title: 4C_DMPK_u16_GM06077_rep3

description: GM06077 (DM1-A) DMPK_u16 4C viewpoint replicate 3


title: 4C_DMPK_u16_GM04648_rep3

status: Public on Apr 07 2020

type: SRA

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: GM04648 (DM1-B) DMPK_u16 4C viewpoint replicate 3

library_source: genomic

data_processing:
Demultiplexing, trimming, and mapping were performed using the BBCF HTSstation (David et al., 2014). Reads were trimmed to keep the first 40 bp. The 4C fragments surrounding the viewpoints (±2.5 kb) were excluded from the rest of the analysis. The demultiplexed reads were mapped to the GRCh38 human reference genome using bowtie2 (v 2.2) (Langmead & Salzberg, 2012).
Fragment read counts were obtained using FourCSeq (v 1.18.0) (Klein et al., 2015). Fragment counts were normalized (reads per million) and smoothed with a running mean (window size = 5 fragments).
Significant chromatin interactions were identified with two 4C-seq data analysis packages: FourCSeq (v 1.18.0) (Klein et al., 2015) and 4C-ker (v 0.0.0.9000) (Raviram et al., 2016).
For the FourCSeq analysis, we defined significant interactions as fragments with a z-score equal to or greater than 1.96 and a false-discovery rate of 0.1, using the following parameters: minCount=20 and fitFun="distFitMonotone" in getZScores function; zScoreThresh=1.96, fdrThresh = 0.1 in addPeaks function.
For the 4C-ker analysis, we used k=5 in the nearBaitAnalysis function, and plotted the high-interacting regions.
Differential interactions were identified with the differentialAnalysis function of 4C-ker, which is based on the DESeq2 (Love et al., 2014) framework, using default parameters (including a p-value threshold of 0.5). The UN-B cell line was used as the reference condition for all comparisons except for Fig. 1 and Fig. S2 where the reference condition was the UN-A cell line.
For plotting the data, the smoothed and normalized fragment counts were averaged among replicates of the same 4C library samples and visualized with gFeatBrowser (http://www.gfeatbrowser.com).
Genome_build: hg38
Supplementary_files_format_and_content: Smoothed and normalized 4C fragment count data (bedGraph) of the cis chromosome, one per viewpoint and per replicate.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: All LCLs were obtained from the Coriell Institute for Medical Research Cell Repository. They were grown at 37ºC and 5% CO2 in RPMI 1640 medium supplemented with 15% FBS, 2 mM L-glutamine, and 1% penicillin-streptomycin. Cells were counted and passaged every 3-4 days depending on cell density. The GFP(CAG)270 and GFP(CAG)15 cell lines were maintained at 37°C and 5% CO2 in DMEM with Glutamax, 1% penicillin-streptomycin, 15 μg mL−1 blasticidine, and 150 μg/mL hygromycin. Transcription of the GFP mini-gene was activated by culturing GFP(CAG)n cells with doxycycline at a final concentration of 2 µg/mL for five days.

extract_protocol:
Samples of 10 million cells were crosslinked in 2% formaldehyde for 10 minutes at room temperature and quenched with glycine to a final concentration 0.13 M. Cross-linked samples were rinsed once with PBS and were either used immediately or flash-frozen in liquid nitrogen and stored at -80ºC for later use. Cells were lysed for 15 minutes on ice in lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, 1x protease inhibitors). The first digestion was performed with 200 U DpnII (NEB) and incubating for 4 hours at 37ºC, then 200 U DpnII and overnight incubation at 37ºC, and finally 200 U DpnII and incubating 4 hours at 37ºC. DpnII digestion efficiency was assessed by agarose gel electrophoresis and DpnII was subsequently heat inactivated. The first ligation was performed at 16ºC overnight with 50 U T4 DNA ligase (Thermo Scientific) in 7 mL. Ligated samples were de-crosslinked with 30 µL Proteinase K (10 mg/mL) at 65ºC overnight followed by RNAse A treatment and phenol-chloroform purification. The second digestion was performed with 50 U of BfaI (NEB) at 37ºC overnight followed by BfaI heat inactivation. The second ligation was performed at 16ºC overnight with 100 U T4 DNA ligase in 14 mL. The resulting 4C template samples were precipitated and purified with the QIAquick PCR purification kit.
4C libraries were generated by amplifying 1 µg total of purified 4C template using the Expand Long Template PCR System (Roche) with 4C viewpoint primers with Illumina sequencing adapters that permitted multiplexing (in 50 µL PCRs), pooling reactions and purifying the PCR products with AMPure XP beads to exclude products less than 130 bp. Single-end sequencing of pooled 4C libraries was performed on Illumina HiSeq 2500.

tag: cell type

value: Lymphoblastoid Cell Line

tag: disease


title: 4C_DMPK_u16_GM04648_rep2

description: GM04648 (DM1-B) DMPK_u16 4C viewpoint replicate 2


title: 4C_DMPK_u16_GM04604_rep3

description: GM04604 (UN-B) DMPK_u16 4C viewpoint replicate 3

value: Unaffected


title: 4C_DMPK_u16_GM04648_rep1

description: GM04648 (DM1-B) DMPK_u16 4C viewpoint replicate 1


title: 4C_DMPK_u16_GM04604_rep2

description: GM04604 (UN-B) DMPK_u16 4C viewpoint replicate 2


title: 4C_DMPK_u16_GM04604_rep1

description: GM04604 (UN-B) DMPK_u16 4C viewpoint replicate 1


title: 4C_DMPK_u16_GM02180_rep3

description: GM02180 (UN-C) DMPK_u16 4C viewpoint replicate 3


title: 4C_DMPK_u65_GM04648_rep2

description: GM04648 (DM1-B) DMPK_u65 4C viewpoint replicate 2


title: 4C_DMPK_u16_GM02180_rep2

description: GM02180 (UN-C) DMPK_u16 4C viewpoint replicate 2


title: 4C_FMR1_u195_GM09236_rep1

description: GM09236 (UN-A) FMR1_u195 4C viewpoint replicate 1


title: 4C_DMPK_u16_GM02180_rep1

description: GM02180 (UN-C) DMPK_u16 4C viewpoint replicate 1


title: 4C_DMPK_d73_GM06077_rep2

description: GM06077 (DM1-A) DMPK_d73 4C viewpoint replicate 2


title: 4C_DMPK_d73_GM06077_rep1

description: GM06077 (DM1-A) DMPK_d73 4C viewpoint replicate 1


title: 4C_DMPK_d73_GM04648_rep1

description: GM04648 (DM1-B) DMPK_d73 4C viewpoint replicate 1


title: 4C_DMPK_d73_GM04648_rep2

description: GM04648 (DM1-B) DMPK_d73 4C viewpoint replicate 2


title: 4C_DMPK_d73_GM02180_rep2

description: GM02180 (UN-C) DMPK_d73 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM06077_rep3

description: GM06077 (DM1-A) DMPK_d11 4C viewpoint replicate 3


title: 4C_DMPK_u65_GM02180_rep1

description: GM02180 (UN-C) DMPK_u65 4C viewpoint replicate 1


title: 4C_DMPK_d73_GM04604_rep1

description: GM04604 (UN-B) DMPK_d73 4C viewpoint replicate 1


title: 4C_DMPK_d73_GM02180_rep1

description: GM02180 (UN-C) DMPK_d73 4C viewpoint replicate 1


title: 4C_DMPK_d11_GM04648_rep3

description: GM04648 (DM1-B) DMPK_d11 4C viewpoint replicate 3


title: 4C_DMPK_d73_GM04604_rep2

description: GM04604 (UN-B) DMPK_d73 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM04648_rep2

description: GM04648 (DM1-B) DMPK_d11 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM06077_rep1

description: GM06077 (DM1-A) DMPK_d11 4C viewpoint replicate 1


title: 4C_DMPK_d11_GM06077_rep2

description: GM06077 (DM1-A) DMPK_d11 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM04604_rep3

description: GM04604 (UN-B) DMPK_d11 4C viewpoint replicate 3


title: 4C_DMPK_d11_GM04648_rep1

description: GM04648 (DM1-B) DMPK_d11 4C viewpoint replicate 1


title: 4C_DMPK_d11_GM02180_rep2

description: GM02180 (UN-C) DMPK_d11 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM04604_rep1

description: GM04604 (UN-B) DMPK_d11 4C viewpoint replicate 1


title: 4C_DMPK_d11_GM02180_rep3

description: GM02180 (UN-C) DMPK_d11 4C viewpoint replicate 3


title: 4C_DMPK_d11_GM04604_rep2

description: GM04604 (UN-B) DMPK_d11 4C viewpoint replicate 2


title: 4C_DMPK_d11_GM02180_rep1

description: GM02180 (UN-C) DMPK_d11 4C viewpoint replicate 1


title: 4C_ACTA1_GM14044_rep2

description: GM14044 (HD-C) ACTA1 4C viewpoint replicate 2

value: HD


title: 4C_ACTA1_GM14044_rep3

description: GM14044 (HD-C) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM14044_rep1

description: GM14044 (HD-C) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM09237_rep2

description: GM09237 (FXS) ACTA1 4C viewpoint replicate 2

value: FXS


title: 4C_ACTA1_GM09237_rep1

description: GM09237 (FXS) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM09236_rep3

description: GM09236 (UN-A) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM09237_rep3

description: GM09237 (FXS) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM09236_rep2

description: GM09236 (UN-A) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM06077_rep3

description: GM06077 (DM1-A) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM09236_rep1

description: GM09236 (UN-A) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM06077_rep2

description: GM06077 (DM1-A) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM06077_rep1

description: GM06077 (DM1-A) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM04648_rep3

description: GM04648 (DM1-B) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM03620_rep2

description: GM03620 (HD-B) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM04604_rep3

description: GM04604 (UN-B) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM04648_rep1

description: GM04648 (DM1-B) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM04648_rep2

description: GM04648 (DM1-B) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM03620_rep3

description: GM03620 (HD-B) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM03620_rep1

description: GM03620 (HD-B) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM04604_rep1

description: GM04604 (UN-B) ACTA1 4C viewpoint replicate 1


title: 4C_ACTA1_GM02180_rep2

description: GM02180 (UN-C) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM02164_rep3

description: GM02164 (HD-A) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM02164_rep2

description: GM02164 (HD-A) ACTA1 4C viewpoint replicate 2


title: 4C_ACTA1_GM02164_rep1

description: GM02164 (HD-A) ACTA1 4C viewpoint replicate 1


title: Y 3

status: Public on Mar 31 2020

city: Harbin

first: Chuanyu

last: Han

state: Heilongjiang

address: Changjiang 600

country: China

institute: School of life science

library_source: transcriptomic

data_processing:
Raw reads were filtered using FastQC.
MultiQC V1.8 was used to evaluate the data quality
Paired-end clean reads were aligned to the reference genome using Hisat2. The reference genome selects the file  "GCA_000240135.3_ASM24013v3_genomic.fa" on NCBI, and the annotation file selects file "GCA_000240135.3_ASM24013v3_genomic.gtf".
FeatureCounts v1.5.0 was used to count the numbers of readsmapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene by featureCounts v1.5.0.
Genome_build: reference genome used WGS AACM02000001:AACM02000435
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Fusarium graminearum

source_name: mycelia

growth_protocol: Two 5-mm mycelial plugs cut from the edge of a 3-day-old colony of F. graminearum strain PH-1 were inoculated into 250 mL baffle Erlenmeyer flasks containing 50 mL of sterilized PDB broth and cultivated with shaking at 180 rpm for 36 hours. After that, Frenolicin B with the final concentration of 0.51 μg·mL-1 was added in the broth, and the same volumes of methanol were served as the control. Then incubated together 6 hours shaking at 180 rpm.

extract_protocol:
The sequencing libraries were generated using the KAPA Stranded RNA-Seq Kit for Illumina following the manufacturer’s recommendations.
These libraries were sequenced on Illumina Novaseq 6000 and 150 bp paired-end reads were generated.

treatment_protocol: The mycelia of F. graminearum strain PH-1 was collected by centrifuged (4000 rpm, 10 min) and frozen in liquid nitrogen more than an hour for transcriptome studies. Three biological replicates were employed in the transcriptome experiments.

tag: strain

tag: age

value: 42 hours

tag: treatment

value: Frenolicin B


title: Y 1


title: ck 2

value: methanol


title: ck 3


title: ck 1


title: SUM159R_H2_P0_DMSO

status: Public on Mar 30 2020

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Library strategy: CRISPR screen
Raw sequencing data are pre-processed by using MAGeCK (PMID:25476604) to obtain the read counts for each sgRNA. Control sgRNAs are used to normalize the data.
MAGeCK TEST algorithm is used to compare treatment with control samples to obtain the significant enriched and depleted sgRNAs and genes.
Genome_build: hg19
Supplementary_files_format_and_content: tsv files contain the abundant of each sgRNA in each sample, as well as the sgRNA sequences and target genes

source_name: breast cancer cells

growth_protocol: SUM149, SUM159, SUM149R, SUM159R cells were grown in SUM Medium

extract_protocol:
For the pooled genome-wide CRISPR screen, 100 million SUM149 and SUM159 Parental and resistant cells were infected with the pooled lentiviral H1 and H2 libraries essentially as described (Jeselsohn et al., 2018) at a multiplicity of infection of 0.3. After 3 d of puromycin selection, half of the surviving cells were stored as 0-d control samples, and the rest of cells were cultured for an additional 5 passages with or without different concentrations of JQ1 treatment.
PCR was performed on genomic DNA to construct the sequencing library.

treatment_protocol: SUM149, SUM159, SUM149R, SUM159R cells were continously treated with JQ1 or DMSO treatment.

tag: cell line

tag: agent

value: DMSO

tag: dose

tag: passage

tag: crispr library


title: SUM159R_H2_P5_JQ1_10uM


title: SUM159R_H2_P5_DMSO


title: SUM159R_H1_P5_JQ1_10uM


title: SUM159_H2_P5_JQ1_1000nM_Rep

tag: replicate

value: Replicate


title: SUM159R_H1_P5_DMSO


title: SUM159R_H1_P0_DMSO


title: 4C_ACTA1_GM04604_rep2

description: GM04604 (UN-B) ACTA1 4C viewpoint replicate 2


title: SUM159_H2_P5_DMSO_Rep


title: SUM159_H1_P5_JQ1_500nM_Rep


title: SUM159_H2_P0_Rep


title: SUM159_H1_P5_JQ1_1000nM_Rep


title: SUM159_H1_P5_DMSO_Rep


title: SUM159_H1_P0_Rep


title: SUM159_H2_P5_JQ1_1uM


title: SUM159_H2_P5_DMSO


title: 4C_ACTA1_GM02180_rep3

description: GM02180 (UN-C) ACTA1 4C viewpoint replicate 3


title: 4C_ACTA1_GM02180_rep1

description: GM02180 (UN-C) ACTA1 4C viewpoint replicate 1


title: Y 2


title: SUM159_H2_P0_DMSO


title: SUM159_H2_P5_JQ1_500nM


title: SUM159_H1_P5_JQ1_1uM


title: SUM159_H1_P5_JQ1_500nM


title: SUM149R_H2_P5_JQ1_10uM


title: SUM149R_H1_P5_JQ1_10uM


title: SUM149R_H2_P0_DMSO


title: SUM149R_H1_P5_DMSO


title: SUM159_H2_P5_JQ1_500nM_Rep


title: SUM159_H1_P5_DMSO


title: SUM149_H2_P5_JQ1_800nM_Rep


title: SUM149_H2_P5_DMSO_Rep


title: SUM149_H2_P0_DMSO_Rep


title: SUM149_H2_P5_JQ1_400nM_Rep


title: SUM149_H1_P5_JQ1_800nM_Rep


title: SUM149R_H1_P0_DMSO


title: SUM149_H1_P5_JQ1_400nM_Rep


title: SUM149_H1_P5_DMSO_Rep


title: SUM149_H2_P5_DMSO


title: SUM149_H2_P5_JQ1_200nM


title: SUM149_H2_P0_DMSO


title: SUM149_H1_P0_DMSO_Rep


title: SUM149_H1_P5_JQ1_200nM


title: SUM149_H2_P5_JQ1_100nM


title: SUM159_H1_P0_DMSO


title: SUM149_H1_P5_DMSO


title: input_control

status: Public on Mar 18 2020

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Reads were aligned to hg19 using bowtie (Langmead et al., 2009) with the following parameters: -m 1 -t –best -q -S -l 32 –e 80 -n 2.
MACS2 (Zhang et al., 2008) was used to call peaks with a p-value cutoff of 1e-10 and the mfold parameter bounded between 5 and 50. The broad peak calling feature was used for H3K27ac ChIP-seq.
Bedtools (Quinlan and Hall, 2010) was used to count reads in peaks. A window of 2 kb centered on the summit was used for counting H3K27ac reads within peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

source_name: Ishikawa (Endometrioid adenocarcinoma)

growth_protocol: Ishikawa cell lines containing deletions of individual ER binding sites were generated as described previously (Carleton et al., 2017). Ishikawa cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco) and 1% pencillin/streptomycin (Gibco). Cells were placed in hormone-depleted RPMI (phenol red-free RPMI-1640 supplemented with 10% Charcoal/Dextran treated fetal bovine serum (HyClone) and 1% penicillin-streptomycin) for at least 6 days prior to 17beta-estradiol (E2) treatment. The input control used in peak-calling was derived from the parental Ishikawa line.

extract_protocol:
To crosslink chromatin, 37% formaldehyde (Sigma-Aldrich) was added directly to the media and allowed to incubate at room temperature for 10 minutes. Glycine was added at a final concentration of 125 mM to stop crosslinking, and cells were washed with cold 1X PBS. Plates were scraped in Farnham lysis buffer with 1X protease inhibitor (Thermo Fisher). Chromatin was sonicated using an Active Motif EpiShear Probe Sonicator with 6 cycles of 30 s, at 40% amplitude, with 30 s of rest. ChIP was performed as previously described (Reddy et al., 2009) using anti-ER (Santa Cruz HC-20) and anti-H3K27ac (Active Motif 39133) antibodies.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009. The following antibodies were used: H3K27ac (Active Motif pAb Cat #39133) and ER (Santa Cruz HC-20) Libraries were sequenced on an Illumina HiSeq 2500 as single-end 50 basepair reads

treatment_protocol: For ER ChIP-seq, a 1 h 10 nM E2 induction was performed prior to harvest. For H3K27ac ChIP-seq, an 8 h 10 nM estradiol or DMSO treatment was performed prior to harvest.

value: Ishikawa

tag: enhancer deleted

tag: antibody target


title: NOD_8_wks_2

status: Public on Mar 27 2020

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

organism: Mus musculus

source_name: Pancreatic islets

extract_protocol:
Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics).
Samples were processed using the Chromium Single Cell 3’ Library & Gel Bead Kit following the manufacturer’s protocol. 10X Single Cell 3' v2.

tag: strain/background

value: NOD/ShiLtJ (NOD)

value: 8 weeks

tag: Sex

value: female

value: Pancreatic islet-infiltrating cells


title: SUM149_H1_P0_DMSO


title: SUM149R_H2_P5_DMSO


title: NOD_8_wks_1


title: h3k27ac_ChIP_E2_M2-5

value: 10nM E2 8hr

value: Histone 3 Lysine 27 acetylation (H3K27ac)


title: h3k27ac_ChIP_E2_M1-9-1


title: h3k27ac_ChIP_E2_M2-3


title: h3k27ac_ChIP_E2_M1-66


title: h3k27ac_ChIP_E2_C2-3


title: h3k27ac_ChIP_E2_C1-5


title: h3k27ac_ChIP_E2_C2-14


title: h3k27ac_ChIP_E2_C1-12


title: h3k27ac_ChIP_DMSO_M2-3

value: DMSO 8hr


title: h3k27ac_ChIP_DMSO_M2-5


title: h3k27ac_ChIP_DMSO_M1-66


title: h3k27ac_ChIP_DMSO_M1-91


title: h3k27ac_ChIP_DMSO_C1-8


title: h3k27ac_ChIP_DMSO_C1-5


title: h3k27ac_ChIP_DMSO_C2-14


title: ER_ChIP_E2_C1-5

value: 10nM E2 1hr

value: Estrogen Receptor alpha


title: SUM149_H1_P5_JQ1_100nM


title: ER_ChIP_E2_C2-14


title: ER_ChIP_E2_M2-3


title: ER_ChIP_E2_M1-66


title: ER_ChIP_E2_M1-9-1


title: ER_ChIP_E2_C1-12


title: ER_ChIP_E2_C2-3


title: ER_ChIP_E2_M2-5


title: Transcriptome-H1-WT-vNPC

status: Public on Feb 12 2020

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

description: total RNA

data_processing:
(CLIP only; samples 1-12) FASTQ files were first quality filtered using fastq_quality_filter of FASTX Toolkit (v0.0.14) with parameters “-q25 -p80”. Adapter sequences were then removed from reads using cutadapt (v1.7.1) with parameters “-n 3 -e 0.1 -O 5 -q 6 -m 20 -a AGATCGGAAGAGCACACG”. PCR duplicates were removed using fastx_collapser of FASTX Toolkit. Finally 5’ adapter sequences were trimmed from reads using fastx_trimmer of FASTX Toolkit with parameters “-f 13 -l 94”
Reads were mapped to GRCh38 whole genome using STAR v2.5.3a with parameters  --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 -alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype SAM --quantMode GeneCounts --outSAMattributes All --outFilterType BySJout --outSAMattrRGline ID:foo --alignEndsType EndToEnd
Differentially expressed genes and target enrichment were generated using DESeq2 v1.16.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include raw reads count

growth_protocol: NPCs and neurons were differentiated from hPSCs using a modified dual SMAD method. dNPCs were patterned with cyclopamine and vNPCs were patterned using SHH and purmorphamine. dNeurons and vNeurons were further differentiated from dNPCs and vNPCs.

extract_protocol:
Total RNAs from NPCs and neurons were extracted using Trizol reagent.
1 ug of total RNA per sample was depleted of ribosomal RNAs and converted to strand-specific cDNA libraries using the TruSeq Stranded Total RNA library prep kit with RiboZero depletion (Illumina)

value: hPSC-derived MGE-NPCs

tag: genotype

value: WT

tag: clip antibody


title: Transcriptome-H1-KO-dNeuron

description: total RNA

tag: cell type

value: hPSC-derived dorsal neurons

value: FMRP-KO


title: Transcriptome-H1-KO-vNeuron

description: total RNA

value: hPSC-derived interneurons


title: Transcriptome-H1-WT-dNPC

description: total RNA

value: hPSC-derived dorsal NPCs


title: Transcriptome-H13-WT-vNPC

description: total RNA


title: Transcriptome-H1-WT-vNeuron

description: total RNA


title: Transcriptome-H1-WT-dNeuron

description: total RNA


title: Transcriptome-H1-KO-vNPC

description: total RNA


title: h3k27ac_ChIP_DMSO_C2-3


title: Transcriptome-H13-WT-vNeuron

description: total RNA


title: Transcriptome-H13-WT-dNPC

description: total RNA


title: Transcriptome-H13-KO-vNPC

description: total RNA


title: Transcriptome-H13-KO-vNeuron

description: total RNA


title: Transcriptome-H13-WT-dNeuron

description: total RNA


title: Transcriptome-H13-KO-dNPC

description: total RNA


title: PREMIERE-Trans-SV-008 [scRNA-seq]

status: Public on Mar 03 2020

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: kidney biospecimen were placed in 1 ml Hypothermasol™ (Stemcell Technologies) and immediately transferred to the laboratory and cryopreserved in DMSO containing Cryostor CS 10 (Stemcell Technologies) solution for long term storage in liquid nitrogen

data_processing:
Further data analyses were performed on the CellRanger output data files using Seurat 3 R package. As a quality control step, cells with less than 500 genes per cell were filtered out. The percentage of mitochondrial gene read content has emerged as a quality measure for the cell viability in single-cell studies. High percentage of mitochondrial reads indicates that the cells are less viable, as much of their cytoplasmic mRNAs were lost due to the breakage of plasma membrane during dissociation process. For the tumor-nephrectomy data generated by 10Xgenomics version2, a threshold of < 20% mitochondrial reads per cell was used, whereas, a cutoff of < 50% mitochondrial reads per cell was applied for the data from 10X genomics version 3. It has been observed by us and other groups that for certain tissues, including kidney, 10X genomics version 3 chemistry results in higher percentage of mitochondrial reads irrespective of the viability status of the cells. This issue was circumvented by deeper sequencing of the samples to obtain more genes per cell. After the quality control step, the data from the three sample types (tumor-nephrectomy, surveillance biopsy and pre-perfusion biopsy) were merged and further analyzed. In order to exclude cells that were doublets or multiplets from the analysis, we used a cutoff of > 500 and < 5000 genes per cell.
Genome_build: Grch38
Supplementary_files_format_and_content: read counts

source_name: Surveillance biopsy

extract_protocol:
For tissue dissociation, samples were quickly thawed in a 37˚C waterbath for one minute, transferred to a small dish containing 1 ml DMEM/F12 medium (with L-Glutamine, HEPES, and high glucose) supplemented with 10% heat inactivated FBS, and incubated for 10 minutes at room temperature. Tissue/biopsy samples were cut into 1 mm3 small pieces to increase the surface area before they were transferred to a 1.5 ml tube containing 500 µl DMEM/F12 digestion media containing 125 ng Liberase TL (Sigma) enzyme (conc.: 0.25 mg/mL). Samples were incubated on an orbital shaker (500 rpm) for 12 minutes at 37˚C with a mild trituration step using a wide bore 1000P tip applied after 6 minutes. Digestion was stopped by adding 500 µl DMEM/F12 medium containing 10% FBS and incubated at room temperature for 1 minute. The cell suspension was then filtered through a 30 µl strainer (Milteny Biotech) into a 15 ml conical tube. Remaining solid tissue was passed through the nylon mesh using the rubber end of a 5 ml syringe pestle and the filter was washed with 10 ml DMEM/F12/10%FBS medium. Cells were pelleted by centrifugation for 10 minutes at 200 x g and 4˚C. The supernatant was immediately, completely removed by vacuum suction using a glass Pasteur pipet. The cell pellet was then gently re-suspended in 55 µl DMEM/F12/10%FBS medium and cell viability was analyzed with a Countess II FL automated cell counter exploiting the Trypan Blue dye exclusion method.
Single cell samples were immediately transferred to the University of Michigan Sequencing Core facility (in up to 46 µl DMEM/F12/10%FBS) per sample were added to each channel of a chip on the droplet based high-throughput 10XGenomics™ Chromium™ platform allowing cell lysis, individual cell barcoding, and reverse RNA transcription. We used the 10X Single Cell 3' GEX – version 2 chemistry for all tumor-nephrectomy samples and the enhanced 10X Single Cell 3' GEX – version3 for the more recently processed transplant surveillance biopsies and pre-perfusion biopsies. Single cell library preparation based on 10X Genomics technology  included emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter and Illumina sample index addition. Libraries have been pooled and sequenced on an Illumina HiSeq4000 platform as asymmetric paired end runs (26x115 bases) with a median of 100 million raw sequencing reads per sample. The output from the sequencer was first processed by CellRanger, the proprietary 10X Chromium single cell gene expression analysis software
Bulk glomerular RNAseq expression data were obtained for 74 participants with biopsy proven FSGS enrolled in the NEPTUNE study. Briefly, mRNA samples were prepared using the Illumina TruSeq mRNA Sample Prep v2 kit (Illumina, San Diego, CA, USA). Multiplex amplification was used to prepare cDNA with a paired‐end read length of 100 bases using an Illumina HiSeq2000 (Illumina Inc., San Diego, CA, USA). RNA‐sequencing was performed by the University of Michigan DNA Sequencing Core (http://seqcore.brcf.med.umich.edu/). Quality of the sequencing data was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read counts were extracted from the fastq files using HTSeq (version 0.11). The objectives and study design of NEPTUNE can be found in the clinicaltrials.gov database under NCT1209000 (42).

tag: subject status

value: normal/healthy

tag: tissue

value: adult kidney


title: Transcriptome-GM1-WT-vNPC

description: total RNA


title: Transcriptome-GM1-WT-dNeuron

description: total RNA


title: Transcriptome-GM1-KO-vNeuron

description: total RNA


title: H1-WT-vNPC

description: RNA isolated by CLIP

data_processing:
Library strategy: HITS-CLIP
(CLIP only; samples 1-12) FASTQ files were first quality filtered using fastq_quality_filter of FASTX Toolkit (v0.0.14) with parameters “-q25 -p80”. Adapter sequences were then removed from reads using cutadapt (v1.7.1) with parameters “-n 3 -e 0.1 -O 5 -q 6 -m 20 -a AGATCGGAAGAGCACACG”. PCR duplicates were removed using fastx_collapser of FASTX Toolkit. Finally 5’ adapter sequences were trimmed from reads using fastx_trimmer of FASTX Toolkit with parameters “-f 13 -l 94”
Reads were mapped to GRCh38 whole genome using STAR v2.5.3a with parameters  --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 -alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype SAM --quantMode GeneCounts --outSAMattributes All --outFilterType BySJout --outSAMattrRGline ID:foo --alignEndsType EndToEnd
Differentially expressed genes and target enrichment were generated using DESeq2 v1.16.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include raw reads count

extract_protocol:
FMRP-target RNAs were isolated from whole cell lysates using antibody.
CLIP-isolated RNAs were converted to cDNA libraries for Illumina sequencing. Briefly, CLIP-isolated RNAs were PNK-treated and ligated to a 3'-adapter. The RNAs were then converted to cDNAs. cDNAs were circularized using CircLigase II ssDNA Ligase and amplified with barcoded primers for Illumina sequencing.

value: FLAG (Sigma# F1804)


title: Transcriptome-GM1-KO-dNPC

description: total RNA


title: Transcriptome-GM1-KO-vNPC

description: total RNA


title: Transcriptome-GM1-KO-dNeuron

description: total RNA


title: H1-SMI-vNPC

description: Size-matched input control RNA

value: FMRP-FLAG


title: H1-WT-dNPC

description: RNA isolated by CLIP


title: Transcriptome-GM1-WT-vNeuron

description: total RNA


title: Transcriptome-H13-KO-dNeuron

description: total RNA


title: H1-WT-vNeuron

description: RNA isolated by CLIP


title: H1-WT-dNeuron

description: RNA isolated by CLIP


title: H1-SMI-vNeuron

description: Size-matched input control RNA


title: H1-FLAG-vNeuron

description: RNA isolated by CLIP


title: H1-SMI-dNeuron

description: Size-matched input control RNA


title: H1-FLAG-vNPC

description: RNA isolated by CLIP


title: H1-FLAG-dNPC

description: RNA isolated by CLIP


title: Transcriptome-H1-KO-dNPC

description: total RNA


title: H13-WT-dNPC

description: RNA isolated by CLIP


title: H13-WT-vNPC

description: RNA isolated by CLIP


title: H13-WT-vNeuron

description: RNA isolated by CLIP


title: Transcriptome-GM1-WT-dNPC

description: total RNA


title: H13-SMI-vNPC

description: Size-matched input control RNA


title: H13-SMI-dNPC

description: Size-matched input control RNA


title: H13-SMI-dNeuron

description: Size-matched input control RNA


title: H13-FLAG-vNPC

description: RNA isolated by CLIP


title: H13-FLAG-vNeuron

description: RNA isolated by CLIP


title: H13-FLAG-dNPC

description: RNA isolated by CLIP


title: GM1-WT-vNeuron

description: RNA isolated by CLIP


title: H13-FLAG-dNeuron

description: RNA isolated by CLIP


title: GM1-WT-dNPC

description: RNA isolated by CLIP


title: H1-SMI-dNPC

description: Size-matched input control RNA


title: H1-FLAG-dNeuron

description: RNA isolated by CLIP


title: GM1-SMI-dNeuron

description: Size-matched input control RNA


title: GM1-WT-dNeuron

description: RNA isolated by CLIP


title: GM1-SMI-vNPC

description: Size-matched input control RNA


title: GM1-FLAG-vNPC

description: RNA isolated by CLIP


title: GM1-SMI-dNPC

description: Size-matched input control RNA


title: GM1-FLAG-dNeuron

description: RNA isolated by CLIP


title: GM1-FLAG-vNeuron

description: RNA isolated by CLIP


title: H13-SMI-vNeuron

description: Size-matched input control RNA


title: H13-WT-dNeuron

description: RNA isolated by CLIP


title: wt_e85_embryo_large.demultiplexed

status: Public on Feb 05 2020

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: 10 E8.25 mouse embryos processed with single-nucleus ATAC-seq

data_processing:
To make a consistent annotation of barcodes between the different platforms, we reverse complemented the I2 barcode sequence of the reads obtained with HiSeq2500.
Fastq files were merged and mapped using bowtie2 with -t -X 2000 --no-mixed --no-discordant and the mm10 genome.
Next, SAM files were pre-processed using samtools and the snATAC_pre script developed in (Preissl et al., 2018) (https://github.com/r3fang/snATAC/blob/master/bin/snATAC_pre) with parameters -m 20 (filter out MAPQ < 20) -f 2000 (maximum fragment length) -e 75 (read extension) and with slight modifications. More specifically, we centred the reads in the cutting site (i.e. 5’ end of each read) and considered each one a fragment: for reads in the forward strand, we considered the start position of the read + 4 bp as the centre of the fragment and extended +/- 75 bp each way; for reads in the reverse strand, we considered the end position of the read – 5 bp as the centre of the fragment and extended +/- 75 bp each way.
Barcodes were filtered out if they satisfied the following two criteria: (a) a total number of reads less than or equal to 2,000 and (b) coverage of constitutive promoters less than or equal to 3% (Supplementary Fig. 2a) – the list of constitutive promoters contains the coordinates of 5,006 promoters (TSS / TSS – 2 kb) that are accessible in the majority of datasets based on ENCODE DNase Hypersensitive Sites and ATAC-seq data, and that was generated in ref. 44 (Supplementary Table 4). Next, we called peaks on the pooled sample of high-quality barcodes using macs2 callpeak (macs2 2.1.0.20150420) with p-value 0.05, --nomodel, --shift 0, --extsize 150 and discarded peaks falling in blacklisted mm10 genomic regions from the ENCODE Project Consortium37 using bedtools intersect (v2.21.0). The resulting peak summits were extended +/- 250 bp and subsequently merged with the promoter coordinates of genes from ensembl GRCm38.92 (from TSS to TSS – 500 bp) using bedtools merge (v2.21.0). An accessibility matrix was then generated using the snATAC_bmat script (https://github.com/r3fang/snATAC/blob/master/bin/snATAC_bmat). Using the binary accessibility matrix as input, doublet scores were computed using the scrublet module v0.2 (Python). Nuclei with a score above 0.4 were considered a doublet and were removed. The remaining nuclei were then visualised by computing the steps in the “Visualisation” section, and clustered using tl.louvain from Scanpy v1.4.4 with resolution = 1 on the matrix obtained after running cisTopic. For each cluster, peaks were subsequently called and only those with – log(q-value) > 30 were retained. Peak summits were extended +/- 250 bp and merged with the previous list of coordinates using bedtools merge (v2.21.0), which resulted in a final list of 305,187 genomic regions. An accessibility matrix was then generated using the snATAC_bmat script (https://github.com/r3fang/snATAC/blob/master/bin/snATAC_bmat). Nuclei with a percentage of reads in called genomic regions less than or equal to 24% were discarded and 19,453 nuclei were retained. All metadata for these nuclei, including cell type annotation, can be found in Supplementary Table 5 of the manuscript.
Visualisation: A binary accessibility matrix was taken as input. Regions with 0 counts were discarded. cisTopic was applied to the binarized data by running “runModels” (cisTopic v0.2.2, R package) on a cisTopic object containing the data. In all cases, the best model was selected using “selectModel” (cisTopic v0.2.2, R package). A neighbourhood graph was subsequently calculated on the resulting topics using pp.neighbours with default parameters from Scanpy v1.4.4 (Python), and a UMAP was then computed with tl.umap (Scanpy v1.4.4; Python) using default parameters.
Genome_build: mm10
bigWig files for each cell type (total of 18) - Sparse matrices for peak counts: one contains the raw counts (embryo_revision1_allPeaks_afterClusterPeak_raw.mtx) and the other is a binary matrix (embryo_revision1_allPeaks_afterClusterPeak.mat.bin.mtx). Two additional files containing peak names (row names of sparse matrix: embryo_revision1_allPeaks_passedQC_peakNames.txt, and BED file: peaks_celltypes_extended500bp_qvalThreshold_overlapped_TSSGeneralPeaks_merged_noblacklist.bed) and barcodes (columns of sparse matrix; embryo_revision1_allPeaks_passedQC_barcodeNames.xgi) are also provided. Note: The matrices contain all the cells after the first QC. They need an additional filtering step using the file embryo_revision1_readsPeaks24.xgi, which contains the barcodes that passed all QC. TF enrichment scores are also provided as a sparse matrix: CHROMVAR_embryo_allPeaks_jointTogether_chromVAR_devScores_pwm_chromVar_sparse_raw_round4_peaksAll.mtx. Barcodes corresponding to column names are in CHROMVAR_embryo_allPeaks_jointTogether_chromVAR_devZscores_colnames_cellNames_pwm_chromVar_raw_round4_peaksAll.tab and TF names corresponding to row names are in CHROMVAR_embryo_allPeaks_jointTogether_chromVAR_devScores_rownames_motifs_pwm_chromVar_raw_round4_peaksAll.tab. Metadata files for nuclei and OCRs are also provided: Supplementary_Table5_metadata.xlsx and Supplementary_Table6_OCRs.xlsx

source_name: E8.25 mouse embryos

extract_protocol:
Mouse embryos were dissected at embryonic day (E) 8.25 in 1X PBS + 2% FCS and placed individually onto a parafilm strip. Overflowing liquid was removed and each parafilm strip was inserted into a cryovial, which was subsequently snap-frozen in liquid nitrogen. Frozen cryovials were stored at -80C. For single-nucleus ATAC-seq, 10 mouse embryos were thawed, pooled and processed using the snATAC-seq protocol with slight modifications. Briefly, after permeabilization with OMNI buffer, 1,500 nuclei were placed per well in two 96-well plates. Nuclei were then tagmented with Tn5 to introduce a first barcode (T7), as in (Preissl et al., 2018), and pooled into one tube. Nuclei were then stained with DRAQ7 (1:200; Cell Signaling Technology #7406; LOT# 31DR71000) for 5 min, and 40 nuclei per well were subsequently sorted into six 96-well plates using SH800 sorter, and a second barcode (i5) was introduced by PCR. During the sort, two populations corresponding to small and large size nuclei were detected. To make sure nuclear size did not affect subsequent bioinformatics analysis, we sorted two extra plates, where small and large nuclei were specifically sorted. You will see that sample titles contain "all", "large" and  "small" in their names. "all" refers to the FACS gating where nuclei were sorted indiscriminately; "large" refers to the FACS gating strategy to sort for large size nuclei; "small" refers to the FACS gating strategy to sort for small size nuclei. Libraries were sequenced using three NextSeq500, 50 paired-end sequencing runs, and one HiSeq2500 100 paired-end run.
Nuclei were tagmented with Tn5 in two 96 well-plates to introduce a first barcode (T7). After pooling, 40 nuclei were sorted into each well of six 96-well plates and a second barcode (i5) was introduced by PCR. Libraries were sequenced on a HiSeq2500 or NextSeq500 (Illumina) with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2). Index1 corresponded to the T7 barcode and Index2 corresponded to the i5 barcode.

tag: strain

tag: developmental stage

value: embryo

tag: facs sorting

value: large nuclei


title: wt_e85_embryo_small.demultiplexed

value: small nuclei


title: GM1-FLAG-dNPC

description: RNA isolated by CLIP

tag: cell line


title: 180823_NB501692_small.demultiplexed.R1.repl1


title: 180823_NB501692_large.demultiplexed.R1.repl1


title: 180823_NB501692_all.demultiplexed

value: all


title: HiSeq2500_all.demultiplexed


title: HiSeq2500_small.demultiplexed


title: GM1-WT-vNPC

description: RNA isolated by CLIP


title: HiSeq2500_large.demultiplexed


title: GM1-SMI-vNeuron

description: Size-matched input control RNA


title: XH69_3.demultiplexed


title: RNA-seq_Dis_08

status: Public on Feb 03 2020

first: JAE WON

last: CHO

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Read mapping: STAR-2.5.2a
Quantification: FeatureCounts
Genome_build: GRCH37.p13, release 19
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample.

source_name: NSCLC biopsies

extract_protocol:
Next-Gen Sequecing Sample Specification and Submission Guideline: RNA extraction protocol
TruSeq RNA Access Library Prep Guide Part # 15049525 Rev. B with TruSeq RNA Access Library Prep Kit

value: NSCLC

tag: treatment status

value: pre-treatment

tag: patient response

value: non-responder

tag: sample

value: FFPE


title: RNA-seq_Dis_09


title: RNA-seq_Dis_18


title: RNA-seq_Dis_06


title: DDX43 KH 89aa 1_ChIP

city: Saskatoon

first: Yuliang

last: Wu

state: Saskatchewan

address: Rm 4D01.1, HSB, 107 Wiggins Road

department: BMI

country: Canada

institute: University of Saskatchewan

description: S00C5C0: DDX43 KH 89aa 1_ChIP

data_processing:
[SELEX DNA insert extraction] The paired-end SELEX reads were trimmed using cutadapt (v1.18) to remove primers and extract the DNA insert.
[SELEX Sequence selection] The set of k-mers present in the control-read pool were removed from the set of k-mers present in the positive-read pool. P-values were assigned to the remaining k-mers using Fisher’s exact test. The resulting P-values were adjusted for multiple comparisons using the Benjamini-Hochberg (BH) procedure and a false-discovery rate of 5%.
[SELEX Motif detection] The resulting set of significantly enriched k-mers was submitted to MEME for motif discovery using the following parameters: classic mode; zoops (Zero or One occurrence per sequence); 3 motifs. Under advanced options, the minimum width was set to 6 and maximum width was set to 8.
[ChIP/CLIP-Seq Adapter trimming] The adaptors of the paired-end FASTQ reads were trimmed using cutadapt (v1.18).
[ChIP/CLIP-Seq Alignment] The trimmed reads were mapped to the hg38 human reference genome using Bowtie2 (v2.3.5).
[ChIP/CLIP-Seq SAM to BAM / filtering] Mapped reads were converted from SAM format to BAM format and filtered based on mapping quality (>=10) using samtools view. Subsequent sorting was performed using samtools sort.
[ChIP/CLIP-Seq BAM indexing] BAM files were indexed using samtools index.
[ChIP/CLIP-Seq Peak calling] Peak-calling was performed using MACS2 (v2.2.1) and the following parameters: A genome size of 2.7e9, which is the recommended setting for the human genome; the -revcomp option; and a P-value cutoff of 1e-5. A negative control was supplied alongside the target data to correct for background.
[ChIP/CLIP-Seq Motif detection] Motifs were extracted from the FASTA sequences of the peaks using MEME and the following options: fasta file uploaded as alphabet:custom;  "zoops" selected; number of motifs: 3; minimum width: 6; maximum width: 8
Genome_build: hg38
Supplementary_files_format_and_content: For the SELEX analysis, the CSV tables of k-mer counts for both target and control are 89aa.csv and NC.csv, respectively. For the ChIP-Seq analysis, there are bedGraph files containing fragment pileup for both target and control. The bedGraph files were produced by MACS2 and used by MACS2 to determine statistically significant peaks.

source_name: HEK293T cells

growth_protocol: SELEX: Using purified recombinant DDX43-KH-89 protein to pull down ssDNA from a oligonucleotides library (TriLink Biotechnologies, O-32001-20), and a library was constructed and sequenced. ChIP/CLIP: HEK293T cells were grown in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 units/ml each).

extract_protocol:
The DNA was extracted with phenol-chloroform, precipitated with 2×volume of ethanol, washed with 70% ethanol, and dissolved in 50 µL of ddH2O. For RNA extraction and purification, Trizol reagent (Invitrogen) was used to isolate the sheared RNA. The isolated RNA was eluted in nuclease-free water.
For the DNA library, 20 ng of ChIP-ed DNA was end repaired using NEBNext Ultra II End Prep buffer and Enzyme mix, adaptor-ligated, cleaned with 0.9×AMPure beads, and size selected using 0.4×beads. The size-selected DNA was then amplified using (Index 3, 4, 5, 6, 7 and 8) NEBNext Multiplex Oligos for Illumina and universal primers (E7335, NEB). The products were cleaned using 0.9×AMPure beads. The RNA library was prepared using the NEBNext Ultra II directional library prep kit (E7760, NEB) and DNA library by NEBNext ultra II DNA library prep kit (E7645, NEB) according to the manufacturer's instructions

treatment_protocol: SELEX: Six rounds of binding, elution, amplification, and enrichment were performed. ChIP/CLIP: The PEI transfection method was used for transfecting pcDNA3-DDX43-KH-FLAG pasmid DNA into HEK293T cells, and overexpression was confirmed by Western blotting using an anti-FLAG antibody. The pcDNA3 empty vector (containing 3×FLAG only) served as a control. The overexpressed protein was cross-linked with chromatin or RNA using formaldehyde (37%, 40 µL/mL of media) for 15 min and quenched with 1.5 M glycine (60 µL/mL).

tag: passage

tag: ip reagent

value: M2-FLAG beads (A2220, Sigma)


title: DDX43 KH 89aa 2_CLIP RNA

description: S00C5C7: DDX43 KH 89aa 2_CLIP RNA


title: DDX43 KH Negative control 2_CLIP RNA (No KH domain protein)

description: S00C5E2: Negative control 2_CLIP RNA


title: DDX43 KH Negative control 1_CLIP RNA (No KH domain protein)

description: S00C5DB: Negative control 1_CLIP RNA


title: DDX43 KH 89aa 2_ChIP

description: S00C5C1: DDX43 KH 89aa 2_ChIP


title: DDX43 KH 89aa Negative control 2_ChIP (No KH domain protein)

description: S00C5C5: Negative control 2_ChIP


title: DDX43 KH Negative control 1_ChIP (No KH domain protein)

description: S00C5C4: Negative control 1_ChIP


title: wt_e85_embryo_all.demultiplexed


title: RNA-seq_Dis_10

value: responder

value: fresh


title: RNA-seq_Dis_07


title: RNA-seq_Dis_03


title: RNA-seq_Dis_17


title: RNA-seq_Dis_16


title: RNA-seq_Dis_12


title: RNA-seq_Dis_15


title: RNA-seq_Dis_11


title: RNA-seq_Dis_01


title: DDX43 KH 89aa 1_CLIP RNA

description: S00C5C6: DDX43KH 89aa 1_CLIP RNA


title: DDX43-KH-89 DNA Negative Control (No KH domain protein)

description:
synthesized Oligo
S00C5BF: Negative control_DNA SELEX

molecule: other

organism: synthetic construct

source_name: Oligo library, TriLink Biotechnologies (O-32001-20)

tag: library

value: 20 nucleotide random sequences, 1x10e15

tag: amplification

value: PCR-amplified

value: Ni-NTA affinity beads


title: RNA-seq_Dis_02


title: Par_RNA_REP2

status: Public on Feb 01 2020

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

description:
STAR.counts.geo.txt
DESeq2.results.geo.txt
par.rna.merge.hg19.bw

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned using STAR aligner v2.7.0 to hg38 using standard parameters and quant mode for gene counts
Reads were aligned using STAR aligner v2.7.0 to hg19 using standard parameters for bigwig signal tracks
DEseq2 was used to determine differential gene expression using counts.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig (Merged), txt (DESeq2 results comparing metastatic sub-population and Par), txt (raw counts)

source_name: MDA-MB-231 breast cancer cell line

growth_protocol: Cells were grown in monolayer in DMEM + 10% FBS + Penicillin-streptomycin at 37ºC, 5% CO2 for 3 days for each replicate

extract_protocol:
Cells were harvested in QIAzol reagent, homogenized using QIAshredder, and RNA isolated using miRNeasy kit with on-column DNAse digestion
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina)

value: mammary gland/breast epithelial cell


title: RNA-seq_Dis_05


title: Par_RNA_REP3


title: Par_RNA_REP1


title: LM_RNA_REP3

description:
STAR.counts.geo.txt
DESeq2.results.geo.txt
lm.rna.merge.hg19.bw

source_name: MDA-MB-231 breast cancer cell line lung metastatic variant

value: MDA-MB-231 LM2


title: DDX43-KH-89 DNA SELEX

description:
synthesized Oligo
S00C5BE: DDX43 KH 89_DNA SELEX


title: LM_RNA_REP2


title: LM_RNA_REP1


title: RNA-seq_Dis_04


title: BrM_RNA_REP1

description:
STAR.counts.geo.txt
DESeq2.results.geo.txt
brm.rna.merge.hg19.bw

source_name: MDA-MB-231 breast cancer cell line brain metastatic variant

value: MDA-MB-231 BrM2


title: BrM_RNA_REP3


title: BrM_RNA_REP2


title: NACT tms077

status: Public on Jan 25 2020

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

value: Tissue

value: LumB Breast Cancer

tag: nact

value: Partial Regression

tag: t

tag: n

tag: age

tag: recist

value: PR


title: NACT tms090

tag: cell type

tag: tissue

value: Stabilization

value: SD


title: NACT tms046


title: NACT tms048


title: NACT tms094


title: NACT tms050


title: NACT tms078


title: NACT tms096


title: NACT tms047


title: NACT tms035


title: NACT tms042


title: NACT tms044


title: NACT tms032


title: NACT tms031


title: NACT tms033


title: NACT tms030


title: NACT tms029


title: NACT tms025


title: NACT tms023


title: NACT tms021


title: NACT tms018


title: NACT tms088


title: NACT tms014


title: NACT tms010


title: NACT tms013


title: Wild type MEFs [WT_2]

status: Public on Jan 01 2020

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

description: Actb +/+

data_processing:
Raw reads were analyzed using FastQC and quality trimmed using Trimmomatic with the parameters “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
Surviving paired reads were then aligned against the mouse reference genome (GRCm38) using Burrows-Wheeler Aligner BWA-MEM 9
BAM alignments were cleaned, sorted and deduplicated (PCR and Optical duplicates) with PICARD tools
RPKM normalized bamCoverage files were produced using deeptools2
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: bigwig files containing RPKM normalized ATAC-Seq signal for each sample

source_name: connective tissue - MEFs

growth_protocol: All MEFs  were cultured in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin (all from Millipore-Sigma), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Samples with 50,000 cells per condition were shipped in frozen medium (DMEM with 50 % FBS and 10% DMSO) on dry ice to Novogene (Beijing, China). All subsequent processing was performed by Novagene using standard DNA extraction and library preperation protocols
All processing was performed by Novagene (Beijing, China). Cell nuclei were isolated, mixed with Tn5 Transposase with two adapters and tagmentation was performed for 30 minutes at 37⁰C. The fragmented DNA was purified and amplified with limited PCR cycle using index primers. Llibraries were prepared according to recommended Illumina NovaSeq6000 protocols.

tag: strain

value: BALB/c

tag: genotype

value: wild type


title: Wild type MEFs [WT_1]

description: Actb +/+


title: β-actin heterozygous MEFs [HET_2]

description: Actb +/-

value: beta-actin heterozygous


title: β-actin heterozygous MEFs [HET_1]

description: Actb +/-


title: germinal center B cells, SAP5

status: Public on Dec 28 2019

city: Rehovot

first: Ziv

last: Shulman

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: tab-deimited text files
raw_counts.txt:  raw counts values for each sample
Deseq_all_results_umi.txt:  normalized abundance measurements and DESeq2 analysis

source_name: Peyer's patches

extract_protocol:
Peyer's patches were harvested and processed for flow cytometry analysis. Cell suspensions were stained and sorted into 50µl of lysis/binding buffer (Life Technologies). mRNA was captured with 12 ml of oligo(dT) Dynabeads (Life Technologies), washed, and eluted at 85°C with 10 µl of 10 mM Tris-Cl (pH 7.5).
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.
RNA sequencing 3' end

value: Peyer's patches

value: germinal center B cell

value: SAPKO


title: germinal center B cells, SAP6


title: germinal center B cells, SAP4


title: germinal center B cells, WT6

value: WT


title: germinal center B cells, WT5


title: β-actin knockout MEFs [KO_1]

description: Actb -/-

value: beta-actin knockout


title: germinal center B cells, SAP3


title: germinal center B cells, SAP1


title: germinal center B cells, WT3


title: germinal center B cells, WT4


title: germinal center B cells, WT2


title: germinal center B cells, WT1


title: First instar larval brain cells, Starvation condition (scRNAseq) 3 - sample 7

status: Public on Nov 15 2019

city: Fribourg

first: Simon

last: Sprecher

state: Fribourg

address: Chemin du Musée 10

department: Biology

institute: University of Fribourg

description: Sample 7

data_processing:
Sequenced libraries with processed with cell ranger pipeline (10X Genomics)
Each time, cell ranger count ran with the specific expected number of cells to recover.
Single datasets were later aggregated with cell ranger aggr pipeline.
Genome_build: The reference genome was built based on the 3rd 2018 FlyBase release (D. melanogaster r6.22)
Supplementary_files_format_and_content: Matrix files originated with cell ranger aggr pipeline

organism: Drosophila melanogaster

source_name: Brain cells

growth_protocol: All flies were kept at 25°C in a 12h/12h light-dark cycle in vials containing conventional cornmeal agar medium

extract_protocol:
Dissected brains in PBS were dissociated into single-cell suspensions by an enzimatic treatment with collagenase. mRNAs were obtained by applying 10X Genomics protocol for scRNAseq, Chromium Single Cell 3’ Library & Gel Bead Kit v2.
Libraries were constructed accoring to the manufacturer's guideline, for sequencing on a Illumina NovaSeq 6000
Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics)

treatment_protocol: Larvae were collected at 11 ALH, quickly washed to remove food leftovers and transferred to a Petri dish with 2% of agar, humidified with PBS, for 4 hours at 25 °C.

value: Wild type CS

tag: development stage

value: First instar larval

value: brain

tag: stress

value: starvation


title: First instar larval brain cells, Normal condition (scRNAseq) 4 - sample 6

description: Sample 6

value: control


title: β-actin knockout MEFs [KO_2]

description: Actb -/-


title: First instar larval brain cells, Normal condition (scRNAseq) 3 - sample 3

description: Sample 3

tag: developmental stage


title: First instar larval brain cells, Starvation condition (scRNAseq) 2 - sample 5

description: Sample 5


title: First instar larval brain cells, Starvation condition (scRNAseq) 1 - sample 4

description: Sample 4


title: Y317F4LZ

status: Public on Nov 13 2019

data_processing:
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019)
Reads were trimmed using Cutadapt and mapped to the Mus_musculus genome  using STAR v2.4.2a with default parameters.
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.txt: tab delimited files include raw counts values for each sample; Deseq_all_results_umi.txt:  normalized abundance measurements and DESeq2 analysis

source_name: popliteal lymph node

extract_protocol:
Popliteal lymph nodes from immunized chimeric mice were harvested and processed for flow cytometry analysis. Cell suspensions were stained and sorted into 50µl of lysis/binding buffer (Life Technologies). mRNA was captured with 12 ml of oligo(dT) Dynabeads (Life Technologies), washed, and eluted at 85°C with 10 µl of 10 mM Tris-Cl (pH 7.5).
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.

value: popliteal lymph node

tag: zone

value: LZ

value: germinal center B cells


title: Y317F2LZ


title: Y317F4DZ

value: DZ


title: First instar larval brain cells, Normal condition (scRNAseq) 2 - sample 2

description: Sample 2


title: Y317F1LZ


title: Y317F1DZ


title: germinal center B cells, SAP2


title: WT5DZ


title: WT5LZ


title: WT4DZ


title: WT3LZ


title: WT1LZ


title: WT3DZ


title: WT2DZ


title: HAECs_BEGM_ALI14_D267

status: Public on Sep 20 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Sample was prepared 14 days after air-liquid interface in BEGM medium. HAECs were cultivated as described in Revinsky et al. (Nature Communications, 2018). Cells were incubated with 0.10% protease type XIV from Streptomyces griseus in HBSS for 4 hours at 4°C degrees. Cells were  detached from the Transwells by pipetting and then transferred to a microtube. 50 units of DNase I per 250µl, were directly added and cells were further incubated at room temperature for 10 min. Cells were washed in 500 µL HBSS 10% Fetal Bovine Serum then in 500 µL HBSS before being mechanically dissociated through a 26G syringe (4 times). Finally, cell suspensions were filtered through a Scienceware® Flowmi™ Cell Strainer (40µm porosity), then centrifuged (150g for 5 min) and resuspended in 500 µL of cold HBSS. Cell concentration measurements were performed and 1500 cells were used for single-cell sequencing.

data_processing:
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger command used to produce output directory for each sample was executed using --cells=1000 and --transcriptome based on human genome release.GRCh37.p13
Cell Ranger aggregated dataset has been produced with default normalization method based on mapped reads.
BAM: cellranger possorted_genome alignment bam file
Genome_build: hg19
Supplementary_files_format_and_content: HDF5: cellranger filtered gene/barcode matrix.

source_name: Human airway epithellial cells differentiated in BEGM medium for 12 days

extract_protocol:
Samples were run on the Chromium machine from 10x Genomics following the  User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry).
Single cell RNA-Seq libraries were made following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry). Library was sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 57bp Read 2 (transcript), and 8bp i7 sample barcode for each scRNA-Seq library.

value: airway epithelial cells  (HAECs)

tag: differentiation day

tag: cell origin

value: Primary culture

tag: donor


title: WT2LZ


title: HAECs_BEGM_ALI14_D252


title: First instar larval brain cells, Normal condition (scRNAseq) 1 - sample 1

description: Sample 1


title: HAECs_BEGM_ALI14_D266


title: Control Sample 1 (snRNAseq)

status: Public on Sep 10 2019

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

description: snRNAseq

data_processing:
Count matrices were generated with zUMIs v2.0 and saved as .rds files
Seurat objects were created from the count matrices and filtered using min.cells=3 and low.thresholds=500 (Seurat v2.3.4)
Seurat objects from control and diabetic samples were combined using the RunMultiCCA function to generate combined.rds
Genome_build: GRCh38
Supplementary_files_format_and_content: individual rds files were generated from count matrices using zUMIs v2.0 and Seurat v2.3.4

source_name: Human Kidney

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 10e6 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Samples were cut into <2-mm pieces and homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and then centrifuged at 500×g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1× PBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-μm cell strainer (43–50020–50; pluriSelect), and counted.
Libraries were prepared according to Illumina's instructions and accompanying 10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit
Single Nucleus RNA Sequencing (snRNAseq)

value: kidney

tag: disease state

tag: gfr

tag: global glomerulosclerosis

value: None <10%

tag: ifta

tag: gender

value: M


title: F_Mef2c_fb1

status: Public on Sep 13 2019

first: Brynn

middle: Nicole-Yoshiko

last: Akerberg

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Fetal Mef2c-fbio ChIPSeq

data_processing:
fastq files were aligned to the mm9 genome using Bowtie2
bam files were sorted and blacklisted regions were filtered out from .bam files (samtools)
bigwig files were generated using peakcaller MACS2 and deeptools
Genome_build: mm9

source_name: dissected E12.5 mouse ventricle

extract_protocol:
Tissue was homogenized and crosslinked for 30', RT in 1% formaldehyde/1XPBS, quenched with 500mM glycine 5', RT and washed multiple times with 1XPBS.
KAPA HiFi Hyperprep library construction

value: mixed

value: dissected E12.5 mouse ventricle

tag: Stage

value: embryonic

tag: chip antibdoy

value: M280 Streptavidin Dynabeads


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C29 - VF95

status: Public on Aug 30 2019

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: small RNA

data_processing:
Fastq files were quality-checked using the FastQC software.
The QC-passed reads were clipped from the adapter sequences using Cutadapt by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15.
Trimmed reads were mapped with BWA algorithm v. 0.7.12 against an in-house reference of human sRNA sequences composed of 1,881 precursor hsa-miRNAs from miRBase v21; 32,826 hsa-piRNA sequences from piRBase v1.0; 5,171 hsa-sncRNAs sequences shorter than 80 bp from Database of Small Human non-coding RNAs (DASHR) database v1.0
The reads unmapped on these annotations were aligned against the human hg38 genome using BWA in default settings.
Differential expression analysis was performed with DESeq2 R package v.1.22.2 using the LRT function.
The sRNA-Seq reads not aligned on human annotations were mapped against microbial genomes using Kraken algorithm. Kraken was applied in default setting by considering bacteria, archaea, and viral genomes from NCBI.The Kraken output in Metaphlan format obtained with option –mpa-format was used in the analysis. For each taxonomic level, the number of reads assigned to microbial annotations by Kraken was converted in relative abundances using the total number of assigned reads.
The expression level of BSRD annotations was quantified using BWA by aligning human-unmapped reads against their sequence.
Genome_build: hg38
Supplementary_files_format_and_content: The processed tab-delimited files include the bacteria relative abundances computed using sRNA-Seq (Kraken) or metagenomic data (Metaphlan).

source_name: Stool sample

extract_protocol:
RNA was extracted using the Stool Total RNA Purification Kit (Norgen Biotek Corp). The RNA quality and quantity were verified according to the MIQE guidelines (http://miqe.gene-quantification.info/). The RNA concentration was quantified by Qubit with Qubit microRNA Assay Kit (Invitrogen).
Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA). For each sample, 250 ng of RNA was used as starting material to prepare libraries. Multiplex adapter ligations, reverse transcription primer hybridization, reverse transcription reaction and the PCR amplification were processed with regard to the protocol for library preparation. After PCR pre-amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol. Further quality control check and size selection were performed following the NEBNext Multiplex Small RNA Library Prep Protocol (Protocol E7330, New England BioLabs Inc., USA). A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) permitted to check DNA libraries final size, purity, and concentration.

value: Patient with colorectal carcinoma

tag: sample type

value: Stool sample


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C28 - VF77

description: small RNA


title: Control Sample 2 (snRNAseq)

description: snRNAseq

tag: tissue

tag: age


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C27 - VF73

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C26 - VF71

description: small RNA


title: Control Sample 3 (snRNAseq)

description: snRNAseq

value: F


title: Y317F2DZ

tag: strain

tag: genotype

tag: cell type


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C23 - VF29

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C22 - VF281

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C24 - VF300

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C21 - VF273

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C20 - VF270

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C17 - VF234

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C19 - VF264

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C16 - VF232

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C14 - VF216

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C15 - VF217

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C13 - VF208

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C12 - VF207

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C11 - VF192

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C9 - VF174

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C10 - VF176

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C8 - VF166

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C25 - VF65

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C6 - VF145

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C4 - VF114

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C3 - VF107

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C5 - VF120

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C2 - VF100

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C18 - VF251

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C1 - GF15

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A24 - VF69

description: small RNA

value: Patient with colorectal adenoma


title: sRNA-Seq of stool sample from the colorectal adenoma patient A25 - VF70

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A26 - VF90

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A27 - VF97

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A23 - VF66

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A22 - VF60

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A19 - VF50

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A20 - VF55

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A21 - VF56

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A18 - VF47

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A17 - VF38

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A16 - VF37

description: small RNA


title: sRNA-Seq of stool sample from the colorectal carcinoma patient C7 - VF154

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A15 - VF35

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A14 - VF32

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A13 - VF30

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A11 - VF214

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A12 - VF301

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A10 - VF197

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A9 - VF172

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A8 - VF102

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A6 - VF04

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A3 - GF17

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A7 - VF07

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A5 - VF02

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A4 - GF18

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A1 - GF12

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H24 - VF84

description: small RNA

value: Healthy subject


title: sRNA-Seq of stool sample from the healthy subject H22 - VF43

description: small RNA


title: sRNA-Seq of stool sample from the colorectal adenoma patient A2 - GF16

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H21 - VF40

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H19 - VF28

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H20 - VF31

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H23 - VF82

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H18 - VF279

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H17 - VF265

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H12 - VF255

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H13 - VF259

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H16 - VF263

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H10 - VF206

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H15 - VF262

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H11 - VF212

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H9 - VF18

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H8 - VF189

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H6 - VF170

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H4 - VF10

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H7 - VF171

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H3 - VF06

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H5 - VF140

description: small RNA


title: sRNA-Seq of stool sample from the healthy subject H1 - GF06

description: small RNA


title: LNCaP_NMYC_EtOH_d42_1

status: Public on Aug 26 2019

city: New York

first: Nicholas

last: Brady

state: NY

address: 1188 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to GRCh38 or GRCm38 using STAR
BAM file creation, sorting, and indexing were performed using SAMtools
Transcript abundances in FPKM were caluculated using Cufflinks
Genome_build: GRCh38 / GRCm38
Supplementary_files_format_and_content: Transcript abundances in FPKM caluculated using Cufflinks

source_name: LNCaP cells

growth_protocol: 22Rv1-N-Myc xenografts were injected into NU/J mice (Jackson Laboratories) and the animals were castrated when tumor size reached 150 mm^3. GEMM were created by crossing mice carrying an integrated CAG-LSL-MYCN gene at the Rosa26 locus with mice harboring homozygously-floxed Pten alleles and expressing Cre recombinase under the control of the probasin promoter. Castration was performed between 3 and 6 months of age. LNCaP-N-Myc and parental LNCaP cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco).

extract_protocol:
RNA extraction was performed using the NucleoSpin RNA Plus Extraction Kit (Macherey-Nagel) following the manufacturer’s recommendation.
Libraries were generated using the TruSeq RNA Library Prep Kit [Non-stranded, polyA+] (Illumina) following the manufacturer's recommended protocol.

treatment_protocol: For androgen deprivation, LNCaP or LNCaP-N-Myc cells were cultured in phenol-red-free RPMI medium (Gibco) supplemented with 5% charcoal-stripped serum (Gibco), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco) for 41 days. The medium was then supplemented with 10 nM DHT (Sigma-Aldrich) or equivalent volume of ethanol for 24 hours.

value: LNCaP cells

value: NMYC +

tag: treatment

value: EtOH

tag: timepoint

value: day 42


title: LNCaP_CTL_DHT_d42_1

value: CTL

value: DHT


title: GEMM_CTL-C-2

source_name: GEMM

treatment_protocol: For androgen deprivation, LNCaP or LNCaP-N-Myc cells were cultured in phenol-red-free RPMI medium (Gibco) supplemented with 5% charcoal-stripped serum (Gibco), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco) for 72 hours. The medium was then supplemented with 10 nM DHT (Sigma-Aldrich) or equivalent volume of ethanol for 24 hours.

value: GEMM

value: Pb-Cre+ ; Pten fl/fl

value: Castrated


title: LNCaP_CTL_DHT_d42_2


title: GEMM_NMYC-C-1

value: Pb-Cre+ ; Pten fl/fl ; MYCN +


title: LNCaP_NMYC_DHT_d42_2


title: GEMM_CTL-C-1


title: LNCaP_NMYC_DHT_d42_1


title: LNCaP_CTL_EtOH_d42_2


title: GEMM_NMYC-C-3


title: LNCaP_NMYC_EtOH_d4_1


title: GEMM_CTL-C-3


title: sRNA-Seq of stool sample from the healthy subject H14 - VF261

description: small RNA


title: LNCaP_CTL_EtOH_d4_3


title: LNCaP_NMYC_EtOH_d4_3


title: LNCaP_NMYC_EtOH_d4_2


title: LNCaP_NMYC_DHT_d4_3


title: sRNA-Seq of stool sample from the healthy subject H2 - VF00TL

description: small RNA


title: LNCaP_NMYC_DHT_d4_2


title: GEMM_NMYC-C-2


title: LNCaP_CTL_EtOH_d4_1


title: LNCaP_CTL_EtOH_d4_2


title: LNCaP_CTL_DHT_d4_3


title: LNCaP_NMYC_DHT_d4_1


title: 22RV1_NMYC-I-3

source_name: 22Rv1 xenografts

value: 22Rv1 xenografts

value: Intact


title: LNCaP_CTL_EtOH_d42_1


title: LNCaP_CTL_DHT_d4_2


title: LNCaP_NMYC_EtOH_d42_2


title: 22RV1_NMYC-I-2


title: 22RV1_NMYC-C-3


title: 22RV1_NMYC-C-1


title: 22RV1_NMYC-C-2


title: 22RV1_CTL-I-2


title: 22RV1_CTL-C-3


title: 22RV1_CTL-I-1


title: 22RV1_CTL-I-3


title: 22RV1_CTL-C-2


title: 22RV1_CTL-C-1


title: LNCaP_NMYC_EtOH_FOXA1_IP

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to GRCh38 using Bowtie2
BAM file creation, sorting, removal of PCR duplicates and indexing were performed using samtools
ChIP-seq peaks were called using MACS2 with input chromatin as the control for each set of data.
Genome_build: GRCh38
Supplementary_files_format_and_content: ChIP-seq signal (bedGraph) called by MACS2 using input chromatin as control

growth_protocol: LNCaP-N-Myc and parental LNCaP cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco). 22Rv1-N-Myc xenografts were injected into NU/J mice (Jackson Laboratories) and the animals were castrated when tumor size reached 150 mm^3. Organoids were cultured in prostate specific culture media composed of Advanced DMEM (Invitrogen) with GlutaMAX (1x, Invitrogen), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco), Primocin 100ug/mL (InvitroGen), B27 (Gibco), N-Acetylcysteine 1.25mM (Sigma-Aldrich), Mouse Recombinant EGF 50ng/mL (Invitrogen), Human Recombinant FGF-10 20ng/mL (Peprotech), Recombinant Human FGF-basic 1ng/mL (Peprotech), A-83-01 500nM (Tocris), SB202190 10uM (Sigma-Aldrich), Nicotinaminde 10mM (Sigma-Aldrich, (DiHydro) Testosterone 1nM (Sigma-Aldrich) PGE2 1uM (R&D Systems), Noggin conditioned media (5%) and R-spondin conditioned media (5%).

extract_protocol:
Cells were collected and crosslinked with 1% methanol-free formaldehyde for 10 minutes and fixation was quenched using 125 mM glycine for 8 minutes. The cell pellets were centrifuged and washed twice in cold PBS. Each pellet was resuspended in 1 ml of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors (Thermo Scientific)) and lysed for 20 minutes at 4°C. The nuclei were collected by centrifugation and resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors (Thermo Scientific)). The protein-bound chromatin was sheared by sonication (Diagenode, Bioruptor Pico). Input sheared chromatin was reserved as a control for downstream ChIP-seq analysis. Equal volumes of sheared chromatin were immunoprecipitated with specified antibodies.
Libraries were generated using the Hyper Prep Kit (Kapa Biosystems) following the manufacturer's recommended protocol.

treatment_protocol: For androgen deprivation, LNCaP or LNCaP-N-Myc cells were cultured in phenol-red-free RPMI medium (Gibco) supplemented with 5% charcoal-stripped serum (Gibco), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco) for 72 hours or 41 days. The medium was then supplemented with 10 nM DHT (Sigma-Aldrich) or equivalent volume of ethanol for 24 hours.

tag: chip antibody

value: FOXA1 (Abcam, ab23738)


title: PM154_H3K4me3_IP

source_name: PM154 organoids

value: PM154 organoids

value: H3K4me3 (Millipore, 17-678)


title: PM154_H3K27me3_IP

value: H3K27me3 (Abcam, ab6002)


title: LNCaP_CTL_DHT_HOXB13_IP

value: HOXB13 (Cell Signaling, 90944)


title: LNCaP_NMYC_DHT_FOXA1_IP

value: LNCaP cells


title: LNCaP_CTL_EtOH_HOXB13_IP


title: LNCaP_CTL_DHT_d4_1


title: LNCaP_NMYC_EtOH_HOXB13_IP


title: LNCaP_NMYC_DHT_HOXB13_IP


title: LNCaP_CTL_EtOH_d42_H3_Input


title: LNCaP_CTL_DHT_d42_H3K4me3_IP


title: LNCaP_CTL_EtOH_d42_H3K4me3_IP


title: LNCaP_CTL_EtOH_d42_H3K27me3_IP


title: LNCaP_CTL_DHT_d42_H3K27me3_IP


title: LNCaP_NMYC_EtOH_d42_H3_Input


title: 22RV1_NMYC-I-1

value: NMYC +


title: LNCaP_CTL_DHT_d42_H3_Input


title: LNCaP_NMYC_EtOH_d42_H3K27me3_IP

value: EtOH


title: LNCaP_NMYC_EtOH_d42_H3K4me3_IP


title: LNCaP_NMYC_DHT_d42_H3_Input


title: LNCaP_NMYC_DHT_d42_H3K27me3_IP


title: LNCaP_NMYC_DHT_d42_H3K4me3_IP


title: PM154_Input


title: PM154_NMYC_IP

value: MYCN (Santa Cruz, sc-53993)


title: 22Rv1-xeno_N-Myc_Intact_NMYC_IP_2


title: 22Rv1-xeno_N-Myc_Intact_NMYC_IP_1


title: 22Rv1-xeno_N-Myc_Intact_Input_2


title: 22Rv1-xeno_N-Myc_Intact_Input_1


title: 22Rv1-xeno_N-Myc_Castrated_Input_2


title: 22Rv1-xeno_N-Myc_Castrated_NMYC_IP_2


title: LNCaP_CTL_EtOH_d4_H3K27me3_IP


title: 22Rv1-xeno_N-Myc_Castrated_Input_1


title: LNCaP_CTL_EtOH_d4_H3_Input


title: LNCaP_CTL_DHT_d4_H3K27me3_IP


title: LNCaP_CTL_DHT_d4_H3K4me3_IP


title: LNCaP_CTL_DHT_d4_H3_Input


title: LNCaP_N-Myc_EtOH_d4_H3K4me3_IP


title: LNCaP_N-Myc_DHT_d4_H3K4me3_IP


title: LNCaP_N-Myc_DHT_d4_H3K27me3_IP


title: LNCaP_N-Myc_EtOH_d4_H3K27me3_IP


title: LNCaP_CTL_DHT_NMYC_IP


title: LNCaP_CTL_DHT_Input


title: LNCaP_N-Myc_DHT_d4_H3_Input


title: LNCaP_CTL_EtOH_NMYC_IP


title: LNCaP_CTL_EtOH_Input


title: LNCaP_N-Myc_EtOH_d4_H3_Input


title: LNCaP_N-Myc_EtOH_Input_1


title: LNCaP_N-Myc_EtOH_Input_2


title: 22Rv1-xeno_N-Myc_Castrated_NMYC_IP_1


title: LNCaP_N-Myc_EtOH_NMYC_IP_1


title: LNCaP_N-Myc_EtOH_NMYC_IP_2


title: LNCaP_CTL_EtOH_d4_H3K4me3_IP


title: LNCaP_N-Myc_DHT_Input_2


title: LNCaP_N-Myc_DHT_NMYC_IP_1


title: QXT64

status: Public on Jun 27 2019

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
Library strategy: gDNA capture-seq
R1 and R2 reads were mapped to the mm9 genome separately, each both in under settings that only allows non-duplicated, uniquely mappable reads (Bowtie -m 1 --best --strata; samtools rmdup -s) and under settings that allows multimapping and duplicated reads (Bowtie --best).
Of the multimapping reads, only reads that overlap (min. 50% of read) with RLTRETN, MMETn-int, ETnERV-int, ETnERV2-int or ETnERV3-int repeats were kept.
Non-duplicated and uniquely mappable reads whose paired read partners were overlapping ETn repeats were then clustered (as bed files) using bedtools (bedtools merge -i -n -d 1000) to receive a list of all potential annotated and non-annotated new ETn insertions.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with clustered ETn-paired reads

source_name: tail

extract_protocol:
Genomic DNA was purified from Proteinase K digested lysates using the gDNA Clean & Concentrator kit (Zymo)
Libraries were constructed and enriched using the SureSelectQXT Target Enrichment kit (Agilent) and custom RNA capture probes complementary to ETn LTRs.

value: tail

tag: mouse id

tag: Sex

value: M

value: Chr2-cl KO/KO

tag: ancestry


title: LNCaP_N-Myc_DHT_NMYC_IP_2

value: DHT


title: QXT63

value: Chr4-cl KO/KO


title: QXT62

value: F


title: QXT56

source_name: ear

value: ear


title: QXT57


title: QXT61


title: QXT60

value: Chr2-cl WT


title: QXT59


title: QXT54


title: QXT55


title: QXT52


title: QXT21


title: QXT45


title: QXT30

value: Chr4-cl WT


title: QXT28


title: QXT18

source_name: spleen

value: spleen


title: QXT17


title: LNCaP_N-Myc_DHT_Input_1


title: QXT11

value: Chr4-cl KO/WT


title: QXT12


title: QXT6

source_name: blood

value: blood


title: SL143962: SH-SY5Y 100 uM Mn

status: Public on Jun 20 2019

city: Atlanta

first: Dean

middle: P.

last: Jones

address: 615 Michael Street Room 205

department: Department of Medicine

institute: Emory University

data_processing:
Initial RNA samples were poly(A) selected to eliminate rRNA, and the cDNA library was prepared using random hexamers and further ribosomal depletion. The platform used for sequencing was the Illumina HiSeq 2500 that ran technical replicates (4 forward and 4 reverse) for each of the 18 samples in pair-end mode. This resulted in 144 raw .fastq files.
Initial data quality control was performed using the 104 FASTQC tool (Babraham Bioinformatics, version 0.11.4 (Andrews, 2010)). Following quality control and assurance of technically sound sequencing files, the trimming of the low-quality read-ends was executed to ensure a Phred score > 30. The trimming was completed with the TrimGalore!  tool (Babraham Bioinformatics, version 0.4.1 (Krueger)). The trimmed reads were then aligned to the human genome (December 2013, hg38) with the STAR alignment algorithm, version 2.5.2a 109 (Dobin et al., 2013), and by using the RefSeq annotation of genes downloaded from the UCSC genome browser (http://genome.ucsc.edu/index.html).
The read counts were then calculated using HTSeq, version 0.6.1 (Anders et al., 2015) with the default union mode. In total, 39,287 transcripts were detected.
The read counts were normalized by the variance stabilization transformation as implemented in the DESeq2 R/Bioconductor package (Love 114 et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

molecule: polyA RNA

source_name: SH-SY5Y cells -ATCC

growth_protocol: SH-SY5Y, human neuroblastoma cell line, obtained from the American Type Culture Collection (ATCC-Manassas, VA) were cultured as previously described (PMID: 30715528, PMID: 29684492, PMID: 27701121)

extract_protocol:
Total RNA was extracted and isolated using miRNeasy Mini Kit (Qiagen). Quality control analyses were performed for each of the samples and were acceptable for downstream sequencing if they met the following criteria: 260/280 ratio (nucleic acid purity) > 2 and RIN score (RNA Integrity number) > 8.5
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SH-SY5Y, human neuroblastoma cell line, obtained from the American Type Culture Collection (ATCC-Manassas, VA) were exposed to Mn dose as previously described (PMID: 30715528, PMID: 29684492, PMID: 27701121)

tag: cell line

value: neuroblastoma

tag: mn_treatment (um)

tag: passage

tag: sample id


title: SL143961: SH-SY5Y 50 uM Mn


title: QXT58

value: Chr2-cl KO/WT


title: SL143958: SH-SY5Y 1 uM Mn


title: SL143960: SH-SY5Y 10 uM Mn


title: SL143959: SH-SY5Y 5 uM Mn


title: SL143956: SH-SY5Y 100 uM Mn


title: SL143955: SH-SY5Y 50 uM Mn


title: SL143954: SH-SY5Y 10 uM Mn


title: SL143957: SH-SY5Y no Mn


title: QXT51


title: QXT53


title: SL143953: SH-SY5Y 5 uM Mn


title: SL143952: SH-SY5Y 1 uM Mn


title: SL143950: SH-SY5Y 100 uM Mn


title: QXT29


title: SL143951: SH-SY5Y no Mn


title: SL143963: SH-SY5Y 50 uM Mn


title: QXT9


title: SL143948: SH-SY5Y 5 uM Mn


title: QXT5


title: QXT10


title: WT, Aged uterus, replicate2

status: Public on Jun 19 2019

city: Fukuoka

first: Teruhiko

last: Kawamura

address: Maidashi 3-1-1,  Higashi-ku

department: Obstetrics and Gynecology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

data_processing:
RNA-sequencing reads were trimmed to remove adaptor sequences and low-quality bases by fastp (Chen et al., 2018) and mapped to the GRCm38 reference genome using STAR (Dobin et al., 2013). Mapped reads were assigned to all exons using featureCounts (Liao et al., 2014). The normalized expression levels of genes as cpm values were generated and the differential analysis was conducted using the Bioconductor package edgeR (Robinson et al., 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample

source_name: 60-75 weeks of age WT mouse, uterus

growth_protocol: Healthy wild type (WT) C57BL/6J mice at 5, 8, 60-75 and 79-week-old were obtained from CLEA Japan, Inc. The mice were housed in groups of five at 23±3 ºC and 55±15% humidity under a 12 h/12 h light/dark cycle. They were maintained in a P2 level area for recombinant DNA experiments

extract_protocol:
Tissue slices were homogenized using a BioMasher®II (Wako Pure Chemical, Osaka, Japan) or TRIzol Reagent (Invitrogen) prior to purification of total RNA using an RNeasy® Mini Kit (QIAGEN, Hilden, Germany) or SV Total RNA Isolation System (Promega) according to the manufacturer’s protocol.
cDNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA). Sequencing was performed using HiSeq1500 (Illumina) with a single-read sequencing length of 60bp. Cluster amplification and 150 bp paired-end sequencing was performed according to the manufacturer’s protocol (Illumina) for NovaSeq 6000 (Illumina).

treatment_protocol: To induce estrus cycles, 5 or 7.5 units of pregnant mare serum gonadotropin (PMSG; Serotropin, ASKA Animal Health Co., Ltd., Tokyo, Japan) were injected into the abdominal cavity 48 hours before uterine dissection. After the euthanasia by cervical dislocation, their uteri were resected and each uterine horn was divided in half. One half was cut into 5 mm slices, transferred to RNAlater® Stabilization Solution (Thermo Fisher Scientific, Waltham, MA, USA) and stored at -80 ºC for RNA isolation.

value: wild type

value: 60-75 weeks (old)

value: whole uterus


title: SL143947: SH-SY5Y 1 uM Mn


title: WT, 8 weeks of age uterus, replicate 2

source_name: 8 weeks of age WT mouse, uterus

value: 8 weeks


title: WT, Aged uterus, replicate1


title: WT, 8 weeks of age uterus, replicate 1


title: WT, 5 weeks of age uterus, replicate 2

source_name: 5 weeks of age WT mouse, uterus

value: 5 weeks


title: heart_rnaseq_mkmyn_c

status: Public on May 31 2019

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St, 4A

institute: Gladstone Institutes

data_processing:
Illumina Casava v1.8 was used for basecalling.
Reads were trimmed and aligned with STAR (v2.5.2).
Transcritps were quantified using Cufflinks (v2.2.1) and differential expression was computed using Cuffdiff (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: cuffdiff output; normalized abundance estimates and differential expression

extract_protocol:
The Zymo Direct-zol kit was used to extract RNA and DNaseI was used to eliminate residual DNA.
Takara Stranded Total RNA Sample Prep (cat# 634876)

treatment_protocol: The atria were trimmed off and the Next Advance Bullet Blender was used to dissociate the remaining mouse ventricular tissue.

tag: genotype/variation

value: triple mutant

tag: timepoint/age

value: post natal day 7

value: heart ventricular tissue


title: heart_rnaseq_mkmyn_b

tag: tissue


title: heart_rnaseq_mkmy_b

value: double mutant


title: heart_rnaseq_mkmy_a


title: heart_rnaseq_wt_b


title: WT, 5 weeks of age uterus, replicate 1

tag: age


title: heart_rnaseq_mkmyn_a

tag: strain


title: 3132_Rep_A

description:
norm_counts_by_rep.txt
dau3132_0

data_processing:
Illumina Casava v1.8 was used for basecalling.
The 3' end of the reads were trimmed with cutadapt and aligned with Bowtie 2 (v2.2.4)
Transcritps were quantified using Cufflinks (v2.2.1) and differential expression was computed using Cuffdiff (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: normalized counts table, reported for each replicate

source_name: hiPSC derived cardiomyocytes

tag: disease state

value: childhood-onset left ventricular non-compaction (LVNC)

value: hiPSC derived cardiomyocytes


title: 3132_Rep_B

description:
norm_counts_by_rep.txt
dau3132_1

tag: cell type


title: 3132_Rep_C

description:
norm_counts_by_rep.txt
dau3132_2


title: 254_Rep_B

description:
norm_counts_by_rep.txt
mom254_1

value: unaffected


title: SL143949: SH-SY5Y 10 uM Mn


title: 254_Rep_A

description:
norm_counts_by_rep.txt
mom254_0


title: 254_Rep_C

description:
norm_counts_by_rep.txt
mom254_2


title: 113_Rep_B

description:
norm_counts_by_rep.txt
dad113_1

value: asymptomatic


title: SL143946: SH-SY5Y no Mn


title: 113_Rep_C

description:
norm_counts_by_rep.txt
dad113_2


title: 113_Rep_A

description:
norm_counts_by_rep.txt
dad113_0


title: Hu1113.RIP.Ctrl

status: Public on Mar 01 2019

city: Indianapolis

first: Debbie

middle: Carolyn

last: Thurmond

state: IN

address: 635 Barnhill Drive, MS 2031

department: Pediatrics

institute: Indiana University

description:
RNA-Seq data, Islets from Donor 12 , GFP Vector Control
Stranded, polyA library

data_processing:
RTA v1.18.64 and bcl2fastq v2.18 was used to base calling and FASTQ generation.
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).  For unstranded counts, strand was to "no" for "Unstranded" counts / FPKM (and strand was set to "reverse" for "Stranded" counts / FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

source_name: Islets from Hu1113 , GFP Vector Control

growth_protocol: human islets were cultured in CMRL, 10% FBS and 1% PSG

extract_protocol:
RNAs were isolated by qiagen RNAeasy plus mini Kit
for samples 1-2: TruSeq unstranded polyA kit, for samples 3-8: KAPA stranded polyA kit
for samples 1-2: unstranded polyA RNA-Seq, for samples 3-8: stranded polyA RNA-Seq

treatment_protocol: 100 moi of adenoviral particles conferring beta cell specific expression of STX4, compared tosimilar moi of control adenovirus (same vector backbone) were applied to human islets for 1 hr. Cells were then washed to remove excess adenovirus and growth media applied for 2 days.

tag: treatment

value: GFP Vector Control

tag: subject

tag: disease status

value: Non-Diabetics

tag: delivery vector

value: AdRIP