS) and polybrene (8 μg/mL; Sigma-Aldrich). The following day media was changed to fresh fibroblast media (2 mL per well) supplemented with Dox. After 2 days, fresh fibroblast media was changed and supplemented with Dox and antibiotics for respective vectors (see Table 1). Seven days post-transduction, cells were first washed 2x with 3 mL sterile PBS, then 1 ml of 0.25% Trypsin (Gibco) was added to each plate then placed in an incubator. Cells were monitored every 2 minutes, as soon as cells began to detach (no more than 6 minutes), 4 ml of MEF media supplemented with 1 μg/mL Dox was added to each plate. Cells were transferred to Primaria modified 10 cm plates (Corning) and 5 ml fresh fibroblast media supplemented with 1 μg/mL Dox was added to a final volume of 10 ml. The following day media was changed to Neuronal Media (Sciencell) supplemented with Dox, valproic acid (1 mM; EMD Millipore) dibutyryl cAMP (200 μM; Sigma-Aldrich), BDNF, and NT-3 (all 10 ng/ml, Peprotech), Retinoic Acid (1 uM; Sigma-Aldrich), and 4% FBS. Dox was replenished every two days and half the media was changed every 4 days.

tag: cell line


title: melXmel_cyc14C_sl19


title: RNAseq_Fibroblast_B

description:
Induced with non-specific miRNA for 10 days.
mRNA

tag: cell type


title: melXmel_cyc14C_sl07


title: melXmel_cyc14C_sl14


title: RNAseq_Fibroblast_A


title: RNAseq_miNs_D30_A


title: melXmel_cyc14C_sl12


title: melXmel_cyc14C_sl13


title: melXmel_cyc14C_sl20


title: melXmel_cyc14C_sl11


title: melXmel_cyc14C_sl10


title: melXmel_cyc14C_sl05


title: melXmel_cyc14C_sl09


title: melXmel_cyc14C_sl02


title: melXmel_cyc14C_sl03


title: ATAC_miNs_D10_B

description: Induced with miR-9/9*-124 for 10 days.


title: melXmel_cyc14C_sl08


title: melXmel_cyc14C_sl01


title: melXmel_cyc14C_sl04