title: m3_Aged_F6_new_384

description: Aged (19 month old)


title: CicsfGFP_ChIP_rep1

status: Public on Mar 05 2020

type: SRA

city: Princeton

first: Stanislav

middle: Y

last: Shvartsman

state: NJ

address: Carl Icahn Lab, Washington Road

department: Chemical and Biological Engineering

country: USA

institute: Princeton University/ Lewis-Sigler Institute for Integrative Genomics

library_source: genomic

data_processing:
Reads were trimmed for adaptors using Galaxy: TrimGalore!
Reads were mapped to the drosophila dm6 genome using Galaxy: BWA-MEM, Version: 0.7.17-r1188, -t 6 -v 1
SAMtools view (Galaxy Version 1.9) was used to remove reads with a quality score lower than 20.
PicardMarkDuplicates (Galaxy version  2.18.2.1) was used to remove duplicates from each sample
Replicate BAM files were merged into a single BAM files using SAMtools
Peaks were called using MACS2 (Zhang et al. 2008), parameters: -q 0.01 --keep-dup all –nomodel –extsize 145.  Peak calling control was OreR ChIP replicates.  we only considered peaks with a log2(fold change) of 5 or greater
Other analysis was done using several R packages including: GenomicRanges and ChIPSeeker.  Many peaks called by MACS2 had low read counts and we did not trust these in our analysis as true Cic targets.  Therefore, we only considered peaks with a log2(fold change) of 5 or greater.  Additionally, we only kept peaks in chromosomes: 2R, 2L, 3R, 3L, 4, and X.  Lastly, we removed peaks found in the dsor1 and rl coding regions as our lab consistently clones with these genes, and they were suspected to be contamination.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files were generated using R.  Coverage of reads across 10 bp windows of the genome were determined using the coverage function in the GenomicRanges package. Scores represent counts per million total read counts in that condition

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryo

growth_protocol: Embryos were collected for 3-4 hours in the dark.  After fixation, embryos that were at NC 14 were selected from the general pool.  Stage was determined based on nuclear density and membrane length

extract_protocol:
Embryos were sonicated 7 times, 20 seconds each, at 20% output.  Cic-DNA complexes were isolated using magnetic protein G dynabead and GFP antibody.  DNA was uncrosslinked from protein and purified.
Purified ChIP and input DNA were prepared for Illumina sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S).  The primers used for multiplexing the library came from the NEBNext Multiplex Oligos for Illumina Kit (E7335S).

treatment_protocol: Embryos were dechorionated in bleach in red light (keeps optogenetic constructs turned off) for 2 minutes.  Embryos were exposed to blue light for varying lengths of time (dependent on condition).  They were then fixed in a mixture of paraformaldehyde, PBS/0.5% TritonX-100, and heptane for 15 minutes

tag: tissue

value: embryo

tag: chip-antibody

value: GFP (Millipore, AB3080)

tag: embryonic stage

value: early nuclear cycle 14

tag: genotype


title: m3_Aged_E5_new_384

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

description: Aged (19 month old)

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table, genes X cells

molecule: total RNA

organism: Mus musculus

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: primary murine brain endothelial cells


title: m3_Young_I23_new_384

description: Young (3 month old)


title: m3_Aged_F17_new_384

description: Aged (19 month old)


title: ORGN-Lgr5-plate09-unlabeled

city: Utrecht

first: Nico

last: Battich

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 5-ethymyluridin labeling

data_processing:
Library strategy: scEU-Seq
Read 2 of Sequencing liberties were using STAR 2.5 with default parameters. If the length of the poly-T track in read 1 was less than 19 bases, the read was discarded.
Genome_build: ensemble release 90 of the homo sapiens GRCh38 genome, extended with ERCC92 spike-ins and ensemble release 90 of the mus musculus GRCm38 genome, extended with ERCC92 spike-ins
Supplementary_files_format_and_content: The number of UMI count per gene was obtained by pooling all reads mapping to the same gene and having the same cell barcode as previously (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637) using only uniquely mapped reads. The minimal number of UMI detected in a cell for the RPE1-FUCCI cell-cycle analysis was of 2,300, while the threshold used for murine in intestinal organoid cells was of 1,000. The UMI for a given gene in a cell was considered to be unspliced if at least one base of any read belonging to that UMI mapped outside of the exons of the gene.

molecule: polyA RNA

source_name: Intestinal organoids treated with DSMO for 120 min, with EU for 120 minutes, or EU for ~22 hours with a U chase 0, 45 or 360 minutes

growth_protocol: RPE1-FUCCI cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/F12, supplemented with GlutaMAX (Gibco), FBS (Gibco), and penicillin/streptomycin (Gibco), following standard procedures. Organoids were expanded in medium termed ENR, consisting of Advanced Dulbecco’s modified Eagle’s medium/F12 (Advanced DMEM) with HEPES (10mM, Sigma), penicillin/streptomycin (1x, Thermofisher) and Glutamax. Advanced DMEM was supplemented with 1x B27 (Thermofisher), 1 mM N-acetylcysteine (Sigma), 50 ng/ml murine recombinant epidermal growth factor (PeproTech), R-spondin 1 conditioned medium (5% of final volume) and Noggin conditioned medium (5% of final volume) to generate ENR medium. To generate conditioned media, HEK293T cells were stably transfected with Rspo1-Fc (gift from Calvin Kuo, Stanford University) or transient transfection with mouse Noggin-Fc expression vector and grown for 1 week in Advanced DMEM supplemented with penicillin/streptomycin, and Glutamax. Organoids were plated in Reduced Growth Factor Basement Membrane Matrix (BME) Type 2 (Trevigen)

extract_protocol:
After incubation with EU, cells were dissociated, fixed with paraformaldehyde, and azide-biotin was clicked in situ after cell permeabilization to mark EU-labeled RNA. We then sorted single cells in 384-well plates and performed first strand synthesis with poly-T primers containing a cell barcode, a unique molecular identifier, a 5’ sequencing adapter, and the T7 promoter. Cells were pooled and streptavidin magnetic beads were used to separate EU labeled and unlabeled mRNA/cDNA hybrids. Library preparation was performed for both fractions separately.
Runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode. Illumina TruSeq adapaters

treatment_protocol: Cells were incubated with the EU and/or DMSO for the desired time (e.g. 60 min). The final concentration of EU was 200 µM for RPE1-FUCCI chase experiments, 400 µM for RPE1-FUCCI pulse experiments, 166 µM for chase experiments in organoids and 1.6 mM for pulse experiments in Organoids. The U chase phase of the was done with 400 µM U. Cells were dissociated using TrypLE enzyme mix (Gibco) and mechanical sheering if required.

tag: cell line

value: Murine intestinal organoids, Lgr5DTR-eGFP line

tag: genetic tag


title: ORGN-Lgr5-plate10-unlabeled

description: 5-ethymyluridin labeling


title: ORGN-Lgr5-plate08-unlabeled

description: 5-ethymyluridin labeling


title: CAOV2P_siYAP-12: CAOV2 primary ovarian cancer cells; biological replicate #3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to mm9 reference genome using Hisat2 with default parameters
Quntification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include results of differential analysis using DESeq2.

organism: Homo sapiens

growth_protocol: CAOV2 ovarian cancer cells were grow in DMEM media (11995-DMEM, ThermoFisher Scientific) and supplement with 10% heat-inactivated fetal bovine serum (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, #74104) according to the manufacturer's instructions.
1μg of total RNA was used to generate cDNA library with Illumina TruSeq Stranded mRNA LT Sample Prep Kit – Set A (Illumina, RS-122-2101) according to manufacturer’s instructions.

treatment_protocol: Human ovarian cancer cells (1x10^5 CAOV2 cells) were seeded in a well on 6-well plate and transfected with 100 pmole of siRNAs (YAP silencing (siYAP): D-012200, Dharmacon; or non-targeting siRNA control (siNT): AllStars Negative Control siRNA, SI03650318) and 6μL of Lipofectamine RNAiMAX (ThermoFisher Scientific, #13778150) reagent for 2 days. Cells were collected at day 3 for RNAseq.

value: ovarian cancer cell line

tag: genotype/variation

value: siRNA targeting YAP (siYAP)


title: CAOV2P_siYAP-11: CAOV2 primary ovarian cancer cells; biological replicate #2


title: m3_Aged_B19_new_384

description: Aged (19 month old)


title: m3_Young_G11_new_384

description: Young (3 month old)


title: CAOV2P_siYAP-9: CAOV2 primary ovarian cancer cells; biological replicate #1


title: m3_Aged_F18_new_384

description: Aged (19 month old)


title: m3_Aged_J12_new_384

description: Aged (19 month old)


title: m3_Aged_K20_new_384

description: Aged (19 month old)


title: m3_Aged_G17_new_384

description: Aged (19 month old)


title: m3_Aged_B8_new_384

description: Aged (19 month old)


title: m3_Aged_N9_new_384

description: Aged (19 month old)


title: ORGN-Lgr5-plate07-unlabeled

description: 5-ethymyluridin labeling


title: m3_Young_G22_new_384

description: Young (3 month old)


title: CAOV2P_siNT-2: CAOV2 primary ovarian cancer cells; biological replicate #1

source_name: CAOV2 primary ovarian cancer cell

value: non-targeting siRNA


title: ORGN-Lgr5-plate05-unlabeled

description: 5-ethymyluridin labeling


title: CAOV2P_siNT-3: CAOV2 primary ovarian cancer cells; biological replicate #2


title: m3_Aged_N21_new_384

description: Aged (19 month old)


title: m3_Aged_H5_new_384

description: Aged (19 month old)


title: ORGN-Lgr5-plate03-unlabeled

description: 5-ethymyluridin labeling


title: ORGN-Lgr5-plate06-unlabeled

description: 5-ethymyluridin labeling


title: ORGN-Lgr5-plate04-unlabeled

description: 5-ethymyluridin labeling


title: m3_Young_B14_new_384

description: Young (3 month old)


title: ORGN-Lgr5-plate02-unlabeled

description: 5-ethymyluridin labeling


title: TB40 Exp 3 72 h Flavo

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

description: other: nascent RNA

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils
hg38 bigwigs were uploaded to the UCSC genome browser.
Custom UCSC track hubs were set up for Towne and TB40 data.
For analysis of host transcription effects upon infection or depletion of IE2 and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. truQuant source code is avaliable on GitHub at https://github.com/meierjl/hubs/tree/master/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne, KF297339.1 (HCMV TB40), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups. BED file contains an annotation of human gene bodies queried for effects on transcription.

source_name: HCMV-infected primary human foreskin fibroblast

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Nuclei isolation was carried out as described in Ball et. al. (2019, PMID: 30743000) and Parida et. al. (2019, PMID: 30755505).
PRO-Seq library preparation to extract and sequence nascent RNAs is carefully detailed in the manuscript and was carried out as previously described by Parida et. al. (2019, PMID: 30755505), with noted modifications.
Other: PRO-Seq

treatment_protocol: HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: hcmv strain

tag: infection duration

value: 72 hours

tag: sequencing method

value: PRO-Seq


title: m3_Aged_K11_new_384

description: Aged (19 month old)


title: m3_Young_G17_new_384

description: Young (3 month old)


title: ORGN-Lgr5-plate01-unlabeled

description: 5-ethymyluridin labeling


title: CAOV2P_siNT-4: CAOV2 primary ovarian cancer cells; biological replicate #3


title: TB40 Exp 3 24h Flavo

description: other: nascent RNA

value: 24 hours


title: m3_Young_L23_new_384

description: Young (3 month old)


title: m3_Aged_O18_new_384

description: Aged (19 month old)


title: 10_TAL1

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description: Treatment with adenoviruses expressing ETS1, SOX18, SOX7 and TAL1 at 20 MOI for 48h

data_processing:
Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the human genome assembly using STAR read aligner v2.5.2a
RefSeq annotated genes were quantified with samtools v1.5 and in-house scripts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene

growth_protocol: Expansion medium consisting of StemPro with 50 ng/mL of VEGFA was used for the first cell division, after which cells were cultured using VascuLife VEGF Endothelial Medium Complete Kit (LifeLine Cell Technology). The final composition of supplements added to the media was as follows: 10% FBS, 4 mM L-glutamine, 0.75 U/mL heparin sulfate, 5 ng/mL FGF-2, 5 ng/mL EGF, 5 ng/mL VEGFA, 15 ng/mL IGF1, 1 µg/mL hydrocortizone hemisuccinate, and 50 µg/mL Ascorbic acid. SB431542 (10 µM) was supplemented to the media.

extract_protocol:
Cultured ECs were lysed using 350 μL RLT lysis buffer (Qiagen) with β-mercaptoethanol (1%) and subsequently vortexed for 1 min at room temperature before snap freezing. RNA was isolated from cell lysates using an automated Maxwell Total RNA purification kit (Promega) with DNAse I digestion.
Total RNA was subjected to oligo (dT) capture and enrichment, and the resulting mRNA fraction was used to construct cDNA libraries. Sequencing was performed on an Illumina HiSeq 4000 platform using the standard protocol (TruSeq Stranded Total RNA Library, Illumina) that generates approximately 30 million reads of 50 base pairs per sample.

treatment_protocol: Cells were treated with adenovirus for 48h at MOI 20 or 80.

value: Pluripotent stem-cell derived endothelial cells

tag: sample label

tag: treatment

tag: replicate


title: m3_Aged_J19_new_384

description: Aged (19 month old)


title: TGCGGC: hair_cells_wt_4H11

city: Neuherberg

first: Hernán

last: López-Schier

address: Ingolstaedter Landstr. 1

department: Research Unit Sensory Biology and Organogenesis

country: Germany

institute: Helmholtz Zentrum München

description: Libraries were constructed using the mcSCRB-seq protocol (see Bagnoli et al., 2018)

data_processing:
Fastq reads were processed with the zUMIs pipeline version 0.2.0 (Parekh et al., 2018)
cDNA reads were aligned to the Zebrafish Genome (GRCZ11) with STAR_2.6.0a
Quantification was done with ENSEMBL gene model (GRCz11.94)
Genome_build: Zebrafish: GRCz11, Ensembl 94
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

organism: Danio rerio

source_name: zebrafish neuromast hair cells

growth_protocol: Standardized conditions at 28.5°C in the 0,3 x Danieau’s solution.

extract_protocol:
Enzymatic dissociation of larval trunks and isolation of green fluorescent protein-expressing cells by FAC-sorting.
mcSCRB-seq (Bagnoli et al., 2018)

value: zebrafish neuromast hair cells

tag: developmental day

value: 6 days post fertilization


title: 09_TAL1

source_name: adenoviruses expressing ETS1, SOX18, SOX7 and TAL1 at 20 MOI for 48h


title: m3_Aged_P20_new_384

description: Aged (19 month old)


title: m3_Aged_L15_new_384

description: Aged (19 month old)


title: m3_Aged_H8_new_384

description: Aged (19 month old)


title: TCGGCG: hair_cells_wt_4H10


title: 08_TAL1


title: m3_Aged_N10_new_384

description: Aged (19 month old)


title: TB40 Exp 3 72h Flavo PFA

description: other: nascent RNA


title: m3_Young_A6_new_384

description: Young (3 month old)


title: 07_LEF1

description: Treatment with adenoviruses expressing ETS1, SOX18, SOX7 and LEF1 at 20 MOI for 48h


title: 06_LEF1

source_name: adenoviruses expressing ETS1, SOX18, SOX7 and LEF1 at 20 MOI for 48h


title: GTCGGC: hair_cells_wt_4H8


title: TCCCCG: hair_cells_wt_4H9


title: m3_Young_F17_new_384

description: Young (3 month old)


title: m3_Aged_O15_new_384

description: Aged (19 month old)


title: m3_Aged_H6_new_384

description: Aged (19 month old)


title: GGTGCG: hair_cells_wt_4H7


title: m3_Young_J11_new_384

description: Young (3 month old)


title: GCGGGA: hair_cells_wt_4G11


title: m3_Aged_I22_new_384

description: Aged (19 month old)


title: 04_Ctrl

description: Treatment with adenovirus 80 MOI expressing empty vector for 48h (control)

value: Ctrl


title: m3_Aged_O14_new_384

description: Aged (19 month old)


title: GCGCGT: hair_cells_wt_4G10


title: m3_Aged_G4_new_384

description: Aged (19 month old)


title: m3_Young_C21_new_384

description: Young (3 month old)


title: m3_Aged_G21_new_384

description: Aged (19 month old)


title: 03_Ctrl

source_name: adenovirus 80 MOI expressing empty vector for 48h


title: m3_Aged_D12_new_384

description: Aged (19 month old)


title: GCGACG: hair_cells_wt_4G9


title: 02_Ctrl


title: m3_Aged_G8_new_384

description: Aged (19 month old)


title: GCCGGT: hair_cells_wt_4G8


title: m3_Aged_A13_new_384

description: Aged (19 month old)


title: GCCCGA: hair_cells_wt_4G7


title: m3_Aged_J22_new_384

description: Aged (19 month old)


title: CGGTCC: hair_cells_wt_4F12


title: empty(AOGG-60)

description: treatment with adenovirus 80 MOI expressing empty vector for 48h

treatment_protocol: Cells were treated with adenovirus for 48h at MOI 80.

value: CONTROL


title: m3_Young_D21_new_384

description: Young (3 month old)


title: m3_Young_N6_new_384

description: Young (3 month old)


title: m3_Young_K10_new_384

description: Young (3 month old)


title: CGGCAC: hair_cells_wt_4F10


title: empty(AOGG-61)


title: TAL1(AOGG-100)

description: treatment with adenovirus 80 MOI expressing TAL1 for 48h


title: 01_Ctrl


title: TAL1(AOGG-99)

source_name: adenovirus 80 MOI expressing TAL1 for 48h


title: CGCTCG: hair_cells_wt_4F9


title: m3_Young_C11_new_384

description: Young (3 month old)


title: m3_Young_H23_new_384

description: Young (3 month old)


title: m3_Young_I20_new_384

description: Young (3 month old)


title: m3_Aged_C19_new_384

description: Aged (19 month old)


title: m3_Aged_P23_new_384

description: Aged (19 month old)


title: CGGGAG: hair_cells_wt_4F11


title: m3_Young_F11_new_384

description: Young (3 month old)


title: 05_LEF1


title: empty(AOGG-59)


title: m3_Young_J19_new_384

description: Young (3 month old)


title: CGCGAC: hair_cells_wt_4F8


title: TAL1(AOGG-98)


title: m3_Aged_E18_new_384

description: Aged (19 month old)


title: m3_Aged_F9_new_384

description: Aged (19 month old)


title: m3_Aged_F22_new_384

description: Aged (19 month old)


title: m3_Aged_G13_new_384

description: Aged (19 month old)


title: SOX7(AOGG-71)

description: treatment with adenovirus 80 MOI expressing SOX7 for 48h


title: CCAGGG: hair_cells_wt_4E12


title: CACGCG: hair_cells_wt_4E10


title: m3_Aged_B5_new_384

description: Aged (19 month old)


title: m3_Young_D18_new_384

description: Young (3 month old)


title: m3_Aged_G19_new_384

description: Aged (19 month old)


title: m3_Aged_G7_new_384

description: Aged (19 month old)


title: AGGGCG: hair_cells_wt_4E9


title: AGCGCC: hair_cells_wt_4E8


title: m3_Aged_M20_new_384

description: Aged (19 month old)


title: SOX18(AOGG-84)

description: treatment with adenovirus 80 MOI expressing SOX18 for 48h


title: m3_Aged_O10_new_384

description: Aged (19 month old)


title: SOX18(AOGG-83)

source_name: adenovirus 80 MOI expressing SOX18 for 48h


title: SOX7(AOGG-72)

source_name: adenovirus 80 MOI expressing SOX7 for 48h


title: LMO2(AOGG-82)

description: treatment with adenovirus 80 MOI expressing LMO2 for 48h


title: m3_Young_A18_new_384

description: Young (3 month old)


title: m3_Young_G23_new_384

description: Young (3 month old)


title: LMO2(AOGG-81)

source_name: adenovirus 80 MOI expressing LMO2 for 48h


title: m3_Young_B21_new_384

description: Young (3 month old)


title: m3_Aged_C18_new_384

description: Aged (19 month old)


title: m3_Aged_M9_new_384

description: Aged (19 month old)


title: CGATTG: hair_cells_wt_4D11


title: CATGGT: hair_cells_wt_4D10


title: CAGGCC: hair_cells_wt_4E11


title: CGCCAG: hair_cells_wt_4F7


title: LEF1(AOGG-74)

description: treatment with adenovirus 80 MOI expressing LEF1 for 48h


title: m3_Aged_L7_new_384

description: Aged (19 month old)


title: SOX7(AOGG-70)


title: m3_Young_L20_new_384

description: Young (3 month old)


title: SOX18(AOGG-85)

description: treatement with adenovirus 80 MOI expressing SOX18 for 48h


title: m3_Young_C12_new_384

description: Young (3 month old)


title: m3_Aged_C20_new_384

description: Aged (19 month old)


title: m3_Aged_J21_new_384

description: Aged (19 month old)


title: TTTTCT: hair_cells_wt_4D7


title: KLF11(AOGG-91)

description: treatment with adenovirus 80 MOI expressing KLF11 for 48h


title: TGTTAT: hair_cells_wt_4C12


title: m3_Aged_J8_new_384

description: Aged (19 month old)


title: ACGGCC: hair_cells_wt_4E7


title: m3_Young_F14_new_384

description: Young (3 month old)


title: KLF11(AOGG-90)

source_name: adenovirus 80 MOI expressing KLF11 for 48h


title: GATCGT: hair_cells_wt_4D12


title: KLF11(AOGG-89)


title: m3_Young_E18_new_384

description: Young (3 month old)


title: m3_Aged_I3_new_384

description: Aged (19 month old)


title: LMO2(AOGG-80)


title: m3_Aged_K22_new_384

description: Aged (19 month old)


title: m3_Young_E14_new_384

description: Young (3 month old)


title: m3_Young_A22_new_384

description: Young (3 month old)


title: LEF1(AOGG-75)

source_name: adenovirus 80 MOI expressing LEF1 for 48h


title: m3_Young_K11_new_384

description: Young (3 month old)


title: m3_Young_G8_new_384

description: Young (3 month old)


title: CAAGCT: hair_cells_wt_4D9


title: m3_Aged_I20_new_384

description: Aged (19 month old)


title: m3_Aged_B15_new_384

description: Aged (19 month old)


title: TATTCA: hair_cells_wt_4C8


title: ACCGTA: hair_cells_wt_4D8


title: LEF1(AOGG-73)


title: m3_Young_F19_new_384

description: Young (3 month old)


title: FOXF2(AOGG-87)

description: treatment with adenovirus 80 MOI expressing FOXF2 for 48h


title: m3_Young_K13_new_384

description: Young (3 month old)


title: m3_Aged_H16_new_384

description: Aged (19 month old)


title: TATCTA: hair_cells_wt_4C7


title: FOXC1(AOGG-94)

description: treatment with adenovirus 80 MOI expressing FOXC1 for 48h


title: TCTATA: hair_cells_wt_4C10


title: m3_Aged_G14_new_384

description: Aged (19 month old)


title: FOXC1(AOGG-93)

source_name: adenovirus 80 MOI expressing FOXC1 for 48h


title: m3_Young_H12_new_384

description: Young (3 month old)


title: TGATAA: hair_cells_wt_4C11


title: m3_Young_P19_new_384

description: Young (3 month old)


title: m3_Young_F18_new_384

description: Young (3 month old)


title: GAATTA: hair_cells_wt_4B10


title: m3_Aged_N19_new_384

description: Aged (19 month old)


title: m3_Aged_J11_new_384

description: Aged (19 month old)


title: CTTATA: hair_cells_wt_4B9


title: TCAATT: hair_cells_wt_4C9


title: m3_Aged_L10_new_384

description: Aged (19 month old)


title: m3_Aged_F16_new_384

description: Aged (19 month old)


title: m3_Young_C22_new_384

description: Young (3 month old)


title: CTAATT: hair_cells_wt_4B8


title: m3_Young_K19_new_384

description: Young (3 month old)


title: m3_Aged_D14_new_384

description: Aged (19 month old)


title: FOXF2(AOGG-86)

source_name: adenovirus 80 MOI expressing FOXF2 for 48h


title: CATATT: hair_cells_wt_4B7


title: m3_Aged_F11_new_384

description: Aged (19 month old)


title: m3_Young_P14_new_384

description: Young (3 month old)


title: ETS1(AOGG-67)

description: treatment with adenovirus 80 MOI expressing ETS1 for 48h


title: m3_Aged_P16_new_384

description: Aged (19 month old)


title: m3_Aged_E4_new_384

description: Aged (19 month old)


title: m3_Aged_C10_new_384

description: Aged (19 month old)


title: GTTATT: hair_cells_wt_4B12


title: m3_Aged_G22_new_384

description: Aged (19 month old)


title: FOXF2(AOGG-88)


title: m3_Young_F15_new_384

description: Young (3 month old)


title: m3_Aged_O7_new_384

description: Aged (19 month old)


title: m3_Aged_K9_new_384

description: Aged (19 month old)


title: ETS1(AOGG-69)

source_name: adenovirus 80 MOI expressing ETS1 for 48h


title: ETS1(AOGG-68)


title: m3_Aged_D11_new_384

description: Aged (19 month old)


title: m3_Aged_P12_new_384

description: Aged (19 month old)


title: m3_Young_B12_new_384

description: Young (3 month old)


title: GTAAAT: hair_cells_wt_4B11


title: TB40 Exp 3 24h

description: nascent RNA with moth spike-in cells

data_processing:
Library strategy: PRO-Seq
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils
hg38 bigwigs were uploaded to the UCSC genome browser.
Custom UCSC track hubs were set up for Towne and TB40 data.
For analysis of host transcription effects upon infection or depletion of IE2 and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. truQuant source code is avaliable on GitHub at https://github.com/meierjl/hubs/tree/master/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne, KF297339.1 (HCMV TB40), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups. BED file contains an annotation of human gene bodies queried for effects on transcription.

extract_protocol:
Nuclei isolation was carried out as described in Ball et. al. (2019, PMID: 30743000) and Parida et. al. (2019, PMID: 30755505).
PRO-Seq library preparation to extract and sequence nascent RNAs is carefully detailed in the manuscript and was carried out as previously described by Parida et. al. (2019, PMID: 30755505), with noted modifications.

value: primary human foreskin fibroblast


title: AGTTAA: hair_cells_wt_4A10


title: ATAATG: hair_cells_wt_4A11


title: FOXC1(AOGG-92)


title: ATAGTA: hair_cells_wt_4A12


title: TB40 Exp 3 72h PFA

description: nascent RNA with moth spike-in cells


title: AGATAT: hair_cells_wt_4A9


title: ACTATT: hair_cells_wt_4A8


title: m3_Young_H20_new_384

description: Young (3 month old)


title: m3_Young_J12_new_384

description: Young (3 month old)


title: m3_Aged_G3_new_384

description: Aged (19 month old)


title: TB40 Exp 3 72h

description: nascent RNA with moth spike-in cells


title: TB40 72h IE2F 6h PFA

description: nascent RNA with moth spike-in cells

value: TB40 BAC4


title: m3_Aged_K16_new_384

description: Aged (19 month old)


title: ACAAAT: hair_cells_wt_4A7


title: TGCCCC: hair_cells_wt_2H11


title: m3_Young_D10_new_384

description: Young (3 month old)


title: TB40 Exp 2 72h IE2F dTAG

description: nascent RNA with moth spike-in cells


title: m3_Aged_I15_new_384

description: Aged (19 month old)


title: TCCGGG: hair_cells_wt_2H10


title: m3_Aged_G18_new_384

description: Aged (19 month old)


title: TB40 Exp 1 72h IE2F Flavo

description: nascent RNA with moth spike-in cells


title: m3_Young_E15_new_384

description: Young (3 month old)


title: GTGGCC: hair_cells_wt_2H9


title: TB40 Exp 2 72h IE2F

description: nascent RNA with moth spike-in cells


title: TB40 Exp 1 72h IE2F Flavo dTAG

description: nascent RNA with moth spike-in cells


title: m3_Aged_K18_new_384

description: Aged (19 month old)


title: m3_Aged_D18_new_384

description: Aged (19 month old)


title: m3_Aged_O11_new_384

description: Aged (19 month old)


title: TB40 Exp 1 72h IE2F dTAG

description:
nascent RNA with moth spike-in cells
This sample includes hg38 data.


title: m3_Young_M4_new_384

description: Young (3 month old)


title: GTCCCC: hair_cells_wt_2H8


title: m3_Aged_B10_new_384

description: Aged (19 month old)


title: TB40 72h IE2F 6h PFA dTAG

description: nascent RNA with moth spike-in cells


title: m3_Aged_I17_new_384

description: Aged (19 month old)


title: m3_Young_F10_new_384

description: Young (3 month old)


title: TB40 Exp 1 72h IE2F


title: m3_Aged_L20_new_384

description: Aged (19 month old)


title: m3_Aged_A20_new_384

description: Aged (19 month old)


title: Towne 96h IE2F Flavo dTAG

description: nascent RNA

value: Towne BAC


title: Towne 96h IE2F Flavo

description: nascent RNA

value: 96 hours


title: m3_Young_B8_new_384

description: Young (3 month old)

value: primary murine brain endothelial cells


title: Towne 96h IE2 Flavo dTAG

description: nascent RNA


title: m3_Aged_L14_new_384

description: Aged (19 month old)


title: m3_Young_K14_new_384

description: Young (3 month old)


title: m3_Aged_N6_new_384

description: Aged (19 month old)


title: Towne 96h IE2 Flavo

description: nascent RNA


title: m3_Aged_E14_new_384

description: Aged (19 month old)


title: m3_Young_D20_new_384

description: Young (3 month old)


title: m3_Young_G18_new_384

description: Young (3 month old)


title: GCCGAC: hair_cells_wt_2G8


title: m3_Aged_E13_new_384

description: Aged (19 month old)


title: m3_Aged_N4_new_384

description: Aged (19 month old)


title: GCCCAG: hair_cells_wt_2G7


title: Towne 96h IE2F

description: nascent RNA


title: GGGTGC: hair_cells_wt_2H7


title: GCGGAG: hair_cells_wt_2G11


title: m3_Young_P16_new_384

description: Young (3 month old)


title: CGGGGA: hair_cells_wt_2F12


title: GCGCAC: hair_cells_wt_2G10


title: CGGCGT: hair_cells_wt_2F11


title: m3_Young_I12_new_384

description: Young (3 month old)


title: m3_Aged_I13_new_384

description: Aged (19 month old)


title: Towne 96h IE2 dTAG

description: nascent RNA


title: m3_Aged_L6_new_384

description: Aged (19 month old)


title: Towne 96h IE2

description: nascent RNA


title: m3_Young_K17_new_384

description: Young (3 month old)


title: GCCTCG: hair_cells_wt_2G9


title: m3_Aged_L13_new_384

description: Aged (19 month old)


title: m3_Young_J23_new_384

description: Young (3 month old)


title: CGCGGT: hair_cells_wt_2F9


title: CGCCGA: hair_cells_wt_2F8


title: m3_Aged_F12_new_384

description: Aged (19 month old)


title: Towne 96h IE2F dTAG

description: nascent RNA


title: m3_Aged_F20_new_384

description: Aged (19 month old)


title: CGCACC: hair_cells_wt_2F7


title: CCACCG: hair_cells_wt_2E12


title: m3_Young_A11_new_384

description: Young (3 month old)


title: m3_Young_P13_new_384

description: Young (3 month old)


title: m3_Aged_F15_new_384

description: Aged (19 month old)


title: CAGCCG: hair_cells_wt_2E11


title: m3_Aged_H11_new_384

description: Aged (19 month old)


title: m3_Aged_N22_new_384

description: Aged (19 month old)


title: m3_Young_D5_new_384

description: Young (3 month old)


title: CGGACG: hair_cells_wt_2F10


title: m3_Young_L13_new_384

description: Young (3 month old)


title: m3_Young_K4_new_384

description: Young (3 month old)


title: m3_Young_G9_new_384

description: Young (3 month old)


title: CACCCC: hair_cells_wt_2E10


title: m3_Aged_D10_new_384

description: Aged (19 month old)


title: m3_Young_E17_new_384

description: Young (3 month old)


title: m3_Aged_B12_new_384

description: Aged (19 month old)


title: AGGCCC: hair_cells_wt_2E9


title: AGCCCG: hair_cells_wt_2E8


title: m3_Aged_D23_new_384

description: Aged (19 month old)


title: ACGCCG: hair_cells_wt_2E7


title: CTTCTG: hair_cells_wt_2D12


title: m3_Aged_C11_new_384

description: Aged (19 month old)


title: m3_Aged_P18_new_384

description: Aged (19 month old)


title: m3_Aged_B20_new_384

description: Aged (19 month old)


title: CCGATT: hair_cells_wt_2D11


title: m3_Aged_H20_new_384

description: Aged (19 month old)


title: m3_Aged_H4_new_384

description: Aged (19 month old)


title: m3_Young_C9_new_384

description: Young (3 month old)


title: CAGTCA: hair_cells_wt_2D10


title: AGGGAT: hair_cells_wt_2D9


title: m3_Young_G20_new_384

description: Young (3 month old)


title: m3_Aged_O4_new_384

description: Aged (19 month old)


title: m3_Aged_B22_new_384

description: Aged (19 month old)


title: TCTTTC: hair_cells_wt_2D8


title: m3_Aged_F4_new_384

description: Aged (19 month old)


title: m3_Aged_L5_new_384

description: Aged (19 month old)


title: TTTGTA: hair_cells_wt_2D7


title: m3_Aged_J9_new_384

description: Aged (19 month old)


title: TGTAAA: hair_cells_wt_2C12


title: Sample 2 (Technical Rep2)

city: Charlottesville

first: Omar

last: Guessoum

state: Va

address: MR4, 409 Lane Road

department: Biology

institute: University of Virginia

data_processing:
We used FastQC to assess the quality of FASTQ file reads.
Prior to alignment, we removed low quality reads and adapter sequences using Trimmomatic0.36.
We aligned FASTQ reads to the GRCm38/ENSEMBL mouse genome using Salmon0.7.2.
Samples with less than 300,000 total aligned reads were excluded from downstream analyses.
Transcript-level estimates of expression were scaled up to gene level estimates using the Tximport 1.2.0 R package, with the “lengthScaledTPM” argument for abundance estimation.
Genome_build: mm10

source_name: Recruited Renin Cells

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).
Native renin cells samples underwent next-generation sequencing library preparation as described in the Fluidigm C1 manual using an Illumina NexteraXT library prep and index kits (Catalog Nos. FC-131-1096 and FC-131-1002). Briefly, cDNA samples were diluted, tagmented, and indexed with unique barcodes for downstream analyses. After the addition of indices and amplification, samples were multiplexed and cleaned using AMPure beads.

treatment_protocol: The animals in this study were subjected to low salt diet and captopril in their drinking water (0.5g/L) for one week prior to harvest.

value: primary kidney cells

tag: strain

tag: age

value: Adult


title: Sample 1 (Technical Rep2)


title: m3_Aged_I10_new_384

description: Aged (19 month old)


title: m3_Aged_E16_new_384

description: Aged (19 month old)


title: m3_Aged_I8_new_384

description: Aged (19 month old)


title: m3_Young_P8_new_384

description: Young (3 month old)


title: TGAAAT: hair_cells_wt_2C11

tag: tissue


title: m3_Aged_C5_new_384

description: Aged (19 month old)


title: m3_Aged_H14_new_384

description: Aged (19 month old)


title: TCATTA: hair_cells_wt_2C10


title: m3_Young_K16_new_384

description: Young (3 month old)


title: Low_96

city: New York

first: Saghi

last: Ghaffari

state: NY

address: One Gustave L. Levy Place, Box 1496

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Single end sequencing were carried out using Illumina HighSeq 4000
fastq file was generated using Illumina's bcl2fastq v2.17.1.14 with 1 mismatch barcode
Alignment was done using Star v2.5.2b to mm10

source_name: Hematopoietic Stem Cells

extract_protocol:
FACS sorted cells in 35% suspension reagent at 600 cells/µL were loaded into the 5-10 μm Fluidigm IFC and visually inspected to confirm one cell per capture site at 20X with a fluorescent microscope. Debris, multiple cells, and dead cells (Calcein negative) were excluded for subsequent library preparation.
Single cell cDNA libraries were generated from FACS-purified MMP-low and -high HSCs with the SMART-Seq v4 Ultra Low Input RNA kit, the Fluidigm C1 system and the Nextera XT library preparation kit (Illumina) following the manufactures’ protocols. The captured cells were then subjected to cDNA synthesis on the C1 system and quantified the next day using the Quant-iT Picogreen dsDNA Assay kit. cDNA was tagmented, amplified, pooled, and cleaned up with the Nextera XT kit. Single-cell cDNA libraries were then quantified with the Bioanalyzer (Agilent) and subjected to sequencing on the Illumina High-Seq. 254 single-cell cDNA libraries were multiplexed over 3 lanes (~84 samples/lane) with 100 nt single-end sequencing.

tag: flow purified

tag: fluidigm c1 platform

value: single cell


title: TATTTG: hair_cells_wt_2C9

tag: genotype


title: Sample 1 (Technical Rep1)

tag: cell type


title: m3_Aged_J7_new_384

description: Aged (19 month old)


title: m3_Aged_B13_new_384

description: Aged (19 month old)


title: m3_Aged_L22_new_384

description: Aged (19 month old)


title: Low_94


title: m3_Aged_C9_new_384

description: Aged (19 month old)


title: Sample 2 (Technical Rep1)


title: Low_95


title: m3_Aged_H17_new_384

description: Aged (19 month old)


title: m3_Young_C19_new_384

description: Young (3 month old)


title: Low_93


title: TATATC: hair_cells_wt_2C7


title: m3_Young_B22_new_384

description: Young (3 month old)


title: TATGTT: hair_cells_wt_2C8


title: GTATAA: hair_cells_wt_2B12


title: m3_Aged_B9_new_384

description: Aged (19 month old)


title: m3_Young_A19_new_384

description: Young (3 month old)


title: m3_Young_J21_new_384

description: Young (3 month old)


title: Low_92


title: m3_Aged_K13_new_384

description: Aged (19 month old)


title: m3_Aged_E6_new_384

description: Aged (19 month old)


title: GATATA: hair_cells_wt_2B11


title: m3_Aged_C22_new_384

description: Aged (19 month old)


title: m3_Young_O6_new_384

description: Young (3 month old)


title: m3_Aged_I21_new_384

description: Aged (19 month old)


title: CTATTA: hair_cells_wt_2B9


title: GAAATT: hair_cells_wt_2B10


title: m3_Aged_O21_new_384

description: Aged (19 month old)


title: Low_91


title: Low_89


title: Low_88


title: m3_Young_O14_new_384

description: Young (3 month old)


title: CATTTA: hair_cells_wt_2B8


title: CAATAA: hair_cells_wt_2B7


title: m3_Young_M8_new_384

description: Young (3 month old)


title: m3_Aged_P4_new_384

description: Aged (19 month old)


title: Low_86


title: m3_Young_E9_new_384

description: Young (3 month old)


title: m3_Aged_N15_new_384

description: Aged (19 month old)


title: Low_87


title: m3_Aged_N16_new_384

description: Aged (19 month old)


title: m3_Young_E21_new_384

description: Young (3 month old)


title: ATACTT: hair_cells_wt_2A12


title: ATAACA: hair_cells_wt_2A11


title: m3_Young_O23_new_384

description: Young (3 month old)


title: AGTAAT: hair_cells_wt_2A10


title: m3_Aged_P10_new_384

description: Aged (19 month old)


title: m3_Aged_M4_new_384

description: Aged (19 month old)


title: ACTTTA: hair_cells_wt_2A9


title: ACATAA: hair_cells_wt_2A8


title: Low_90


title: m3_Aged_G10_new_384

description: Aged (19 month old)


title: m3_Aged_K4_new_384

description: Aged (19 month old)


title: AATTGA: hair_cells_wt_2A7


title: High_126


title: High_122


title: m3_Aged_G6_new_384

description: Aged (19 month old)


title: m3_Aged_C16_new_384

description: Aged (19 month old)


title: m3_Aged_I11_new_384

description: Aged (19 month old)


title: GGGAGG: hair_cells_Emx2_mutant_4H4


title: GGGCTC: hair_cells_Emx2_mutant_4H5


title: High_121


title: GGCGGA: hair_cells_Emx2_mutant_4H3


title: m3_Young_C20_new_384

description: Young (3 month old)


title: 170406_p3_c8

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
raw sequencing data was converted to fastq files using Bcl2fastq (version 2.20)
reads were mapped against the reference genome (mm10) using STAR (version 2.4.2a)
gene expression levels were quantified using rpkmforgees (Ramsköld 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix gene-/sample-wise for raw counts

extract_protocol:
Electrophysiological properties were recorded by patch clamping. The cytosols of the cells were extracted and transferred into lysis buffer and converted to cDNA libraries for sequencing.
Patch-seq (Cadwell 2016)

tag: brain region

value: brain


title: 170406_p3_c6


title: m3_Aged_L9_new_384

description: Aged (19 month old)


title: High_120


title: High_124


title: GGCAGC: hair_cells_Emx2_mutant_4H2


title: m3_Aged_A22_new_384

description: Aged (19 month old)


title: 170406_p3_c3


title: High_125


title: 170406_p3_c7


title: High_119


title: 170406_p3_c5


title: GGACGC: hair_cells_Emx2_mutant_4H1


title: High_117


title: High_118


title: GCACCC: hair_cells_Emx2_mutant_4G5


title: m3_Young_D23_new_384

description: Young (3 month old)


title: m3_Aged_N13_new_384

description: Aged (19 month old)


title: 170406_p3_c1


title: 170406_p3_b12


title: High_114


title: GAGCCC: hair_cells_Emx2_mutant_4G4


title: CTCGGG: hair_cells_Emx2_mutant_4G2


title: m3_Aged_J20_new_384

description: Aged (19 month old)


title: High_113


title: 170406_p3_b11


title: 170406_p3_c4


title: m3_Aged_H13_new_384

description: Aged (19 month old)


title: m3_Young_A7_new_384

description: Young (3 month old)


title: High_115


title: GACCCG: hair_cells_Emx2_mutant_4G3


title: CGTGCC: hair_cells_Emx2_mutant_4G1


title: High_112


title: High_123


title: CCTGCG: hair_cells_Emx2_mutant_4F5


title: m3_Aged_M5_new_384

description: Aged (19 month old)


title: CGAGCG: hair_cells_Emx2_mutant_4F6


title: 170406_p3_b5


title: m3_Young_E20_new_384

description: Young (3 month old)


title: High_111


title: m3_Aged_D8_new_384

description: Aged (19 month old)


title: 170406_p3_b8


title: m3_Aged_P15_new_384

description: Aged (19 month old)


title: High_107


title: High_108


title: CCCCCA: hair_cells_Emx2_mutant_4F1


title: 170406_p3_b3


title: High_110


title: High_109


title: High_116


title: m3_Young_K20_new_384

description: Young (3 month old)


title: CCGGTG: hair_cells_Emx2_mutant_4F4


title: m3_Aged_I23_new_384

description: Aged (19 month old)


title: 170406_p3_b10


title: 170406_p3_b6


title: CCCGGA: hair_cells_Emx2_mutant_4F2


title: 170406_p3_b4


title: m3_Aged_K15_new_384

description: Aged (19 month old)


title: GGACCA: hair_cells_Emx2_mutant_4E5


title: 170406_p3_a12


title: m3_Aged_L3_new_384

description: Aged (19 month old)


title: High_105


title: CCGCGA: hair_cells_Emx2_mutant_4F3


title: m3_Aged_L12_new_384

description: Aged (19 month old)


title: High_106


title: ACCGCG: hair_cells_Emx2_mutant_4E6


title: 170406_p3_b7


title: m3_Young_L19_new_384

description: Young (3 month old)


title: m3_Aged_L21_new_384

description: Aged (19 month old)


title: 170406_p3_a11


title: 170406_p3_b1


title: High_104


title: High_102


title: 170406_p3_a7


title: m3_Aged_M8_new_384

description: Aged (19 month old)


title: m3_Aged_E21_new_384

description: Aged (19 month old)


title: 170406_p3_a6


title: High_103


title: High_100


title: GTGACT: hair_cells_Emx2_mutant_4E2


title: TCGAAG: hair_cells_Emx2_mutant_4E3


title: 170406_p3_a8


title: m3_Young_I22_new_384

description: Young (3 month old)


title: GGCAAT: hair_cells_Emx2_mutant_4E1


title: High_99


title: TTTCAA: hair_cells_Emx2_mutant_4D6


title: 170406_p2_h11


title: TTTAAC: hair_cells_Emx2_mutant_4D5


title: High_101


title: m3_Aged_P6_new_384

description: Aged (19 month old)


title: m3_Aged_C12_new_384

description: Aged (19 month old)


title: TTCTAA: hair_cells_Emx2_mutant_4D4


title: m3_Aged_A18_new_384

description: Aged (19 month old)


title: High_97


title: 170406_p3_a2


title: 170406_p3_a4


title: TTAGAA: hair_cells_Emx2_mutant_4D2


title: m3_Aged_N3_new_384

description: Aged (19 month old)


title: TTAAGA: hair_cells_Emx2_mutant_4D1


title: TTTGGC: hair_cells_Emx2_mutant_4E4


title: 170406_p2_h6


title: TATACT: hair_cells_Emx2_mutant_4C6


title: TTATGT: hair_cells_Emx2_mutant_4D3


title: 170406_p2_h8


title: 170406_p2_h9


title: High_96


title: High_95


title: TACATT: hair_cells_Emx2_mutant_4C4


title: m3_Aged_L18_new_384

description: Aged (19 month old)


title: m3_Aged_F23_new_384

description: Aged (19 month old)


title: m3_Young_L22_new_384

description: Young (3 month old)


title: High_94


title: m3_Aged_J6_new_384

description: Aged (19 month old)


title: 170406_p3_a1


title: High_98


title: 170406_p2_h7


title: High_92


title: m3_Young_F12_new_384

description: Young (3 month old)


title: TAGATA: hair_cells_Emx2_mutant_4C5


title: High_93


title: 170406_p2_h4


title: TAACTT: hair_cells_Emx2_mutant_4C2


title: High_88


title: 170406_p2_h10


title: m3_Young_H17_new_384

description: Young (3 month old)


title: High_90


title: TAATCT: hair_cells_Emx2_mutant_4C3


title: m3_Aged_B3_new_384

description: Aged (19 month old)


title: ATTTAC: hair_cells_Emx2_mutant_4B5


title: TAAACA: hair_cells_Emx2_mutant_4C1


title: 170406_p2_h12


title: 170406_p2_h5


title: High_89


title: 170406_p2_h1


title: 170406_p2_h2


title: High_87


title: m3_Young_G21_new_384

description: Young (3 month old)


title: m3_Young_K21_new_384

description: Young (3 month old)


title: Low_121


title: CAAAAT: hair_cells_Emx2_mutant_4B6


title: m3_Young_M7_new_384

description: Young (3 month old)


title: High_91


title: m3_Young_H19_new_384

description: Young (3 month old)


title: m3_Aged_B4_new_384

description: Aged (19 month old)


title: ATTCAT: hair_cells_Emx2_mutant_4B4


title: High_86


title: m3_Aged_M23_new_384

description: Aged (19 month old)


title: 170406_p2_g10


title: 170406_p2_h3


title: ATATTC: hair_cells_Emx2_mutant_4B1


title: 170406_p2_g11


title: Low_122


title: 170406_p2_g12


title: ATTAAG: hair_cells_Emx2_mutant_4B3


title: AATTAG: hair_cells_Emx2_mutant_4A6


title: Low_120


title: 170406_p2_g8


title: m3_Aged_D3_new_384

description: Aged (19 month old)


title: Low_118


title: Low_119


title: Low_117


title: m3_Young_H15_new_384

description: Young (3 month old)


title: AATCAA: hair_cells_Emx2_mutant_4A5


title: 170406_p2_g9


title: 170406_p2_g7


title: m3_Aged_D7_new_384

description: Aged (19 month old)


title: 170406_p2_g6


title: m3_Young_O16_new_384

description: Young (3 month old)


title: Low_115


title: ATCTTA: hair_cells_Emx2_mutant_4B2


title: AACTAA: hair_cells_Emx2_mutant_4A3


title: AAATGT: hair_cells_Emx2_mutant_4A2


title: AATAAC: hair_cells_Emx2_mutant_4A4


title: 170406_p2_g5


title: m3_Young_L3_new_384

description: Young (3 month old)


title: m3_Aged_C7_new_384

description: Aged (19 month old)


title: AAACTA: hair_cells_Emx2_mutant_4A1


title: Low_114


title: m3_Young_N8_new_384

description: Young (3 month old)


title: m3_Young_A4_new_384

description: Young (3 month old)


title: Low_112


title: Low_113


title: 170406_p2_g3


title: Low_116


title: 170406_p2_g2


title: m3_Young_M9_new_384

description: Young (3 month old)


title: m3_Aged_P7_new_384

description: Aged (19 month old)


title: m3_Young_J16_new_384

description: Young (3 month old)


title: GGCTCC: hair_cells_Emx2_mutant_2H4


title: 170406_p2_g1


title: m3_Young_C14_new_384

description: Young (3 month old)


title: 170406_p2_f12


title: GGAGGG: hair_cells_Emx2_mutant_2H2


title: Low_110


title: 170406_p2_f9


title: GCTGCC: hair_cells_Emx2_mutant_2H1


title: GGGCCT: hair_cells_Emx2_mutant_2H5


title: Low_108


title: Low_109


title: 170406_p2_g4


title: m3_Young_H7_new_384

description: Young (3 month old)


title: GAGGCG: hair_cells_Emx2_mutant_2G5


title: GACGCC: hair_cells_Emx2_mutant_2G4


title: 170406_p2_f6


title: CTGGCG: hair_cells_Emx2_mutant_2G3


title: GGCGAG: hair_cells_Emx2_mutant_2H3


title: Low_111


title: m3_Young_O21_new_384

description: Young (3 month old)


title: 170406_p2_f11


title: Low_107


title: m3_Young_J8_new_384

description: Young (3 month old)


title: m3_Young_B4_new_384

description: Young (3 month old)


title: m3_Young_M6_new_384

description: Young (3 month old)


title: 170406_p2_f7


title: CTCCCG: hair_cells_Emx2_mutant_2G2


title: Low_105


title: CGTCCG: hair_cells_Emx2_mutant_2G1


title: m3_Young_D13_new_384

description: Young (3 month old)


title: 170406_p2_f8


title: Low_103


title: Low_104


title: 170406_p2_f2


title: 170406_p2_f4


title: m3_Young_I3_new_384

description: Young (3 month old)


title: Low_106


title: m3_Young_O18_new_384

description: Young (3 month old)


title: CCGTGC: hair_cells_Emx2_mutant_2F5


title: Low_102


title: CCGGCA: hair_cells_Emx2_mutant_2F4


title: Low_101


title: CGACCC: hair_cells_Emx2_mutant_2F6


title: 170406_p2_f1


title: 170406_p2_e10

source_name: unknown


title: m3_Young_O12_new_384

description: Young (3 month old)


title: m3_Young_D14_new_384

description: Young (3 month old)


title: 170406_p2_e11


title: CCCCTG: hair_cells_Emx2_mutant_2F2


title: Low_98


title: Low_100


title: 170406_p2_e12


title: 170406_p2_f3


title: CCGAGG: hair_cells_Emx2_mutant_2F3


title: 170406_p2_e6


title: m3_Aged_E9_new_384

description: Aged (19 month old)


title: m3_Young_B6_new_384

description: Young (3 month old)


title: CCTTCC: hair_cells_Emx2_mutant_2E5


title: 170406_p2_e8


title: High_80


title: High_72


title: m3_Aged_P5_new_384

description: Aged (19 month old)


title: 170406_p2_e7


title: TTCCTC: hair_cells_Emx2_mutant_2E4


title: m3_Young_B10_new_384

description: Young (3 month old)


title: Low_99


title: CCCAGC: hair_cells_Emx2_mutant_2F1


title: High_64


title: Low_97


title: TAGTGG: hair_cells_Emx2_mutant_2E3


title: m3_Young_H18_new_384

description: Young (3 month old)


title: m3_Young_I19_new_384

description: Young (3 month old)


title: GCTTAC: hair_cells_Emx2_mutant_2E1


title: m3_Young_J14_new_384

description: Young (3 month old)


title: 170406_p2_e5


title: m3_Young_K6_new_384

description: Young (3 month old)


title: TTTAGT: hair_cells_Emx2_mutant_2D6


title: ACCCCC: hair_cells_Emx2_mutant_2E6


title: 170406_p2_e4


title: m3_Young_L21_new_384

description: Young (3 month old)


title: TTCAAT: hair_cells_Emx2_mutant_2D4


title: m3_Aged_A5_new_384

description: Aged (19 month old)


title: m3_Aged_A16_new_384

description: Aged (19 month old)


title: TTAAAG: hair_cells_Emx2_mutant_2D1


title: High_71


title: TTATAC: hair_cells_Emx2_mutant_2D3


title: High_63


title: m3_Young_P15_new_384

description: Young (3 month old)


title: 170406_p2_e3


title: TACTTA: hair_cells_Emx2_mutant_2C5


title: High_55


title: m3_Aged_A23_new_384

description: Aged (19 month old)


title: 170406_p2_d6


title: High_56


title: 170406_p2_d5


title: GTACAC: hair_cells_Emx2_mutant_2E2


title: High_48


title: 170406_p2_e9


title: TAAATG: hair_cells_Emx2_mutant_2C2


title: m3_Young_N12_new_384

description: Young (3 month old)


title: m3_Young_G6_new_384

description: Young (3 month old)


title: 170406_p2_d4


title: High_32


title: High_31


title: GTTTTA: hair_cells_Emx2_mutant_2C1


title: m3_Young_J5_new_384

description: Young (3 month old)


title: 170406_p2_e2


title: High_23


title: m3_Young_B13_new_384

description: Young (3 month old)


title: High_24


title: m3_Young_K18_new_384

description: Young (3 month old)


title: 170406_p2_e1


title: m3_Young_L11_new_384

description: Young (3 month old)


title: High_16


title: High_40


title: High_8


title: TTACAT: hair_cells_Emx2_mutant_2D2


title: High_15


title: 170406_p2_d10


title: High_79


title: TAGTTT: hair_cells_Emx2_mutant_2C6


title: m3_Young_J7_new_384

description: Young (3 month old)


title: 170406_p2_d11


title: m3_Aged_A3_new_384

description: Aged (19 month old)


title: 170406_p2_d2


title: 170406_p2_d7


title: 170406_p2_d9


title: 170406_p2_c12


title: m3_Young_L4_new_384

description: Young (3 month old)


title: m3_Young_B7_new_384

description: Young (3 month old)


title: TAAGTA: hair_cells_Emx2_mutant_2C3


title: 170406_p2_c9


title: TAATTC: hair_cells_Emx2_mutant_2C4


title: High_47


title: m3_Young_F5_new_384

description: Young (3 month old)


title: High_39


title: 170406_p2_c10


title: High_62


title: High_54


title: 170406_p2_d3


title: 170406_p2_c1


title: High_46


title: 170406_p2_d1


title: ATTTGT: hair_cells_Emx2_mutant_2B6


title: ATTGAA: hair_cells_Emx2_mutant_2B5


title: m3_Young_O17_new_384

description: Young (3 month old)


title: m3_Young_B15_new_384

description: Young (3 month old)


title: 170406_p2_c3


title: High_7


title: High_30


title: AACAAT: hair_cells_Emx2_mutant_2A3


title: High_78


title: 170406_p2_c4


title: ATGATA: hair_cells_Emx2_mutant_2B3


title: High_70


title: ATCATT: hair_cells_Emx2_mutant_2B2


title: ATATCT: hair_cells_Emx2_mutant_2B1


title: 170406_p2_c11


title: m3_Young_B11_new_384

description: Young (3 month old)


title: 170406_p2_d12


title: m3_Young_P20_new_384

description: Young (3 month old)


title: ATTAGA: hair_cells_Emx2_mutant_2B4


title: AATGAT: hair_cells_Emx2_mutant_2A6


title: 170406_p2_c2


title: m3_Young_B5_new_384

description: Young (3 month old)


title: AATAGT: hair_cells_Emx2_mutant_2A5


title: 170406_p2_c6


title: AAGTAT: hair_cells_Emx2_mutant_2A4


title: m3_Young_D12_new_384

description: Young (3 month old)


title: High_38


title: m3_Young_P4_new_384

description: Young (3 month old)


title: 170406_p2_b12


title: High_77


title: High_22


title: High_69


title: AAATAC: hair_cells_Emx2_mutant_2A2


title: m3_Aged_F7_new_384

description: Aged (19 month old)


title: 170406_p2_c7


title: High_14


title: m3_Aged_L8_new_384

description: Aged (19 month old)


title: High_6


title: AAAATC: hair_cells_Emx2_mutant_2A1


title: High_53


title: LN18.ABCB5+

type: RNA

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
5_ln18_ab5positive
Transcriptome expression levels from ABCB5+ GBM cells

hyb_protocol: GeneChip™ Human Transcriptome Array 2.0

scan_protocol: Microarrays were scanned at the Dana-Farber Microarray Core Facility

data_processing: R Bioconductor oligo package with RMA normalization

label: biotin

source_name: ATCC GBM cell line LN18 ABCB5+ fraction

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the Dana-Farber Microarray Core Facility

growth_protocol: LN-18 and LN-229 were cultured in DMEM, U-87 MG in EMEM, suplemented with 10% (v/v) fetal bovine serum and 1% (v/v) Pen/Strep

extract_protocol: RNeasy Plus isolation kit (Qiagen)

treatment_protocol: FACS based on anti-ABCB5 mAb clone 3C2-1D12

tag: cell line

value: ATCC GBM cell line

value: positive


title: U87MG.ABCB5-

description:
4_u87_ab5negative
Transcriptome expression levels from ABCB5- GBM cells

source_name: ATCC GBM cell line U87MG ABCB5- fraction

value: negative


title: m3_Young_J17_new_384

description: Young (3 month old)


title: 170406_p2_b11


title: m3_Aged_K3_new_384

description: Aged (19 month old)


title: m3_Young_L6_new_384

description: Young (3 month old)


title: 170406_p2_b9


title: m3_Young_B23_new_384

description: Young (3 month old)


title: 170406_p2_b10


title: 170406_p2_b4


title: High_29


title: High_85


title: LN18.ABCB5-

description:
6_ln18_ab5negative
Transcriptome expression levels from ABCB5- GBM cells

source_name: ATCC GBM cell line LN18 ABCB5- fraction


title: HeatShock-42C-Tot-EU-45min-K562-plate4

data_processing:
Read 2 of Sequencing liberties were using STAR 2.5 with default parameters. If the length of the poly-T track in read 1 was less than 19 bases, the read was discarded.
Genome_build: ensemble release 90 of the homo sapiens GRCh38 genome, extended with ERCC92 spike-ins and ensemble release 90 of the mus musculus GRCm38 genome, extended with ERCC92 spike-ins
The number of UMI count per gene was obtained by pooling all reads mapping to the same gene and having the same cell barcode as previously (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637) using only uniquely mapped reads. The minimal number of UMI detected in a cell for the RPE1-FUCCI cell-cycle analysis was of 2,300, while the threshold used for murine in intestinal organoid cells was of 1,000. The UMI for a given gene in a cell was considered to be unspliced if at least one base of any read belonging to that UMI mapped outside of the exons of the gene.
Supplementary_files_format_and_content: The number of UMI count per gene

growth_protocol: RPE1-FUCCI cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/F12, supplemented with GlutaMAX (Gibco), FBS (Gibco), and penicillin/streptomycin (Gibco), following standard procedures. K562 cells were cultured in RPMI medium supplemented with penicillin/streptomycin and FBS. Organoids were expanded in medium termed ENR, consisting of Advanced Dulbecco’s modified Eagle’s medium/F12 (Advanced DMEM) with HEPES (10mM, Sigma), penicillin/streptomycin (1x, Thermofisher) and Glutamax. Advanced DMEM was supplemented with 1x B27 (Thermofisher), 1 mM N-acetylcysteine (Sigma), 50 ng/ml murine recombinant epidermal growth factor (PeproTech), R-spondin 1 conditioned medium (5% of final volume) and Noggin conditioned medium (5% of final volume) to generate ENR medium. To generate conditioned media, HEK293T cells were stably transfected with Rspo1-Fc (gift from Calvin Kuo, Stanford University) or transient transfection with mouse Noggin-Fc expression vector and grown for 1 week in Advanced DMEM supplemented with penicillin/streptomycin, and Glutamax. Organoids were plated in Reduced Growth Factor Basement Membrane Matrix (BME) Type 2 (Trevigen)

treatment_protocol: Cells were incubated with the EU and/or DMSO for the desired time (e.g. 60 min). The final concentration of EU was 200 µM for RPE1-FUCCI chase experiments, 400 µM for RPE1-FUCCI or K562 pulse experiments, 166 µM for chase experiments in organoids and 1.6 mM for pulse experiments in Organoids. The U chase phase of the was done with 400 µM U. Cells were dissociated using TrypLE enzyme mix (Gibco) and mechanical sheering if required.

value: Incubated at 37C for 45min prior fixation; Incubated with EU

tag: molecule subtype

value: Unlabeled mRNA


title: m3_Young_C7_new_384

description: Young (3 month old)


title: TTGATT: hair_cells_Emx2_mutant_2D5

description: Libraries were constructed using the mcSCRB-seq protocol (see Bagnoli et al., 2018)

source_name: zebrafish neuromast hair cells

value: zebrafish neuromast hair cells

value: 6 days post fertilization


title: LN229.ABCB5-

description:
2_ln229_ab5negative
Transcriptome expression levels from ABCB5- GBM cells

source_name: ATCC GBM cell line LN229 ABCB5- fraction


title: 170406_p2_b3


title: 170406_p2_b8


title: m3_Young_N3_new_384

description: Young (3 month old)


title: 170406_p2_b6


title: LN229.ABCB5+

description:
1_ln229_ab5positive
Transcriptome expression levels from ABCB5+ GBM cells

source_name: ATCC GBM cell line LN229 ABCB5+ fraction


title: m3_Aged_O12_new_384

description: Aged (19 month old)


title: HeatShock-42C-NS-EU-45min-K562-plate4

value: EU Labeled mRNA


title: High_45


title: m3_Young_L8_new_384

description: Young (3 month old)


title: High_37


title: 170406_p2_b1


title: 170406_p2_b7


title: High_61


title: HeatShock-37C-NS-EU-45min-K562-plate2


title: High_5


title: 170406_p2_a12


title: U87MG.ABCB5+

description:
3_u87_ab5positive
Transcriptome expression levels from ABCB5+ GBM cells

source_name: ATCC GBM cell line U87MG ABCB5+ fraction


title: m3_Aged_O16_new_384

description: Aged (19 month old)


title: High_21


title: m3_Young_D6_new_384

description: Young (3 month old)


title: RPE1-CellSeq2-Plate04

data_processing:
Library strategy: CEL-seq2
Read 2 of Sequencing liberties were using STAR 2.5 with default parameters. If the length of the poly-T track in read 1 was less than 19 bases, the read was discarded.
Genome_build: ensemble release 90 of the homo sapiens GRCh38 genome, extended with ERCC92 spike-ins and ensemble release 90 of the mus musculus GRCm38 genome, extended with ERCC92 spike-ins
Supplementary_files_format_and_content: The number of UMI count per gene was obtained by pooling all reads mapping to the same gene and having the same cell barcode as previously (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637) using only uniquely mapped reads. The minimal number of UMI detected in a cell for the RPE1-FUCCI cell-cycle analysis was of 2,300, while the threshold used for murine in intestinal organoid cells was of 1,000. The UMI for a given gene in a cell was considered to be unspliced if at least one base of any read belonging to that UMI mapped outside of the exons of the gene.

source_name: RPE1-FUCCI cells

extract_protocol: Runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode. Illumina TruSeq adapaters

tag: genetic tag

value: FUCCI


title: HeatShock-42C-Tot-DMSO-45min-K562-plate3

value: Incubated at 37C for 45min prior fixation; Incubated with DMSO


title: RPE1-CellSeq2-Plate03


title: m3_Young_H6_new_384

description: Young (3 month old)


title: HeatShock-37C-Tot-EU-45min-K562-plate2


title: High_13


title: RPE1-CellSeq2-Plate02


title: 170406_p2_b2


title: m3_Young_G12_new_384

description: Young (3 month old)


title: HeatShock-37C-Tot-DMSO-45min-K562-plate1


title: 170406_p2_a7


title: RPE1-CellSeq2-Plate01


title: High_84


title: 170406_p2_a11


title: m3_Young_I14_new_384

description: Young (3 month old)


title: High_76


title: 170406_p2_a8


title: 170406_p2_a6


title: High_68


title: High_60


title: 170406_p2_a9


title: Ctrl_WB_1217

city: Las Vegas

first: Łukasz

middle: J.

last: Sznajder

state: Nevada

address: 4505 S. Maryland Pkwy.

department: Chemistry and Biochemistry

institute: University of Nevada-Las Vegas (UNLV)

description: rRNA and globin depleted total RNA

data_processing:
Basecalling was done using Illumina Real-Time Analysis (RTA) and demultiplexed fastq files were obtained from BaseSpace with BaseMount.
STAR was used to map reads to the reference genome.
Salmon and DEseq2 were used to quantify and normalize gene expression followed by differential analysis.
rMATS turbo was used for differential alternative splicing.
IRFinder was used for retained intron quantification.
Genome_build: mm10 and hg38.
Supplementary_files_format_and_content: Sznajder_Supplementary_Data.xlsx contains STAR statistics as well as DESeq2, rMATS and IRFinder results.

source_name: Whole blood

extract_protocol:
Total RNA from DNA/RNA Shield Blood Collection Tubes was isolated by using Quick-DNA/RNA Blood Tube Kit with DNase treatment according to manufacturer’s provided protocol (Zymo Research). Total RNA from PBMCs was isolated by using TRIzol Reagent and the Direct-zol RNA MiniPrep Kit with DNase treatment according to manufacturer’s provided protocol (Zymo Research). Total RNA from mouse thymus was isolated using PolyTron (Kinematica) homogenization in TRI Reagent (Sigma) followed by treatment with the RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA was quantitated on a Nanodrop, Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher) and/or Qubit RNA BR Assay Kit (Thermo Fisher Scientific).
Thymic RNA-seq (2 × 50 paired-end reads) were performed by The New York Genome Center from total RNA. For human PBMC and whole blood strand-specific, rRNA- and globin- (only whole blood) depleted RNA-seq libraries were prepared using the KAPA Stranded RNA-seq Kit with RiboErase HMR Globin (Kapa Biosystems) per manufacturer’s instructions, except for the use of custom Illumina-compatible index primers to allow multiplexing. Library size distribution was assessed using the High Sensitivity NGS Fragment Analysis Kit (DNF-747) on a Fragment Analyzer (Agilent) and 2 × 76 paired-end sequencing was performed using an Illumina NextSeq 500.

tag: condition

value: Control

tag: sampling age

value: 58 years of age


title: m3_Aged_A7_new_384

description: Aged (19 month old)

value: primary murine brain endothelial cells


title: 170406_p2_a3


title: High_52


title: High_28


title: m3_Young_L16_new_384

description: Young (3 month old)


title: High_36


title: m3_Young_P5_new_384

description: Young (3 month old)


title: m3_Young_F3_new_384

description: Young (3 month old)


title: 170406_p2_a5


title: m3_Young_D4_new_384

description: Young (3 month old)


title: High_20


title: Ctrl_WB_1212

description: rRNA and globin depleted total RNA

value: 48 years of age


title: High_44


title: 170406_p2_a2


title: DM2_WB_1228

description: rRNA and globin depleted total RNA

value: 37 years of age


title: 170406_p1_h10


title: High_4

value: single cell


title: m3_Young_J15_new_384

description: Young (3 month old)


title: m3_Young_P10_new_384

description: Young (3 month old)


title: Liver, BALB/c, Control Water + 20% Fructose, 12h (JC130)

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
group 26, rep 5
JC130

data_processing:
Illumina Casava was used for basecalling.
Raw reads were filtered by removing read which:  (1) contained adaptors; (2) contained N > 10% (N represents base that could not be determined); and (3) The Qscore (Quality value) of over 50% bases of the read was <= 5.
STAR v2.5 was used to align clean data to mm10 reference genome with parameter mismatch = 2
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. Then FPKM of each gene was calculated.
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv files including raw counts, FPKM values for each sample, and FPKM values for each group

source_name: Liver

extract_protocol:
Completely dissolve approximately 5mg of frozen liver tissue powder in 500 uL of Trizol reagent at room temperature; Add 100uL of chloroform to the Trizol-liver mixture and incubate the mixture at RT for 2 min; Spin down at 12krpm for 15 minutes at 4°C; Isolate the top layer (aqueous) and mix it with 100% ethanol at 1:1 ratio and load the mixture to the RNeasy mini column from the Qiagen kit (catalogue No. 74106); Thereafter follow the protocol part 1 step 3 from the same kit to finish the extraction of total RNA.
Standard Illumina protocol using NEBNext Library Prep Kit for Illumina
Illumina NovaSeq 6000 paired with an S4 flowcell

treatment_protocol: Mice at 8 weeks of age were purchased and trained for 1 week for regulated fasting (from 10 pm to 7 pm) and feeding of regular chow (10 % of calories from fat and 64.5% of calories from carbohydrates) (from 7 pm to 10 pm). On the day of the experiment, mice were fasted from 10 pm the day before to 7 pm on the day of the experiment. They were deprived of water from 4 pm to 7 pm only on the day of the experiment. At 7 pm, they were provided with regular chow and water with or without 20% of glucose or sucrose or fructose. Mice were sacrificed at 7 pm as controls and 3, 6 or 12 hours following feeding.

value: BALB/c

tag: gender

value: male

value: 8 weeks

value: wild type

tag: treatment (drink)

value: Control Water + 20% Fructose

tag: time (feed duration)


title: DM1_WB_1196

description: rRNA and globin depleted total RNA

value: 35 years of age


title: DM1_WB_1198

description: rRNA and globin depleted total RNA

value: 33 years of age


title: 170406_p1_h12

value: brain


title: 170406_p1_h9


title: DM2_WB_1194

description: rRNA and globin depleted total RNA

value: 57 years of age


title: Liver, BALB/c, Control Water + 20% Sucrose, 12h (JC129)

description:
group 25, rep 5
JC129

value: Control Water + 20% Sucrose


title: High_12


title: DM1_WB_1195

description: rRNA and globin depleted total RNA

value: 46 yeras of age


title: High_83


title: 170406_p1_h8


title: Ctrl_WB_1186

description: rRNA and globin depleted total RNA

value: Control

value: 23 years of age


title: DM2_WB_1218

description: rRNA and globin depleted total RNA

value: 44 years of age


title: Liver, BALB/c, Control Water, 12h (JC127)

description:
group 23, rep 5
JC127

value: Control Water


title: High_67


title: High_75


title: DM2_WB_1220

description: rRNA and globin depleted total RNA

value: 46 years of age


title: Liver, C57BL6/J, Control Water + 20% Fructose, 12h (JC126)

description:
group 22, rep 5
JC126


title: High_51

value: single cell


title: Ctrl_WB_1215

description: rRNA and globin depleted total RNA

value: 58 years of age


title: 170406_p1_g10


title: 170406_p1_h5


title: High_59


title: 170406_p1_h6


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 12h (JC125)

description:
group 21, rep 5
JC125a

value: male


title: 170406_p1_h3


title: Liver, C57BL6/J, Control Water + 20% Glucose, 12h (JC124)

description:
group 20, rep 5
JC124a

value: 8 weeks

value: Control Water + 20% Glucose


title: Ctrl_WB_1205

description: rRNA and globin depleted total RNA


title: High_11


title: High_19


title: Liver, BALB/c, Control Water + 20% Glucose, 12h (JC128)

description:
group 24, rep 5
JC128

value: BALB/c

value: wild type


title: DM1_WB_1207

description: rRNA and globin depleted total RNA

value: 31 years of age


title: High_43


title: DM1_WB_1208

description: rRNA and globin depleted total RNA


title: 170406_p1_h4

value: brain


title: Liver, BALB/c, Control Water, 6h (JC119)

description:
group 15, rep 5
JC119


title: 170406_p1_h7


title: High_35


title: Liver, BALB/c, Control Water + 20% Fructose, 6h (JC122)

description:
group 18, rep 5
JC122

value: Control Water + 20% Fructose


title: DM1_WB_1206

description: rRNA and globin depleted total RNA

value: 29 years of age


title: High_27


title: Liver, BALB/c, Control Water + 20% Sucrose, 6h (JC121)

description:
group 17, rep 5
JC121

value: Control Water + 20% Sucrose


title: 170406_p1_g9


title: Liver, BALB/c, Control Water + 20% Glucose, 6h (JC120)

description:
group 16, rep 5
JC120


title: High_3


title: DM2_WB_1201

description: rRNA and globin depleted total RNA

value: 42 years of age


title: 170406_p1_g12


title: Liver, C57BL6/J, Control Water, 12h (JC123)

description:
group 19, rep 5
JC123a


title: High_82


title: Liver, C57BL6/J, Control Water + 20% Fructose, 6h (JC118)

description:
group 14, rep 5
JC118a


title: Ctrl_WB_1204

description: rRNA and globin depleted total RNA

value: Control

value: 60 years of age


title: 170406_p1_h1


title: sALS_PBMC_3601

description:
rRNA depleted total RNA
Stored at ambient temperature >4 hours

source_name: Peripheral blood mononuclear cell (PBMC)

value: sALS


title: DM2_WB_1200

description: rRNA and globin depleted total RNA

value: 53 years of age


title: High_74

value: single cell


title: Liver, C57BL6/J, Control Water + 20% Glucose, 6h (JC116)

description:
group 12, rep 5
JC116


title: sALS_PBMC_2001

value: 77 years of age


title: DM1_PBMC_1127+1128

description:
rRNA depleted total RNA
Stored at ambient temperature >24 hours

value: 19 and 39 years of age


title: Liver, C57BL6/J, Control Water, 6h (JC115)

description:
group 11, rep 5
JC115

value: male

value: 8 weeks

value: Control Water


title: High_66


title: 170406_p1_h2


title: 170406_p1_g7


title: 170406_p1_g11


title: 170406_p1_g5


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 6h (JC117)

description:
group 13, rep 5
JC117a

value: wild type


title: High_58


title: DM1_PBMC_1142

value: 31 years of age


title: Liver, BALB/c, Control Water + 20% Fructose, 3h (JC114)

description:
group 10, rep 5
JC114a

value: BALB/c


title: 170406_p1_g6

value: brain


title: 170406_p1_g1


title: DM1_PBMC_1156


title: DM2-SR_PBMC_1119

value: 41 years of age


title: Liver, BALB/c, Control Water + 20% Glucose, 3h (JC112)

description:
group 8, rep 5
JC112

value: Control Water + 20% Glucose


title: High_42


title: Liver, BALB/c, Control Water + 20% Sucrose, 3h (JC113)

description:
group 9, rep 5
JC113a

value: Control Water + 20% Sucrose


title: 170406_p1_g4


title: High_34


title: Liver, BALB/c, Control Water, 3h (JC111)

description:
group 7, rep 5
JC111a


title: DM2-SR_PBMC_1117

value: 72 years of age


title: 170406_p1_g8


title: Liver, C57BL6/J, Control Water + 20% Fructose, 3h (JC110)

description:
group 6, rep 5
JC110a

value: Control Water + 20% Fructose


title: High_26


title: High_50


title: DM2-LR_PBMC_1161

value: 66 years of age


title: 170406_p1_g3


title: DM2-SR_PBMC_1116

value: 26 years of age


title: 170406_p1_f12


title: High_18

value: single cell


title: High_10


title: PAN GEnC derived EVs3 [miRNA-seq]

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

data_processing:
Pipeline: TIGER https://www.ncbi.nlm.nih.gov/pubmed/30128086
Step 1: Pre-processing: To assess raw data quality, FastQC was performed at the raw read level to check for base quality, total read counts, and adapter identification. Cutadapt was then used to trim 3’ adapters from processed reads (-a TGGAATTCTCGGGTGCCAAGG). Cutadapt was then used to remove the first and last 4 bases from the trimmed reads and all trimmed reads <16 nts in length were removed (-m 16 -u 4 -u -4). After trimming, read length distributions were plotted and FastQC was performed on trimmed reads to validate the efficiency of adapter trimming. To generate identical read files, trimmed reads in each sample were collapsed into non-redundant “identical” reads in FASTQ format and copy numbers were recorded for downstream analysis.
Step 2: Genome Alignment (Human) In the Host Genome & Database alignment module, bowtie (v1.1.2) was used to map reads to a costumed database with option (-a -m 100 --best - strata -v 1) which allows 1 mismatch (MM) and 100 multi-mapped loci, and only the best matches were recorded. Counting and differential expression analysis of miRNAs were performed. All prepossessed quality reads were assigned to different classes of annotated sRNAs using distinct rules -- miRNA: 1 MM, ≥16nt, offset -2, -1, 0, 1, 2. Differential expression of tabulated read counts were performed by DEseq2.
Genome_build: human GRCh37

source_name: Podocytes

growth_protocol: GEnCs were incubated at 33℃ in 5% CO2 to proliferate in microvascular cell growth kit, then thermoswitched at 37℃, 5% CO2 in attachment factor coated plates. Podocytes were incubated at 33℃ in 5% CO2 in RPMI supplemented with 10% PS, 25% FCS, 5% L-glutamine, and 5% ITS. Cells were induced to differentiate at 37℃ in 5% CO2.

extract_protocol:
RNA from 2x10^5 podocytes incubated for 24h with EVs derived from GEnCs was isolated using the Total RNA Purification Kit (Norgen Biotec) according to the manufacturer's instructions.
Libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq Kit v3

treatment_protocol: GENCs were incubated in microvascular cell growth kit media supplemented with 5% exosome depleted FBS. GEnCs were either unstimulated (steady state, SS), or stimulated with glucose (Glu, 30mmol), or puromycin aminonucleoside (PAN, 100ug/mL) for 24hr. Cell supernatants were spun at 300g for 10 min, then 2,000g for 15min, and then ultracentrifuged for 10,000g for 30min to remove cell debris and large EVs. Equal supernatant volumes were then ultracentrifuged at 100,000g for 70min at 4℃. EV pellets were resuspended in 300uL of podocyte media plus 5% exosome depleted FBS. 2x10^5 podocytes were untreated (UT) or treated with EVs from GEnCs from SS, Glu or PAN conditions for 24hr.

tag: podocyte treatment

value: GEnC derived EVs

tag: genc treatment

value: PAN


title: Liver, C57BL6/J, Control Water + 20% Glucose, 3h (JC108)

description:
group 4, rep 5
JC108

tag: strain

value: male

tag: age


title: PAN GEnC derived EVs1 [miRNA-seq]


title: Liver, C57BL6/J, Control Water, 3h (JC107)

description:
group 3, rep 5
JC107a

value: 8 weeks


title: 170406_p1_f10

tag: tissue


title: High_73

tag: flow purified

tag: fluidigm c1 platform


title: High_65


title: PAN GEnC derived EVs2 [miRNA-seq]


title: High_81


title: Liver, C57BL6/J, Control Water, 0h (JC105)

description:
group 1, rep 5
JC105

tag: genotype

value: Control Water


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 3h (JC109)

description:
group 5, rep 5
JC109a

value: wild type


title: LPS GEnC derived EVs3 [miRNA-seq]

value: LPS


title: 170406_p1_f9

tag: brain region


title: Liver, BALB/c, Control Water, 0h (JC106)

description:
group 2, rep 5
JC106a

value: BALB/c


title: 170406_p1_g2

value: brain


title: High_2


title: 170406_p1_f8


title: LPS GEnC derived EVs1 [miRNA-seq]


title: 170406_p1_f11


title: LPS GEnC derived EVs2 [miRNA-seq]


title: Liver, BALB/c, Control Water + 20% Sucrose, 12h (JC103)

description:
group 25, rep 4
JC103


title: High_57


title: High_49


title: Liver, C57BL6/J, Control Water + 20% Fructose, 12h (JC100)

description:
group 22, rep 4
JC100


title: 170406_p1_f7


title: High_41


title: Glucose GEnC derived EVs1 [miRNA-seq]

value: Glucose


title: Liver, BALB/c, Control Water, 12h (JC101)

description:
group 23, rep 4
JC101


title: 170406_p1_f6


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 12h (JC099)

description:
group 21, rep 4
JC099a


title: High_17


title: Glucose GEnC derived EVs2 [miRNA-seq]


title: Steady state GEnC derived EVs2 [miRNA-seq]

value: Steady state


title: Liver, C57BL6/J, Control Water, 12h (JC097)

description:
group 19, rep 4
JC097


title: Glucose GEnC derived EVs3 [miRNA-seq]


title: High_25


title: High_33


title: Liver, C57BL6/J, Control Water + 20% Glucose, 12h (JC098)

description:
group 20, rep 4
JC098

value: Control Water + 20% Glucose


title: 170406_p2_b5


title: Liver, BALB/c, Control Water + 20% Fructose, 6h (JC096)

description:
group 18, rep 4
JC096


title: Steady state GEnC derived EVs3 [miRNA-seq]


title: 170406_p1_f5


title: Liver, BALB/c, Control Water + 20% Sucrose, 6h (JC095)

description:
group 17, rep 4
JC095

value: Control Water + 20% Sucrose


title: High_9


title: Steady state GEnC derived EVs1 [miRNA-seq]


title: Low_80


title: Liver, BALB/c, Control Water, 6h (JC093)

description:
group 15, rep 4
JC093


title: 170406_p1_f3


title: 170406_p1_f1


title: 170406_p1_f4


title: Untreated  3 [miRNA-seq]

value: Untreated


title: High_1


title: Low_72


title: 170406_p1_e12


title: Liver, C57BL6/J, Control Water + 20% Fructose, 6h (JC092)

description:
group 14, rep 4
JC092

value: Control Water + 20% Fructose


title: Untreated  2 [miRNA-seq]


title: 170406_p1_e11


title: 170406_p1_e9


title: Untreated  1 [miRNA-seq]


title: Liver, C57BL6/J, Control Water + 20% Glucose, 6h (JC090)

description:
group 12, rep 4
JC090


title: 170406_p1_e10


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 6h (JC091)

description:
group 13, rep 4
JC091


title: Liver, BALB/c, Control Water + 20% Fructose, 3h (JC088)

description:
group 10, rep 4
JC088


title: RPE1-Pulse-plate09-unlabeled

description: 5-ethymyluridin labeling

source_name: RPE1-FUCCI cells treated with DSMO for 120 min, or EU for 15, 30, 45, 60, 120, 180 minutes

tag: cell type

value: FUCCI


title: 170406_p1_e6


title: 170406_p1_e8


title: RPE1-Pulse-plate10-unlabeled

description: 5-ethymyluridin labeling


title: Low_32

value: single cell


title: Liver, C57BL6/J, Control Water, 6h (JC089)

description:
group 11, rep 4
JC089


title: Low_40


title: Liver, BALB/c, Control Water + 20% Sucrose, 3h (JC087)

description:
group 9, rep 4
JC087


title: 170406_p1_e7


title: Low_64


title: RPE1-Pulse-plate08-unlabeled

description: 5-ethymyluridin labeling


title: RPE1-Pulse-plate09-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Glucose, 6h (JC094)

description:
group 16, rep 4
JC094


title: Liver, BALB/c, Control Water + 20% Glucose, 3h (JC086)

description:
group 8, rep 4
JC086


title: Low_24


title: RPE1-Pulse-plate08-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water, 3h (JC085)

description:
group 7, rep 4
JC085


title: 170406_p1_e5


title: RPE1-Pulse-plate10-labeled

description: 5-ethymyluridin labeling


title: Low_48


title: 170406_p1_e4


title: Liver, C57BL6/J, Control Water + 20% Fructose, 3h (JC084)

description:
group 6, rep 4
JC084


title: 170406_p1_e3


title: RPE1-Pulse-plate07-unlabeled

description: 5-ethymyluridin labeling


title: Low_8


title: Liver, C57BL6/J, Control Water + 20% Glucose, 3h (JC082)

description:
group 4, rep 4
JC082


title: 170406_p1_e2


title: Low_71


title: Low_63


title: Low_55


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 3h (JC083)

description:
group 5, rep 4
JC083a


title: RPE1-Pulse-plate06-unlabeled

description: 5-ethymyluridin labeling


title: Low_56


title: Low_16


title: Low_79


title: RPE1-Pulse-plate06-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_e1


title: RPE1-Pulse-plate05-unlabeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water, 0h (JC080)

description:
group 2, rep 4
JC080


title: RPE1-Pulse-plate05-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_d12


title: Liver, C57BL6/J, Control Water, 3h (JC081)

description:
group 3, rep 4
JC081


title: 170406_p1_d11


title: 170406_p1_f2


title: 170406_p1_d10


title: Liver, C57BL6/J, Control Water, 0h (JC079)

description:
group 1, rep 4
JC079


title: Low_39


title: RPE1-Pulse-plate07-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Fructose, 12h (JC078)

description:
group 26, rep 3
JC078


title: RPE1-Pulse-plate04-unlabeled

description: 5-ethymyluridin labeling


title: RPE1-Pulse-plate04-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_d9


title: Low_31


title: RPE1-Pulse-plate03-unlabeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Sucrose, 12h (JC077)

description:
group 25, rep 3
JC077


title: 170406_p1_d8


title: 170406_p1_d7


title: 170406_p1_d6


title: Low_23


title: Low_78


title: RPE1-Pulse-plate03-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water, 12h (JC075)

description:
group 23, rep 3
JC075


title: Liver, BALB/c, Control Water + 20% Glucose, 12h (JC076)

description:
group 24, rep 3
JC076


title: RPE1-Pulse-plate01-unlabeled

description: 5-ethymyluridin labeling


title: Low_7


title: 170406_p1_d4


title: Liver, C57BL6/J, Control Water + 20% Fructose, 12h (JC074)

description:
group 22, rep 3
JC074


title: RPE1-Pulse-plate02-labeled

description: 5-ethymyluridin labeling


title: RPE1-Pulse-plate02-unlabeled

description: 5-ethymyluridin labeling


title: Low_15


title: Low_70


title: 170406_p1_d3


title: Low_47


title: Liver, C57BL6/J, Control Water + 20% Glucose, 12h (JC072)

description:
group 20, rep 3
JC072


title: RPE1-Pulse-plate01-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_d5


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 12h (JC073)

description:
group 21, rep 3
JC073


title: RPE1-Chase-plate12-unlabeled

description: 5-ethymyluridin labeling

source_name: RPE1-FUCCI cells treated with DSMO for 120 min, or EU for ~22 hours with a U chase 0, 60, 120, 240 or 360 minutes


title: Liver, C57BL6/J, Control Water, 12h (JC071)

description:
group 19, rep 3
JC071


title: Low_54


title: 170406_p1_d2


title: Low_62


title: RPE1-Chase-plate12-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_d1


title: Liver, BALB/c, Control Water + 20% Fructose, 6h (JC070)

description:
group 18, rep 3
JC070


title: Liver, BALB/c, Control Water + 20% Sucrose, 6h (JC069)

description:
group 17, rep 3
JC069


title: RPE1-Chase-plate11-unlabeled

description: 5-ethymyluridin labeling


title: Low_46


title: 170406_p1_c12


title: Low_38


title: 170406_p1_c10


title: 170406_p1_c9


title: Low_30


title: RPE1-Chase-plate11-labeled

description: 5-ethymyluridin labeling


title: Liver, C57BL6/J, Control Water + 20% Fructose, 6h (JC066)

description:
group 14, rep 3
JC066


title: RPE1-Chase-plate10-unlabeled

description: 5-ethymyluridin labeling


title: 170406_p1_c8


title: Low_22


title: RPE1-Chase-plate10-labeled

description: 5-ethymyluridin labeling


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 6h (JC065)

description:
group 13, rep 3
JC065


title: 170406_p1_c7


title: Low_14


title: Liver, C57BL6/J, Control Water + 20% Glucose, 6h (JC064)

description:
group 12, rep 3
JC064


title: Low_6


title: RPE1-Chase-plate09-unlabeled

description: 5-ethymyluridin labeling


title: 170406_p1_c5


title: Liver, C57BL6/J, Control Water, 6h (JC063)

description:
group 11, rep 3
JC063


title: 170406_p1_c6


title: Low_77


title: Low_85


title: RPE1-Chase-plate08-unlabeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Glucose, 6h (JC068)

description:
group 16, rep 3
JC068


title: 170406_p1_c4


title: Low_69


title: Liver, BALB/c, Control Water, 6h (JC067)

description:
group 15, rep 3
JC067


title: Liver, BALB/c, Control Water + 20% Sucrose, 3h (JC061)

description:
group 9, rep 3
JC061


title: RPE1-Chase-plate08-labeled

description: 5-ethymyluridin labeling


title: Low_61


title: RPE1-Chase-plate07-unlabeled

description: 5-ethymyluridin labeling


title: Low_53


title: 170406_p1_c2


title: Liver, BALB/c, Control Water + 20% Glucose, 3h (JC060)

description:
group 8, rep 3
JC060


title: Liver, BALB/c, Control Water, 3h (JC059)

description:
group 7, rep 3
JC059


title: 170406_p1_c3


title: RPE1-Chase-plate07-labeled

description: 5-ethymyluridin labeling


title: RPE1-Chase-plate06-unlabeled

description: 5-ethymyluridin labeling


title: 170406_p1_b12


title: RPE1-Chase-plate06-labeled

description: 5-ethymyluridin labeling


title: Liver, C57BL6/J, Control Water + 20% Fructose, 3h (JC058)

description:
group 6, rep 3
JC058


title: RPE1-Chase-plate09-labeled

description: 5-ethymyluridin labeling


title: Low_45


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 3h (JC057)

description:
group 5, rep 3
JC057


title: Low_37


title: RPE1-Chase-plate05-unlabeled

description: 5-ethymyluridin labeling


title: Liver, C57BL6/J, Control Water + 20% Glucose, 3h (JC056)

description:
group 4, rep 3
JC056


title: RPE1-Chase-plate05-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Fructose, 3h (JC062)

description:
group 10, rep 3
JC062


title: 170406_p1_b10


title: 170406_p1_b9


title: Low_21


title: Liver, BALB/c, Control Water, 0h (JC054)

description:
group 2, rep 3
JC054


title: 170406_p1_c1


title: 170406_p1_b8


title: Low_5


title: Liver, C57BL6/J, Control Water, 0h (JC053)

description:
group 1, rep 3
JC053


title: RPE1-Chase-plate04-labeled

description: 5-ethymyluridin labeling


title: 170406_p1_b7


title: Low_84


title: RPE1-Chase-plate03-labeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water + 20% Fructose, 12h (JC052)

description:
group 26, rep 2
JC052a


title: Liver, C57BL6/J, Control Water, 3h (JC055)

description:
group 3, rep 3
JC055


title: RPE1-Chase-plate03-unlabeled

description: 5-ethymyluridin labeling


title: 170406_p1_b6


title: 170406_p1_b4


title: RPE1-Chase-plate01-unlabeled

description: 5-ethymyluridin labeling


title: Low_76


title: Low_29


title: Liver, BALB/c, Control Water + 20% Sucrose, 12h (JC051)

description:
group 25, rep 2
JC051a


title: 170406_p1_b11


title: Low_68


title: RPE1-Chase-plate01-labeled

description: 5-ethymyluridin labeling


title: Low_60


title: Low_13


title: 170406_p1_b3


title: Liver, BALB/c, Control Water + 20% Glucose, 12h (JC050)

description:
group 24, rep 2
JC050a


title: RPE1-Chase-plate04-unlabeled

description: 5-ethymyluridin labeling


title: Liver, BALB/c, Control Water, 12h (JC049)

description:
group 23, rep 2
JC049a


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_09_mutant_03

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
RNA sequencing (RNA-seq) libraries were sequenced on Illumina NextSeq500 (160-nt single-end), yielding 44.4-49.6 million reads per sample. Many reads show adapter pieces at the 3’ end, which need to be trimmed, Thus, reads were trimmed at the 3’ end to a total length of 100bp since downstream splicing analysis requires reads of equal length rather than individually adapter trimmed reads. Sequencing qualities were checked using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All reads were mapped to the human genome (assembly version hg38/GRCh38) and its annotation (GENCODE release 25) (Harrow et al., 2012) with the splice-aware aliger STAR (version 2.5.4b) (Dobin et al., 2013) with up to 4% allowed mismatches and an overhang of at most 159 base pairs at each splice junction. Reads were sorted using SAMtools (version 1.5) (Li et al., 2009). Uniquely mapped reads were summarized per gene using featureCounts from the subread package (version 1.5.1) (Liao et al., 2014).
Genome_build: hg38

source_name: GS overexpression replicate 3

extract_protocol:
Hela was lysed in 1ml lysis buffer followed by immunoprecipitation as described on previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016)
in vivo iCLIP libraries were prepared from HeLa cells under U2AF65 KD and wild-type conditions according to the previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016). For immunoprecipitation, we used 7.5 µg monoclonal anti-U2AF65 antibody produced in mouse (Sigma cat. no. U4758) per sample. Each iCLIP library was done in triplicates. The libraries were sequenced as single-end reads on an Illumina HiSeq 2500 and NextSeq 500 sequencing system.

tag: cell line

value: Hela

tag: technique

value: RNA-Seq

tag: barcode

value: ATTCCT


title: Low_52

source_name: Hematopoietic Stem Cells


title: 170406_p1_b2


title: Low_44


title: Liver, C57BL6/J, Control Water + 20% Fructose, 12h (JC048)

description:
group 22, rep 2
JC048a

value: male

value: 8 weeks


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 12h (JC047)

description:
group 21, rep 2
JC047a

value: wild type


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_07_mutant_01

source_name: GS overexpression replicate 1

value: CGTACG


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_08_mutant_02

source_name: GS overexpression replicate 2

value: ACTGAT


title: 170406_p1_a7

value: brain


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_06_WT_03

source_name: WT overexpression replicate 3

value: GGCTAC


title: Low_36


title: 170406_p1_b1


title: 170406_p1_a9


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_05_WT_02

source_name: WT overexpression replicate 2

value: TAGCTT


title: Liver, BALB/c, Control Water + 20% Fructose, 6h (JC044)

description:
group 18, rep 2
JC044a

value: BALB/c


title: Liver, C57BL6/J, Control Water + 20% Glucose, 12h (JC046)

description:
group 20, rep 2
JC046a

value: Control Water + 20% Glucose


title: Low_20


title: Liver, C57BL6/J, Control Water, 12h (JC045)

description:
group 19, rep 2
JC045a

value: Control Water


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_04_WT_01

source_name: WT overexpression replicate 1

value: GATCAG


title: 170406_p1_a11


title: Liver, BALB/c, Control Water + 20% Sucrose, 6h (JC043)

description:
group 17, rep 2
JC043a

value: Control Water + 20% Sucrose


title: 170406_p1_a8


title: Low_12

value: single cell


title: 170406_p1_a10


title: Low_4


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_02_control_02

source_name: control replicate 2

value: Hela

value: TTAGGC


title: 170406_p1_a12


title: Low_83


title: Liver, BALB/c, Control Water + 20% Glucose, 6h (JC042)

description:
group 16, rep 2
JC042


title: Liver, BALB/c, Control Water, 6h (JC041)

description:
group 15, rep 2
JC041a


title: 170406_p1_a6


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_01_control_01

source_name: control replicate 1

value: RNA-Seq

value: ATCACG


title: Low_28


title: Liver, C57BL6/J, Control Water + 20% Fructose, 6h (JC040)

description:
group 14, rep 2
JC040a

value: male

value: 8 weeks

value: Control Water + 20% Fructose


title: 170406_p1_a5


title: Low_67


title: 170406_p1_a4