title: mix60_repair

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 60 minute 37C incuabtion prior to RT. A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

molecule: other

organism: synthetic construct

source_name: 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant. These repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: S943Nr6

status: Public on Apr 16 2020

type: SRA

city: Berlin

first: Katrin

last: Kreuzer

address: Max-Dohrn-Str. 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

library_source: transcriptomic

data_processing:
De-multipltiplexing of sequencing reads was accomplished using Illumina bcl2fastq (version 2.19)
Adapter trimming was performed with Skewer (version 0.2.2)
Alignment to the human genome (hg 19) was performed using STAR (version 2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: Counted reads per gene as raw counts and normalized counts. Normalized counts contain all genes which sum of mapped reads across all samples is greater than one. Normalizing was performed with DESeq2.

molecule: total RNA

organism: Homo sapiens

source_name: HepaRG cell line

growth_protocol: HepaRG cells were seeded in 6-well-plates (200 00 cells per well) and cultivated and proliferated in Williams E medium with 2 mM glutamine supplemented with 10 % fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 0.05 % human insulin and 50 µM hydrocortison. After a 2-week proliferation phase, cells were differentiated in the mentioned culture medium additionally containing 1.7 % DMSO, for another 2 weeks.

extract_protocol:
RNA isolation was performed with the RNeasy Mini Kit (Qiagen) according to the manufactures' protocol.
Libraries were prepared from 100 ng of RNA using the TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: Differentiated HepaRG cells were treated with the non toxic concentrations of 1 µM aflatoxin B1, 5 µM benzo[a]pyrene, 1 µM lasiocarpine, 250 µM methyleugenol or 20 mM nitrosopyrrolidine for 24h.

tag: treatment

value: Benzo[a]pyrene

tag: cas number

tag: concentration

value: 5 uM


title: BE1

city: Tromso

first: Peter

last: Utnes

address: Hansine Hansens veg 18

country: Norway

institute: UiT - The Arctic University of Norway

data_processing:
BaseCalling was done with Illumina Casava Pipeline 1.8.2.
Initial quality assessment was based on data passing the Illumina Chastity filter.
Quality assessment was based on the reads using the FASTQC quality control.
Reads were mapped with STAR Aligner 2.5 onto the human reference genome GRCh38.
Duplicate removal was done with Picard’s tool MarkDuplicates (http://broadinstitute.github.io/picard).
Read counting was performed with featureCounts v1.5.0-p2 on ENSEMBL gene annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with CPM values for each sample

source_name: Neuroblastoma cell line

growth_protocol: CHLA cells were grown in Iscove’s modified Dulbecco’s medium supplemented with 20% fetal bovine serum, 4 mM L-glutamine, and 1× ITS (5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL selenous acid). The other cell lines were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 2 mM L-glutamine (final concentrations).    All cell lines were cultured at 37°C in a humidified incubator with 95% air and 5% CO2 atmosphere without antibiotics. The identity of all cell lines was authenticated by short tandem repeat (STR) analysis at the Center of Forensic Genetics, The Arctic University of Norway—UiT, Norway. Cells were tested and confirmed negative for mycoplasma contamination.

extract_protocol:
Total RNA was extracted by adding 1 mL of TRIzol (Invitrogen, Carlsbad, USA) to the samples, vortexed for 1 min, and placed at room temperature for 5 min before adding 200 µL chloroform. The phases were mixed and phase separation was done by centrifuging at 12 000×g, 15 min at 4°C. To maximize yields and reducing the risk of phenol contamination, the lower phenol phase was removed and the sample was re-spun at 12 000×g, 15 min at 4°C. The aqueous phase was moved to a new tube with glycogen (Ambion) and 1 volume of 0.2 M NH4OAc isopropanol. The mixture was chilled at −20°C for 15 min and RNA was co-precipitated with glycogen by centrifuging at 12 000×g, 15 min, 4°C. The visible RNA pellet was washed twice in 1 mL 75 % ethanol and re-acquiring of the pellet was done by spinning down at 7500×g, 5 min at 4°C. The pellet was resuspended in Tris-ethylenediaminetetraacetic acid (EDTA) buffer (10 mM Tris-HCl (pH 8.0), 0.1 mM EDTA). RNA concentration and DNA contamination were assessed using NanoDrop 2000 (Thermo Scientific).
RNA concentrations were measured using Agilent’s Eukaryote Total RNA Pico Assay. After fragmentation, a quality control (QC) was done on Agilent 2100 HS DNA chip. Concentration was determined with smear analysis on the Agilent 2100 and checked for degradation. Samples were prepared using the NEBNext Ultra Directional RNA Library Protocol (New England Biolabs). The paired-end, cDNA libraries were consequently sequenced on the Illumina HiSeq 2000 sequencer.

tag: cell line

tag: Sex

value: male

tag: age (months)


title: S943Nr5


title: NUGC3-control (1)

type: RNA

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression profile of NUGC3-control (1)

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

label: biotin

source_name: PRMT6 wild-type Human gastric cancer cell line NUGC3

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human gastric cancer cell line NUGC3 was purchased from the Human Science Research Resources Bank, and then grown in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting PRMT6 (5'-GACGGTACTGGACGTGGGCG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). PRMT6-konckout clones were obtained by limiting dilution.

tag: cell type

value: Gastric cancer


title: S943Nr8

value: Nitrosopyrrolidine

value: 20 mM


title: KO_2DL_n_2_input

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

country: Canada

institute: University of Montreal

description: Illumina sequencing

library_source: genomic

data_processing:
Libraries were sequenced with 100 bp single-end reads
Sequences were mapped to mm9 using Bowtie 2 (v2.0.5) with default parameters (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
Poor quality reads (MAPQ<=30, reads mapping to chrM, chrY and patch chromosomes were also removed.
Reads were further filtered to remove PCR duplicates using Picard Tool MarkDuplicates (v2.6.0, https://broadinstitute.github.io/picard/). H3K27me3 peaks were called using MACS2 v2.0.10 using the following parameters: --keep-dup all -B -- broad -q 0.05.
The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over the input sample. We then calculated the maximum signal intensity over every peak for conditions being compared using mapBed –o max and quantile normalized them across samples.
Spearman correlation was then calculated between average normalized signal intensity across replicates for each condition which was then plotted in heatmap. Analysis of downstream peak calling were carried out using Bedtools v2.26.0 (https://bedtools.readthedocs.io/en/latest/) and R 3.4.1 (https://www.r-project.org/). Figures were plotted using ggplot2 (https://ggplot2.tidyverse.org/).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: Tert-/- Embryonic stem cells

growth_protocol: Murine embryonic stem cells were thawed (initial cell passage indicated), cultured in LIF containing media for 2 days (2DL), transferred to media containing 5 micromolar ATRA for a further 6 days (6DA) and transferred to LIF-containing media for a further 6 days (6DL).

extract_protocol:
ESC populations were harvested and crosslinked in formaldehyde. Cell pellets (frozen, or fresh) were subjected to chromatin preparation and immunopreciptiation with an antibody against H3K27me3, followed by extraction of genomic DNA.
DNA samples were quantified, and libraries were generated and amplified by PCR, followed by library size determination using a Agilent BioAnalyzer.
Libraries were then pooled, quantified, and sequenced on an Illumina MiSeq to determine the amount required for deep sequencing. Pooled libraries were then diluted accordingly and loaded on an Illumina NovSeq6000 for sequencing.

treatment_protocol: ESC populations were untreated (DMSO) or treated throughout the 14 day differentiation treatment with the compounds indicated: UNC1999, UNC2400, GSK343. The compound concentration was 1 micromolar for UNC1999 and UNC2400, and 3 micromolar GSK343.

tag: strain

tag: sequencing run#

tag: passage numbers

tag: treatment group

tag: sample preparation

value: ChIP-seq


title: AGS-PRMT6-KO (2)

description: Gene expression profile of AGS-PRMT6-KO (2)

source_name: PRMT6 knockout Human gastric cancer cell line AGS

treatment_protocol: Human gastric cancer cell line AGS was purchased from the Human Science Research Resources Bank, and then grown in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting PRMT6 (5'-GACGGTACTGGACGTGGGCG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). PRMT6-konckout clones were obtained by limiting dilution.


title: AGS-control (2)

description: Gene expression profile of AGS-control (2)

source_name: PRMT6 wild-type Human gastric cancer cell line AGS


title: S943Nr4


title: AGS-control (1)

description: Gene expression profile of AGS-control (1)


title: AGS-PRMT6-KO (1)

description: Gene expression profile of AGS-PRMT6-KO (1)


title: Input.rep1

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

institute: The University of Tokyo,

description: Ribosome Profiling

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
random barcode (UMI) triming with UMI-tools v1.0.1
rRNA alignment with bowtie2 v2.2.5
Alignment with TopHat v2.1.1 to Genome
Read quantitation using plastid v0.4.7
Genome_build: sacCer3
Supplementary_files_format_and_content: input.rep1.RPM.csv: Comma-separated text files contain following columns: 1. mrna; 2. codon (assigned by Psite); 3. E-site codon; 4. P-site codon; 5. A-site codon; 6. read count (RPM).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted by TRIzol reagent from the IPed ribosome.
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129.

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 Not4-FTP::natNT2

tag: protocol

value: RNase I footprinting, Sucrose cushion, RNA extraction


title: mix15_repair

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

country: USA

institute: University of Colorado School of Medicine

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 15 minute 37C incuabtion prior to RT. A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/rhumba/tree/master/haircut). Single cell RNA-Seq libraries were preprocessed using the 10x genomics software cellranger (3.0.2). The single cell DNA repair libraries were preprocessed to append the read 1 sequence to the paired read 2 read id using umi_tools extract(v 1.0.0 --bc-pattern CCCCCCCCCCCCCCCCNNNNNNNNNN)(Smith et al. 2017) followed by poly(A) tail and template switching oligo removal from read 2 using cutadapt (v. 1.8.3 -a AAAAAAAAAAA -g AAGCAGTGGTATCAACGCAGAGTACATGGG --minimum-length=2)  (Martin 2011). Reads were next aligned with bowtie2 (v 2.3.2 Langmead B, Salzberg S. 2012) to a repair substrate reference.     Following alignment, BAM files were processed to extract the alignment hairpin and position into a tag (XT) within the BAM file (tag_bam). UMI groups were identified and added as a tag (CB) using umi_tools group (--read-length = True --per-cell --output-bam = True --output-unmapped = True). BAM files were then sorted by cell barcode tag using samtools sort (v 1.5-4 -t CB -@ 23) (Li 2009). UMIs per hairpin_position were enumerated per cell using umi-tools count (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.    Count tables produced by umi_tools are then converted into sparseMatrix format using the scrunchy R package (https://github.com/hesselberthlab/scrunchy, umitools_to_mtx). Matrices are the filtered to include only the cell-associated barcodes using the scrunchy R package (filter_matrix). Cell-associated barcodes are identified from the mRNA data using cellranger (v 3.0.2) from the filtered barcodes.tsv output.
Genome_build: hg38, custom repair substrate reference
Supplementary_files_format_and_content: Text file containing cell barcodes, genes/features, and UMI counts per gene/fetaure per cell are provided

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 15 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant. These repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.

value: 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line


title: mix30_repair

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 30 minute 37C incuabtion prior to RT. A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 30 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant. These repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: Ecoli_Ven_pLtet01_mCh_ATC5_1_39853

city: Liverpool

first: Jonathan

middle: P

last: Bollback

state: Merseyside

address: Crown Street, Biosciences Building, Room 305

department: Functional and Comparative Genomics

country: United Kingdom

institute: University of Liverpool

description:
Baterial culture
Strain also contains mCherry gene under pLtet0-1 promoter, inducer ATC 5ng/mL

data_processing:
Sequence reads with an average read quality of >= 34 were retained for further analysis.
After quality controls, fastq files were aligned to the E. coli MG1655 genome (Genbank U00096.3) using the Bowtie2 aligner using RSEM’s (Langmead & Salzberg 2012) default settings.
The reference genome was modified in silico to contain the chromosomal modifications of tetR and fluorescent protein gene cassettes. Expected counts were calculated by using the defaults in RSEM (B. Li & Dewey 2011).
After between-sample normalization of the counts with the DESeq package of the R statistical software (Anders & Huber 2010), TPM (transcript per million) values for each gene were calculated and used in further analyses (B. Li & Dewey 2011).
Supplementary_files_format_and_content: Tab-delimited text file include normalized TPM values for each sample

organism: Escherichia coli

source_name: E.coli strain chromosomally market with Venus grown until OD:0.12 in M9 medium, replicate#1

growth_protocol: E.coli was grown in 1mL of rich M9 (1x M9 salts, 1% CAA, 0.4% glucose, 2mM MgSO4, 0.1mM CaCl2), with inducer ATC (5ng.mL) until OD0.12, in 96 deep-well plates.

extract_protocol:
16x1mL of bacterial culture was first combined together in a 50mL centrifuge tube, 32mL of Qiagen RNAprotect bacteria reagent was added onto the medium, mixed well. After 5 min of incubation at RT, cells were harvested with centrifugation at 5000xg for 10min. Total RNA was extracted as fl=ollows: 200uL of TE buffer containing lysozyme and 20uL Qiagen proteinase K was added on the pellet and resuspended with pipetting up and down. Vortex 10s, and incubated at RT for 10 min, vortexing every 2 mins. 700uL RLT buffer containing b-mercaptoethanol added and vortexed. 500uL 96% ethanol is added and Qiagen RNAeasy Mini Kit protocol 7 was followed.
RNA libraries were prepared for sequencing using RiboZero, NEB protocol.

tag: genotype

value: contain pZS*plasmid, with mCherry (RFP) under pLtet0-1 promoter


title: KAN

value: KAN

value: female


title: Ecoli_Ven_pLtet01_mCh_ATC5_2_39854

source_name: E.coli strain chromosomally market with Venus grown until OD:0.12 in M9 medium, replicate2


title: S943Nr3

value: Aflatoxin B1

value: 1 uM


title: pbmc60_repair

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 60 minute 37C incuabtion prior to RT. Fresh PBMCs were isolated from a healthy human donor.

source_name: Human PBMCs

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant to clean up the repair fraciton. The repair fraction was split in two to optimize the library prep. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.

value: Human PBMCs


title: pbmc30_repair

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 30 minute 37C incuabtion prior to RT. Fresh PBMCs were isolated from a healthy human donor.

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 30 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant to clean up the repair fraciton. The repair fraction was split in two to optimize the library prep. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: Not4.1

description: Ribosome Profiling

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
random barcode (UMI) triming with UMI-tools v1.0.1
rRNA alignment with bowtie2 v2.2.5
Alignment with TopHat v2.1.1 to Genome
Read quantitation using plastid v0.4.7
Genome_build: sacCer3
Supplementary_files_format_and_content: CSV files contain following columns: 1.Lane No. 2.gene name 3.Codon at Psite 4.Esite codon 5.Psite codon 6.Asite codon 7.Pause score

extract_protocol:
The ribosome was immunoprecipitated from lysate and then treated with RNase I. Total RNA was extracted by TRIzol reagent from the IPed ribosome.
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 .

value: Rnase I footprinting, ribosome IP, RNA extraction


title: Ecoli_CFP_pLtet01_mCh_ATC5_2_39848

source_name: E.coli strain chromosomally market with CFP grown until OD:0.12 in M9 medium, replicate#2


title: Not4.2

description: Ribosome Profiling


title: L7.2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPL7b-TAP::TRP1


title: S943Nr1


title: pbmc15_repair

description: Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with 15 minute 37C incuabtion prior to RT. Fresh PBMCs were isolated from a healthy human donor.

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 15 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant to clean up the repair fraciton. The repair fraction was split in two to optimize the library prep. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: Ecoli_CFP_pLtet01_mCh_ATC5_1_39847

source_name: E.coli strain chromosomally market with CFP grown until OD:0.12 in M9 medium, replicate#1


title: L7.1

description: Ribosome Profiling


title: OrR RNAseq 2

status: Public on Apr 15 2020

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

description: whole transcriptome

data_processing:
Base calling, read trimming and sample de-multiplexing was done using the standard Ion Torrent Suite. The reads were aligned to the Drosophila genome (ENSEMBL assembly BDGP5, downloaded 8 Jan 2015) using the TopHat aligner (v2.0.13) (Kim, 2013). To quantitate gene expression, uniquely aligned reads were assigned to the Drosophila exome (BDGP5) using htseq-count (Anders et al., 2015). Differential was assessed using negative binomial generalised linear models implemented in R/Bioconductor package DESeq2 (Love et al., 2014).
Genome_build: ENSEMBL BDGP5
Supplementary_files_format_and_content: bedgraph coverage

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: WT_L3 laval brain

growth_protocol: Drosophila melanogaster flies were grown at 25 °C on standard cornmeal-agar medium.

extract_protocol:
Brains were removed and flash frozen in liquid nitrogen before lysis. RNA was harvested using RNASpin Mini kit (GE Healthcare). polyA RNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to manufacturer’s instructions.
Libraries were prepared using Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Life Technologies) according to manufacturer's instructions.

treatment_protocol: No treatment

tag: strain background

value: OregonR

tag: genotype/variation

value: WT control

tag: developmental stage

value: wandering L3 larva

tag: tissue

value: brain


title: OrR RNAseq 3

description: whole transcriptome


title: SypN RNAseq 2

description: whole transcriptome

source_name: Syp mutant_L3 laval brain

value: Syp mutant


title: SypN RNAseq 1

description: whole transcriptome


title: OrR RNAseq 1

description: whole transcriptome


title: S943Nr2

tag: treatment

tag: cas number

tag: concentration


title: mix30_mrna

description: Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry) with 30 minute 37C incuabtion prior to RT. A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 30 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: SypN RNAseq 3

description: whole transcriptome


title: WT_5_PairH [10H2Lardelli_2]

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

data_processing:
Illumina BaseSpace was used for base-calling.
Reads were trimmed using AdapterRemoval v2.2.1 setting a minimum quality of 30 and a minimum length of 35.
Trimmed reads were aligned to the Danio rerio genome Ensembl Release 96 (GRCz11) using STAR v2.5.3a.
FeatureCount was used to count the align reads assigned to each gene, specifying that only unique alignments which strictly overlapped exonic regions were counted.
Genome_build: GRCz11
Supplementary_files_format_and_content: An output file was generated from FeatureCount containing the gene counts of all samples.

organism: Danio rerio

source_name: Clutch of larvae

growth_protocol: The larvae were raised in E3 medium for 7 days, allowing complete larval yolk absorption but not food intake

extract_protocol:
Total RNA was extracted from pooled larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).  DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-freeTM Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). PolyA amplification was performed for the construction of sequencing libraries.
Demultiplexed libraries were provided by the sequencing centre at SAHMRI as 75bp single-end reads.

value: wild type

value: larvae

tag: age

value: 7 days post-fertilization


title: WT_3_PairF [6F2Lardelli_2]


title: WT_5_PairH [10H2Lardelli]


title: WT_6_PairI [12I2Lardelli]


title: WT_1_PairB [2B2Lardelli_2]


title: WT_4_PairG [8G2Lardelli_2]


title: Q96K97del_4_PairG [7G1Lardelli_2]


title: WT_6_PairI [12I2Lardelli_2]


title: Q96K97del_1_PairB [1B1Lardelli_2]


title: Q96K97del_2_PairD [3D1Lardelli_2]


title: WT_2_PairD [4D2Lardelli]


title: Q96K97del_6_PairI [11I1Lardelli_2]


title: WT_3_PairF [6F2Lardelli]


title: Q96K97del_5_PairH [9H1Lardelli_2]


title: WT_2_PairD [4D2Lardelli_2]


title: WT_1_PairB [2B2Lardelli]


title: WT_4_PairG [8G2Lardelli]


title: Q96K97del_3_PairF [5F1Lardelli_2]


title: Q96K97del_5_PairH [9H1Lardelli]


title: Q96K97del_6_PairI [11I1Lardelli]


title: Q96K97del_4_PairG [7G1Lardelli]


title: Q96K97del_3_PairF [5F1Lardelli]


title: Q96K97del_1_PairB [1B1Lardelli]


title: Q96K97del_2_PairD [3D1Lardelli]


title: Th17_highsalt_3

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

data_processing:
Alignment: The reads were mapped to the reference transcriptome built from the human genome assembly GRCh38.p12 (Gencode release 28) using STAR v2.6.1a with the following parameters: -runMode alignReads --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted.
Read counting: Transcripts were quantified with salmon v0.11.3 in the alignment-based mode using the "quant" algorithm and library type "IUR".
Differential expression: Transcript abundance estimates were imported using tximport R package. Differentially expressed genes were identified using the R package DESeq2, considering the effect of samples originating from the same donor by using the design "~ replicate + condition". No fold change cutoff was set for determining differentially expressed genes and only the genes with a false discovery rate (FDR) < 0.05 by the Wald Test were considered significantly dysregulated. For GSEA and genes were ranked according to the shrunken fold change values calculated by DESeq2using the adaptive t prior shrinkage estimator ("apeglm").
Genome_build: GRCh38.p12 (Gencode release 28)
Supplementary_files_format_and_content: The files with the raw counts for transcript abundance contain the output from salmon ("quant.sf" file) containing the gene id, length, effective length, calculated TPM and raw counts. The file with the normalized counts for gene abundance is the output from DESeq2 "counts" function with "normalized=T" on the output of the "res" function and contains the normalized counts for all genes in each sample. The file with the differential expression is the output from DESeq2 "res" function containing all genes and their mean of normalized counts for all samples, log2 fold change between high salt versus low salt treatments, standard error, Wald statistic, Wald test p-value and Benjamini & Hochberg-adjusted p-values, along with gene symbol and gene description.

source_name: Sorted Th17 cells

growth_protocol: Fresh peripheral blood was obtained from healthy donors. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation using Ficoll-Paqu<e Plus (GE Healthcare). Th17 cells were isolated from the PBMCs by positive selection with CD4-specific microbeads (Miltenyi Biotec), using an autoMACS Pro Separator. Th17 cells were sorted to at least 98% purity using the following markers: CXCR3–CCR4+CCR6+CD45RA–. Th17 cells were cultured in RPMI-1640 medium supplemented with 2 mM glutamine, 1% (vol/vol) nonessential amino acids, 1% (vol/vol) sodium pyruvate, penicillin (50 U/ml), streptomycin (50 g/ml; all from Invitrogen) and 10% (vol/vol) fetal calf serum (FCS; Biochrom).

extract_protocol:
Total RNA was extracted from cells lysed in TRI reagent (Sigma-Aldrich) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and its quality was verified by an Agilent 2100 Bioanalyzer (Agilent) according to the manufacturer’s guidelines.
Library preparation for RNA-seq was performed using the TruSeq® Stranded Total RNA Sample Preparation Guide (Illumina) starting with 450 ng RNA as the input for each sample. Only 11 cycles were used for PCR amplification to minimize PCR bias. The barcoded libraries were sequenced on a HiSeq 2500 (Illumina) with paired-end, 100-bp reads. Approximately 6 Gb of sequencing reads were produced on average per sample.

treatment_protocol: Th17 cells were stimulated ex vivo for 48 hours with plate-bound anti-CD3 (2 µg/ml, clone TR66) and anti-CD28 (2 µg/ml CD28.2; BD Biosciences) antibodies for a total culture time of 5 days in the presence of low and high NaCl concentrations. Hypersalinity (high NaCl levels) was induced by increasing the NaCl concentration to 185 mM, while the baseline concentrations of NaCl in cell culture medium including supplements were 140 mM (NaCl, Sigma-Aldrich).

value: blood

tag: stimulation


title: Th17_lowsalt_3


title: Th17_highsalt_2


title: NormalFibroblast_primary_03_rep1

city: Budapest

first: Alexandra

last: Fullár

address: Üllői út 26

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

description: Gene expression of primary fibroblast from tumor free cervix tissue

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffers (Agilent) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Patient 03

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Fresh surgical specimens obtained from radical Wertheim hysterectomy were sent for routine pathology service. Tumorous and normal areas of surgical specimens taken from the same patient and not used for diagnosis were excised and cut into small pieces and placed into sixwell tissue culture dishes containing Cytogen Amnio Grow Plus medium (CytoGen GmbH, Sinn, Germany), optimized for development of primary cell culture.

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen). Integrity of RNA was confirmed on Experion Automated Electrophoresis System (Bio-Rad Laboratories GmbH, Münich, Germany).

tag: patient number

value: Patient 03

tag: cell type

value: primary fibroblasts from normal regions of uterine cervix

tag: fibroblast type

value: normal fibroblast


title: Th17_lowsalt_2


title: Th17_lowsalt_1


title: LECKSHV2

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
perform image analysis and base calling with Illumina's RTA v1.17 Software
demultiplex and generate files in FASTQ format, using Illumina's CASAVA v1.8.2 Software
remove reads that didn't pass Illumina's base call quality threshold
align reads, using TopHat v2.08b ( http://tophat.cbcb.umd.edu/ ) along with Bowtie 1.0.0 ( http://bowtie-bio.sourceforge.net/index.shtml ), using Ensembl's GRCh37 release 70 as the reference genome.
generate counts for each gene using htseq-count v0.5.3p9 (using the intersection-strict overlapping mode)
Genome_build: Ensembl's GRCh37 release 70
Supplementary_files_format_and_content: tab-delimited text file includes CPM (counts per million reads) for each sample

source_name: neonatal dermal microvasculature

extract_protocol:
RNA was isolated using the RNA isolation kit by Macherey-Nagel. Samples were cleaned and concentrated, where necessary, using Zymogen kit
RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep Kit v2 following the manufactures protocol.

value: Primary lymphatic-specific endothelial cells

tag: passage

tag: kshv infection

value: WT KSHV 1wpi


title: Jurkat SIX6 KO repl.2

city: Tampere

first: Laura

last: Oksa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: T-ALL cells

data_processing:
Base calling was mabe using CASAVA base recognition software and SecureCRT was used to data demultiplexin. These steps were performed by Novogene Europe (Cambridge, UK).
The quality of the raw reads was ensured with FastaQC (v0.11.08)
STAR software (version 2.7.1a) was used to map the reads to the human reference genome (hg19).
Tag directories were made from the alingment files and raw read counts were calculated using Homer tool kit ( v.4.11)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw read counts of the samples and replicates.

source_name: Jurkat Cas9 cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% FBS (Gibco).

extract_protocol:
Total RNA extraction was performed with PureLink™ RNA Mini Kit and On-Column PureLink® DNase Treatment Protocol was used to avoid contamination by genomic DNA (Ambion® by Life Technologies and Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols (Hiseq-PE150)

treatment_protocol: Cells were transfected with 2µg of empty px321-GFP plasmid or px321-GFP, which contains SIX6 KO gRNA, targeting exon1, containing the N-terminal SIX domain (SD). After 24h, GFP positive cells were single cell sorted. Single cell clones were Sanger sequenced to confirm the mutations and Western blot was used to confirm the decreased level of SIX6 protein. The clone chosen to further studies has 10 nucleotide deletion (chr14:60976402_60976411delTACCAGGAGG) and amino acid changes Y96Lfs*17 resulting an early stop codon.

tag: vector

value: SIX6 KO

tag: replicate


title: Jurkat ctrl repl.1

description: T-ALL cells

value: empty vector


title: DVCYC1

value: KSHV-Dvcyc 1wpi


title: Th17_highsalt_1


title: Jurkat ctrl repl.3

description: T-ALL cells


title: Jurkat SIX6 KO repl.1

description: T-ALL cells


title: Jurkat ctrl repl.2

description: T-ALL cells


title: LY_KSHV3

value: WT KSHV 48hpi


title: LECKSHV3


title: BL_KSHV3

value: Primary blood-specific endothelial cells


title: LY_KSHV2


title: Jurkat SIX6 KO repl.3

description: T-ALL cells


title: LY_KSHV1


title: LECKSHV1


title: DVCYC3


title: BL_KSHV1


title: DVCYC2


title: BL_KSHV2


title: SuvER-4936 native

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

description: Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into R (version 3.5.0) and processed by the RMA workflow implemented in the oligo package (median polish probe set summarization, RMA background correction, quantile normalization). Batch Effects were reduced by Empirical Bayes methods (ComBat) in the sva package. Treatment and phenotype were included as covariates in batch correction.

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days

value: primary lymphoma cells

value: native

tag: genotype

value: Suv39h1- plus Suv39h1ER

tag: phenotype

value: non-senescent


title: SuvER-5043 native


title: WT_6DL_DMSO_n_2

description: Illumina sequencing

source_name: wild-type Embryonic stem cells

extract_protocol:
ESC populations were harvested and crosslinked in formaldehyde. Cell pellets (frozen, or fresh) were subjected to chromatin preparation and immunopreciptiation with an antibody against H3K27me3, followed by extraction of genomic DNA.
DNA samples were quantified, and libraries were generated and amplified by PCR, followed by library size determination using a Agilent BioAnalyzer.
Libraries were then pooled, quantified, and sequenced on an Illumina MiSeq to determine the amount required for deep sequencing. Pooled libraries were then diluted accordingly and loaded on an Illumina NovSeq6000 for sequencing.

tag: strain

tag: sequencing run#

tag: passage numbers

tag: treatment group

tag: sample preparation

value: ChIP-seq


title: SuvER-4936 ADR 4OHT

tag: treatment

value: ADR & 4OHT

value: senescent


title: SuvER-4936 5d ADR

value: 5d ADR


title: SuvER-5043 ADR 4OHT


title: SuvER-4146 ADR 4OHT


title: SuvER-4146 5d ADR


title: SuvER-5043 5d ADR


title: SuvER-4146 native


title: 9250 5d ADR


title: 9584 5d ADR

value: Suv39h1 WT


title: 4936 native


title: 6054 5d ADR


title: 9583 native


title: 9584 native


title: 6054 native


title: 5783 5d ADR


title: 7050 native


title: 9583 5d ADR


title: 1032 5d ADR


title: 7890 5d ADR


title: 5766 5d ADR


title: 9250 native


title: 7890 native


title: 1032 native


title: 5783 native


title: 4936 5d ADR


title: 5766 native


title: 5560 5d ADR


title: 5043 5d ADR


title: 7050 5d ADR


title: 5043 native


title: 403 native


title: 3769 5d ADR


title: 3594 native


title: 3594 5d ADR


title: 3769 native


title: 5560 native


title: 403 5d ADR


title: 2581 native


title: 2581 5d ADR


title: 2949 native


title: 2949 5d ADR


title: 1570 native


title: 1570 5d ADR


title: 1467 native


title: 1467 5d ADR


title: Lung AQ-seq

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Small RNA-seq

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the mouse genome (mm10) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

source_name: Lung

extract_protocol:
Commercially available: Mouse Total RNA Master Panel; Takara
AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs from fifteen mouse tissues (Mouse Total RNA Master Panel; Takara) as described in our previous study (Kim et al., 2019). Briefly, we mixed 5 μg of total RNAs with 10 fmole of thirty equimolar spike-in RNAs which are miRNA-like non-human/mouse/frog/fish RNAs used for bias evaluation. Small RNAs were enriched by size fractionation by 15% urea-polyacrylamide gel electrophoresis and sequentially ligated to the randomized adapter at the 3′ and 5′ ends. The ligated RNAs were reverse-transcribed using SuperScript III reverse transcriptase (Invitrogen), amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), and subjected to high-throughput sequencing on the MiSeq platform (Illumina).

tag: tissue

value: Lung


title: Spinal cord AQ-seq

description: Small RNA-seq

source_name: Spinal cord

value: Spinal cord


title: Kidney AQ-seq

description: Small RNA-seq

source_name: Kidney

value: Kidney


title: Testis AQ-seq

description: Small RNA-seq

source_name: Testis

value: Testis


title: Spleen AQ-seq

description: Small RNA-seq

source_name: Spleen

value: Spleen


title: Salivary gland AQ-seq

description: Small RNA-seq

source_name: Salivary gland

value: Salivary gland


title: Stomach AQ-seq

description: Small RNA-seq

source_name: Stomach

value: Stomach


title: 15-day embryo AQ-seq

description: Small RNA-seq

source_name: 15-day embryo

value: Embryo


title: Eye AQ-seq

description: Small RNA-seq

source_name: Eye

value: Eye


title: 11-day embryo AQ-seq

description: Small RNA-seq

source_name: 11-day embryo


title: Brain AQ-seq

description: Small RNA-seq

source_name: Brain

value: Brain


title: Heart AQ-seq

description: Small RNA-seq

source_name: Heart

value: Heart


title: Day 7 primary patterned replicate 2

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Gene expression quantification (TPM) performed using kallisto
Genome_build: mm10
Supplementary_files_format_and_content: Table of expression values as transcripts per million (TPM) for each sample

source_name: Primary Mouse Myoblast

extract_protocol:
Trizol RNA extraction, Directzol column isolation
NEBNext RNA seq prep kit

value: Primary myoblast

tag: differentiation day

tag: substrate

value: Patterned Gelatin


title: Day 0 replicate 2

source_name: C2C12 mouse myoblast

value: Plastic


title: Day 0 primary replicate 2

source_name: Primary mouse myoblast


title: Day 0 primary replicate 1


title: Day 0 primary replicate 3


title: Day 0 replicate 1


title: Day 0 replicate 3


title: Day 7 primary patterned replicate 3


title: Smooth muscle AQ-seq

description: Small RNA-seq

source_name: Smooth muscle

value: Smooth muscle


title: Day 7 primary patterned replicate 1


title: Day 4 primary patterned replicate 3


title: Day 7 patterned replicate 2


title: Day 4 primary patterned replicate 1


title: Day 7 unpatterned replicate 2

value: Unpatterned Gelatin


title: Day 7 unpatterned replicate 3


title: Day 4 Unpatterned replicate 2


title: Day 4 patterned replicate 2


title: Day 7 unpatterned replicate 1


title: Day 4 patterned replicate 1


title: Day 7 plastic replicate 1


title: Day 7 plastic replicate 3


title: Day 7 plastic replicate 2


title: 17-day embryo AQ-seq

description: Small RNA-seq


title: Day 4 Unpatterned replicate 1


title: Day 4 Plastic replicate 2


title: Day 4 Plastic replicate 1


title: Day 4 Unpatterned replicate 3


title: METTL5_WT_2_Ribo-seq

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

description: Ribosome protected mRNA fragment

data_processing:
Library strategy: Ribo-Seq
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and then mapped to mm10 whole genom using bowtie2 v2.3.4.3 with parameters -W 6:00 -e rsem.mm10 rsem-calculate-expression -p 8 --fragment-length-min 18 --strand-specific
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Embryonic stem cell

extract_protocol:
For RNA-seq, cells were grown to 80% confluence and RNA was harvested using Trizol reagent. For Ribo-seq, sucrose gradient fraction contiaining monoribosomes we teated with Trizol reagent to purify RNA.
RNA libraries were prepared for sequencing using NEB small RNA Kit.

tag: cell type

value: mESC

tag: passages

value: WT


title: METTL5_KO_2_RNA-seq

description: mRNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and then mapped to mm10 whole genom using bowtie2 v2.3.4.3 with parameters -W 6:00 -e rsem.mm10 rsem-calculate-expression -p 8 --fragment-length-min 18 --strand-specific
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

value: METTL5 KO


title: Day 4 Plastic replicate 3


title: Day 4 patterned replicate 3


title: METTL5_KO_1_Ribo-seq

description: Ribosome protected mRNA fragment


title: METTL5_KO_1_RNA-seq

description: mRNA


title: METTL5_WT_1_Ribo-seq

description: Ribosome protected mRNA fragment


title: METTL5_WT_2_RNA-seq

description: mRNA


title: METTL5_KO_2_Ribo-seq

description: Ribosome protected mRNA fragment


title: METTL5_WT_1_RNA-seq

description: mRNA


title: Day 4 primary patterned replicate 2


title: Day 7 patterned replicate 1


title: Day 7 patterned replicate 3


title: Erythroid differentiation CITE-seq cDNA reads

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Cell Ranger (10x genomics)
Scrublet (https://doi.org/10.1016/j.cels.2018.11.005)
Seurat (https://doi.org/10.1038/nbt.4096)
CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (sparse gene x cell matrix, gene names, cell barcodes); CITE-seq-count output file (surface antibody barcode x cell barcode matrix)

source_name: Primary haematopoietic/erythroid progenitor cells

growth_protocol: Cells were dissociated from fetal livers of e13.5 C57BL/6 mouse embryos and partially depleted for Ter119+ cells as described in the Methods section of the paper

extract_protocol: single-cell RNA-seq was performed using the 10x genomics platform as described in the Methods section of the paper

treatment_protocol: Cells were stained with barcode conjugated antibodies against cell surface markers: anti-Ter119 conjugated to ADT2 [GAGGCGATTGAT], anti-CD71 conjugated with ADT9 [CGAAGAAGGAGT], anti-CD41 conjugated with ADT3 [TGTCCGGCAATA], anti-CD45R conjugated with ADT5 [GATCGTAATACC], anti-CD3e conjugated with ADT7 [CATCGGTGTACA], anti CD11b conjugated with ADT1 [CATGATTGGCTC], anti-Ly6G/6C conjugated with ADT4 [TGGTGAACCTGG], anti-CD44 conjugated with ADT8 [GTCTAGACTTCG], anti-cKit conjugated with ADT6 [AAGCGCTTGGCA], and non-specific IgG conjugated with ADT10 [CGGAGTAGTAAT]

tag: developmental stage

value: Fetal liver

value: Primary erythroid progenitor cells isolated from fetal liver


title: Erythroid differentiation MPP3 ATAC-seq

description:
RBAT97
MPP3-expt93.mm9.bw

data_processing:
NGseqBasic pipeline (https://doi.org/10.1101/393413)
Custom scripts (https://github.com/rbeagrie/alpha-tiledc)
Genome_build: mm9 & mm10
Supplementary_files_format_and_content: BigWig files of genome-wide read density

growth_protocol: Cells were FACS-sorted from fetal liver or bone marrow of C57BL/6 mice as described in the Methods section of the paper

extract_protocol:
Cells were transposed with Tn5 transposase for ATAC-seq library preparation as described in the Methods section of the paper
ATAC-seq transposed DNA was amplified using custom barcoded oligonucleotides as described in the Methods section of the paper

value: adult (12w)

value: bone marrow

value: Primary haematopoietic progenitor cells isolated from bone marrow

tag: immunophenotype

value: LSK Flt3- CD48+ CD150-


title: Erythroid differentiation HSPC ATAC-seq

description:
RBAT94
HSPC-expt93.mm9.bw

value: LSK Flt3- CD48- CD150+


title: Erythroid differentiation S3 ATAC-seq replicate 3.2

description:
RBAT60
S3-expt35.mm10.bw
S3-expt35.mm9.bw

value: fetal liver

value: Lin- CD71:high Ter119:high


title: Erythroid differentiation MPP2 ATAC-seq

description:
RBAT96
MPP2-expt93.mm9.bw

value: LSK Flt3- CD48+ CD150+


title: Erythroid differentiation LMPP ATAC-seq

description:
RBAT95
LMPP-expt93.mm9.bw

value: LSK Flt3+


title: Erythroid differentiation S2 ATAC-seq replicate 3.1

description:
RBAT57
S2-expt35.mm9.bw
S2-expt35.mm10.bw

value: Lin- CD71:high Ter119:med


title: Erythroid differentiation S1 ATAC-seq replicate 3.2

description:
RBAT56
S1-expt35.mm10.bw
S1-expt35.mm9.bw

value: Lin- CD71:high Ter119-


title: Erythroid differentiation S0-medium ATAC-seq replicate 3.1

description:
RBAT53
S0_CD71_medium-expt35.mm9.bw
S0_CD71_medium-expt35.mm10.bw

value: Lin- CD71:med Ter119-


title: Erythroid differentiation S0-low ATAC-seq replicate 3.1

description:
RBAT52
S0_CD71_low-expt35.mm10.bw
S0_CD71_low-expt35.mm9.bw

value: Lin- CD71- Ter119-


title: Erythroid differentiation S2 ATAC-seq replicate 3.2

description:
RBAT58
S2-expt35.mm9.bw
S2-expt35.mm10.bw


title: Erythroid differentiation S1 ATAC-seq replicate 1.2

description:
RBAT47
S1-expt10.mm10.bw
S1-expt10.mm9.bw


title: Erythroid differentiation S0-medium ATAC-seq replicate 1.2

description:
RBAT45
S0_CD71_medium-expt10.mm10.bw
S0_CD71_medium-expt10.mm9.bw


title: Erythroid differentiation S0-low ATAC-seq replicate 1.1

description:
RBAT42
S0_CD71_low-expt10.mm9.bw
S0_CD71_low-expt10.mm10.bw


title: Erythroid differentiation S3 ATAC-seq replicate 3.1

description:
RBAT59
S3-expt35.mm10.bw
S3-expt35.mm9.bw


title: Erythroid differentiation S0-medium ATAC-seq replicate 3.2

description:
RBAT54
S0_CD71_medium-expt35.mm9.bw
S0_CD71_medium-expt35.mm10.bw


title: Erythroid differentiation S0-low ATAC-seq replicate 1.2

description:
RBAT43
S0_CD71_low-expt10.mm9.bw
S0_CD71_low-expt10.mm10.bw


title: Erythroid differentiation S1 ATAC-seq replicate 3.1

description:
RBAT55
S1-expt35.mm10.bw
S1-expt35.mm9.bw


title: Erythroid differentiation S3 ATAC-seq replicate 2.2

description:
RBAT40
S3-expt13.mm10.bw
S3-expt13.mm9.bw


title: Erythroid differentiation S3 ATAC-seq replicate 2.1

description:
RBAT39
S3-expt13.mm10.bw
S3-expt13.mm9.bw


title: Erythroid differentiation S0-medium ATAC-seq replicate 1.1

description:
RBAT44
S0_CD71_medium-expt10.mm10.bw
S0_CD71_medium-expt10.mm9.bw


title: Erythroid differentiation CITE-seq ADT (barcoded antibody) reads

description:
Surface protein antibody barcodes
RBAT32

data_processing:
Library strategy: CITE-seq
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Cell Ranger (10x genomics)
Scrublet (https://doi.org/10.1016/j.cels.2018.11.005)
Seurat (https://doi.org/10.1038/nbt.4096)
CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (sparse gene x cell matrix, gene names, cell barcodes); CITE-seq-count output file (surface antibody barcode x cell barcode matrix)


title: Erythroid differentiation S1 ATAC-seq replicate 2.2

description:
RBAT36
S1-expt13.mm9.bw
S1-expt13.mm10.bw


title: Erythroid differentiation S2 ATAC-seq replicate 2.1

description:
RBAT37
S2-expt13.mm10.bw
S2-expt13.mm9.bw


title: Erythroid differentiation S1 ATAC-seq replicate 2.1

description:
RBAT35
S1-expt13.mm9.bw
S1-expt13.mm10.bw


title: Erythroid differentiation S0-low ATAC-seq replicate 2.1

description:
RBAT31
S0_CD71_low-expt13.mm9.bw
S0_CD71_low-expt13.mm10.bw


title: Erythroid differentiation S0-medium ATAC-seq replicate 2.1

description:
RBAT33
S0_CD71_medium-expt13.mm9.bw
S0_CD71_medium-expt13.mm10.bw


title: Erythroid differentiation S0-medium ATAC-seq replicate 2.2

description:
RBAT34
S0_CD71_medium-expt13.mm9.bw
S0_CD71_medium-expt13.mm10.bw


title: Erythroid differentiation S0-low ATAC-seq replicate 2.2

description:
RBAT32
S0_CD71_low-expt13.mm9.bw
S0_CD71_low-expt13.mm10.bw


title: Erythroid differentiation S1 ATAC-seq replicate 1.1

description:
RBAT46
S1-expt10.mm10.bw
S1-expt10.mm9.bw


title: tKO_C1_DM3_BR2_smallRNAseq

city: Charlottesville

first: Roza

middle: Kamila

last: Przanowska

state: Virginia

department: Biomedical Engineering

institute: University of Virginia

data_processing:
cutadapt v1.15 (--nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15)
STAR aligner v2.5.4
unitas v1.5.1 (–species_miR_only –species mus_musculus)
Genome_build: mm10
Supplementary_files_format_and_content: unitas miRNA count table: miRNA count table, generated by unitas

source_name: Murine myotubes C2C12

growth_protocol: C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS. For differentiation to myotubes serum was exchanged to 2%HS.

extract_protocol:
Cells were grown to ~80% confluency for GM or differentiated for 3 days for DM3 and washed briefly twice with ice-cold PBS. Total RNA was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051).
Small RNA-sequencing libraries were prepared following NEBNext Small RNA library kit (NEB #E7300). Briefly, 0.5 μg total RNA was ligated with 3’ pre-adenylated adaptors and then 5’ adaptors. After reverse transcription and PCR amplification with indexed-adaptors, each library was size selected on 8% TBE-PAGE gel (Invitrogen #EC6215BOX) to enrich for 15-50 nt insert.

tag: cell line

value: miR-206, miR-1a-1 and miR-1a-2 triple KO

value: Myotubes


title: Control_2_DM3_BR2_smallRNAseq

value: Wild-type


title: Control_2_GM_BR2_smallRNAseq

source_name: Murine myoblasts C2C12

value: Myoblasts


title: tKO_C2_DM3_BR2_smallRNAseq


title: Erythroid differentiation S2 ATAC-seq replicate 2.2

description:
RBAT38
S2-expt13.mm10.bw
S2-expt13.mm9.bw

value: Primary erythroid progenitor cells isolated from fetal liver


title: Control_1_GM_BR2_smallRNAseq


title: tKO_C1_DM3_BR1_smallRNAseq


title: Control_2_DM3_BR1_smallRNAseq


title: tKO_C2_GM_BR2_smallRNAseq


title: tKO_C1_GM_BR1_smallRNAseq


title: tKO_C2_GM_BR1_smallRNAseq


title: tKO_C2_DM3_BR1_smallRNAseq


title: Control_1_DM3_BR1_smallRNAseq


title: Control_1_GM_BR1_smallRNAseq


title: H3K27Ac_WT

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: H3K27Ac ChIP of WT brain

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm9 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: mm9
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

source_name: CIC WT mouse brain E19

growth_protocol: We harvested mouse brains at indicated ages and cross-linked with 1% paraformaldehyde.

extract_protocol:
After isolation of nucleus with lysis buffer (50 mM HEPES-KOH, 135 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% TritonX100), the chromatin was digested with micrococcal nuclease. The pellet was resuspended with IP buffer (50 mM Tris-HCl, 100 mM NaCl, 10 mM EDTA, 0.1% SDS, and 1% TritonX100) and the nuclear membrane was broken with sonication. IP was performed with respective antibody overnight at  cold room. The antibody-antigen was precipitated with magnetic beads. The ChIPed DNA was eluted and extracted with DNA extraction kit (MN #740609.250).
Libraries were made using KAPA Hyper Prep kit (KAPABiosystems #KR0961) following manufacturer’s instructions. Briefly, 30 ng from each immunoprecipitated or Input DNA, were end-repaired, phosphorylated, A-tailed and ligated to adaptors (Roche SeqCap Adapter kit A #07141530001). Ligated products were size selected with 0.8X SPRI beads to obtain 250~350 bp of DNA. After purification, 8-cycle PCR amplification reaction was performed. PCR product was cleaned by the use of 1X SPRI beads. Final product was resuspended in 30 ul of Tris buffer.

value: Brain

value: Embryonic day 19

tag: mouse genotype

value: Nes-Cre;CIC+/+

tag: chip antibody

value: abcam #ab4729


title: H3K27Ac_KO

description: H3K27Ac ChIP of CIC null brain

source_name: CIC KO mouse brain E19

value: Nes-Cre;CIClox/lox


title: Control_2_GM_BR1_smallRNAseq

tag: genotype


title: Control_1_DM3_BR2_smallRNAseq


title: Liver AQ-seq

description: Small RNA-seq

source_name: Liver

value: Liver


title: 1001200627_H5, pancreatic cells for patch-seq

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Genome_build: GRCh38

source_name: pancreatic islets

extract_protocol: SmartSeq2 (21X-23X PCR cycles)

tag: cryopreserved

value: Yes

tag: diabetes

tag: Sex

value: M

tag: patched


title: 1001200627_H3, pancreatic cells for patch-seq


title: 1001200627_G4, pancreatic cells for patch-seq


title: 1001200627_G5, pancreatic cells for patch-seq


title: 1001200627_G6, pancreatic cells for patch-seq


title: 1001200627_H2, pancreatic cells for patch-seq


title: 1001200627_G3, pancreatic cells for patch-seq


title: 1001200627_G2, pancreatic cells for patch-seq


title: 1001200627_G1, pancreatic cells for patch-seq


title: 1001200627_F6, pancreatic cells for patch-seq


title: tKO_C1_GM_BR2_smallRNAseq


title: 1001200627_H6, pancreatic cells for patch-seq


title: 1001200627_H4, pancreatic cells for patch-seq


title: 1001200627_F5, pancreatic cells for patch-seq


title: 1001200627_F4, pancreatic cells for patch-seq


title: 1001200627_F2, pancreatic cells for patch-seq


title: 1001200627_E5, pancreatic cells for patch-seq


title: 1001200627_E6, pancreatic cells for patch-seq


title: 1001200627_F3, pancreatic cells for patch-seq


title: 1001200627_H1, pancreatic cells for patch-seq


title: 1001200627_E4, pancreatic cells for patch-seq


title: 1001200627_E3, pancreatic cells for patch-seq


title: 1001200627_E2, pancreatic cells for patch-seq


title: 1001200627_E1, pancreatic cells for patch-seq


title: 1001200627_D5, pancreatic cells for patch-seq


title: 1001200627_D4, pancreatic cells for patch-seq


title: 1001200627_D3, pancreatic cells for patch-seq


title: 1001200627_D2, pancreatic cells for patch-seq


title: 1001200627_D1, pancreatic cells for patch-seq


title: 1001200627_C6, pancreatic cells for patch-seq


title: 1001200627_C4, pancreatic cells for patch-seq


title: 1001200627_C5, pancreatic cells for patch-seq


title: patient SPN-13 xenograft B7

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were processed using Partek genomics suite software and RMA background correction were applied to probe intensities, then the corrected intensities were quantile normalized.

source_name: distal lung stem cells

label_protocol: Samples were enzymatically fragmented and biotinylated.

growth_protocol: Cultured stem cell colony on 3T3 feeder layer.

extract_protocol: For the stem cell colony RNA extraction, we have used Arcturus PicoPure RNA isolation kit and for ALI RNA, we have extracted RNA using Trizol and Qiagen RNeasy kit.

treatment_protocol: Not applicable.

value: xenograft cells

tag: genotype/variation

value: wild type

tag: patient


title: patient SPN-13 xenograft B14


title: patient SPN-13 xenograft B5


title: patient SPN-12 xenograft 2


title: 1001200627_C2, pancreatic cells for patch-seq


title: patient SPN-13 xenograft B2


title: patient SPN-13 xenograft B1


title: patient SPN-13 xenograft B6


title: 1001200627_D6, pancreatic cells for patch-seq


title: patient SPN-13 xenograft B11


title: ADAR1_irCLASH_HEK293_Endo_Rep2

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

description: irCLASH-seq of endogenous ADAR1 in HEK293 cell line

data_processing:
Library strategy: irCLASH-seq
Demultiplex raw data by barcodes, then remove PCR duplicates using fastx_toolkit_0.0.13 and  adaptors were trimmed by cutadapt v1.14
Step 1 mapping: irCLASH-seq clean reads were mapped to hg19 transcripts (including rRNA and tRTNA, bowtie -f-S -v 3 -k 10 --best --strata) and discard the mapped reads using bowtie version 1.1.2
Step 2 mapping: map to hg19 genome (-f -S -v 3 -k 10 --best --strata) and discard the continuously mapped reads using bowtie verison 1.1.2
Step 3 mapping: map to hg19 genome using STAR version 020201 (--outSAMprimaryFlag AllBestScore --outSAMattributes All --outFilterMultimapNmax 100  --outFilterMismatchNmax 3 --alignEndsType EndToEnd  --outSAMunmapped Within --alignIntronMin 4)
Step 4 mapping: map to hg19 genome using bowtie version 1.1.2 (--very-sensitive-local -f) and  extract the “recombinant” reads, then reform reads
Step 5 mapping: map to hg19 genome using STAR version 020201 (--outSAMprimaryFlag  AllBestScore --outSAMattributes All  --outFilterMultimapNmax 100  --outFilterMismatchNmax 3  --alignEndsType EndToEnd  --outSAMunmapped Within --alignIntronMin 4)
Get hybrid reads from step 3 and step 5
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing hybrid reads of ADAR1, ADAR2 and ADAR3

source_name: HEK293 cell line

growth_protocol: HEK293 cells were grown in Dulbecco’s modified Eagle medium (DMEM) (Thermo Fisher Scientific, cat# C11995500CP) containing 10% FBS (Thermo Fisher Scientific, cat# 26400044) and cultured in 37℃ with 5% CO2.

extract_protocol:
UV crosslinked RNA was extracted with phenol-chloroform.
Briefly, UV crosslinked RNA were pulled down with anti-FLAG antibody, then digested by RNA I. Digested RNA were 5’ and 3’ dephosphorylated with Thermosensitive Alkaline Phosphatase (TSAP) (Promega, cat# M9910), then 5' end were phosphorylated with T4 PNK (NEB, cat# M0210). Both inter-molecular RNA-RNA ligation and fluorescent dye IR800 labeled preA-DNA-adaptor ligation were applied with T4 RNA ligase I (NEB, cat# M0204). Adaptor ligated RNA were resolved by a 4-12% NuPAGE Bis-Tris gel (Thermo Fisher Scientific, cat# NP0335PK2) and subsequently transferred to NC membrane. Target regions were cut and digested with proteinase K (QIAGEN, cat# 19131). RNA fragments were purified by phenol-chloroform extraction. Reverse transcription was performed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific, cat# 18080051) with customed irCLIP RT primers according to manufacture’s instructions. RNA/cDNA hybrids were captured by Streptavidin Dynabeads (Thermo Fisher Scientific, cat# 65002). cDNA were circularized with Circligase-II (Epicentre, cat# CL9021K) after RNA degradation and cDNA elution. Circularized cDNA was captured by VAHTS DNA clean beads (Vazyme Biotech, cat# N411). irCLASH-seq libraries were amplified by two rounds of PCR and the final products were separated by 2.5% TAE gel. The libraries, ranging from 150bp to 275bp, were cut and recovered using Zymoclean Gel DNA Recovery Kit (Zymo Research, cat# D4002).

treatment_protocol: HEK293 ells were transiently transfected with ADARs’ plasmid by Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, cat# L3000015) according to manufacturer’s instructions.

tag: irclash or hiclip antibody

value: anti-FLAG M2 antibody (Sigma-Aldrich, cat# F1804-1MG)

tag: experiment


title: ADAR1_irCLASH_HEK293_Endo_Rep1


title: Experiment 6 - Interferon-alpha condition (18h)

city: Brussels

first: Maikel

middle: Luis

last: Colli

address: Route de Lennik, 808

department: Faculty of Medicine

country: Belgium

institute: Universite Libre de Bruxelles

data_processing:
Sequencing reads were mapped to the Homo sapiens genome (version GRCh37/hg19) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options the GENCODE 18 annotation of genes transcripts. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify human transcripts from the GENCODE 18 annotation dataset, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

source_name: Pancretic human islets_Interferon-alpha condition (18h)

growth_protocol: Pancreatic human islets were cultured in Ham’s F-10 medium containing 6.1 mM glucose (Gibco, Thermo-Fisher Scientific), 10% fetal bovine serum (FBS) (Gibco, Thermo-Fisher Scientific), 2 mM GlutaMAX (Sigma-Aldrich), 50 mM 3-isobutyl-1-methylxanthine (Sigma-Aldric), 1% BSA fraction V, fatty acid free (Roche), 50 U/ml penicillin and 50 mg/ml streptomycin (Lonza) (Brozzi et al., 2015).

extract_protocol:
Total RNA was isolated from pancreatic human islets using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides. mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2500 system

treatment_protocol: Pancreatic human isltes were exposed or not to interferon-alpha (2.000U/ml) for 2, 8 or 18h.

value: pancreatic human islets

tag: treatment

value: Interferon-alpha condition (18h)

tag: experiement batch

value: Experiment 6


title: Experiment 5 - Interferon-alpha condition (18h)

tag: cell type

value: Experiment 5


title: Experiment 3 - Interferon-alpha condition (18h)

value: Experiment 3


title: Experiment 4 - Interferon-alpha condition (18h)

value: Experiment 4


title: 1001200627_C1, pancreatic cells for patch-seq


title: Experiment 2 - Interferon-alpha condition (18h)

value: Experiment 2


title: 1001200627_B6, pancreatic cells for patch-seq


title: patient SPN-12 xenograft 1


title: Experiment 1 - Interferon-alpha condition (18h)

value: Experiment 1


title: 1001200627_C3, pancreatic cells for patch-seq


title: Experiment 6 - Interferon-alpha condition (8h)

source_name: Pancretic human islets_Interferon-alpha condition (8h)

value: Interferon-alpha condition (8h)


title: 1001200627_B5, pancreatic cells for patch-seq


title: Experiment 5 - Interferon-alpha condition (8h)


title: 1001200627_B4, pancreatic cells for patch-seq


title: 1001200627_B3, pancreatic cells for patch-seq


title: MPSC1 untreated

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

hyb_protocol: Following fragmentation, 14 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MPSC1 untreated

label_protocol: Biotinylated cRNA were prepared using MessageAmp Premier RNA Amplication Kit (ThermoFisher Scientific) according to the manufacturer's protocol with 500ng total RNA as starting material.

growth_protocol: HOC-7 and MPSC1 ovarian cancer cells were grown in RPMI media containing 10% fetal bovine serum, 100 U/ml penicillin, and 100µg/ml streptomycin (Millipore Sigma) in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kit (Qiagen).

treatment_protocol: When cells reached 70% confluency, trametinib was added to a final concentration of 10nM for 18 hours.

tag: kras

value: wild-type

tag: braf

value: mutant


title: MPSC1 10nM trametinib-18hr

source_name: MPSC1 10nM trametinib-18hr

tag: cell line


title: 1001200627_B1, pancreatic cells for patch-seq


title: Experiment 3 - Interferon-alpha condition (8h)


title: HOC7 untreated

source_name: HOC7 untreated


title: Experiment 4 - Interferon-alpha condition (8h)


title: Experiment 1 - Interferon-alpha condition (8h)


title: 1001200627_A6, pancreatic cells for patch-seq


title: 1001200627_B2, pancreatic cells for patch-seq


title: Experiment 4 - Interferon-alpha condition (2h)

source_name: Pancretic human islets_Interferon-alpha condition (2h)

value: Interferon-alpha condition (2h)


title: Experiment 5 - Interferon-alpha condition (2h)


title: 1001200627_A3, pancreatic cells for patch-seq

value: Yes


title: Experiment 3 - Interferon-alpha condition (2h)


title: Experiment 2 - Interferon-alpha condition (8h)


title: 1001200627_A5, pancreatic cells for patch-seq

value: M


title: 1001200627_A4, pancreatic cells for patch-seq


title: 1001200627_A1, pancreatic cells for patch-seq


title: 1001200627_A2, pancreatic cells for patch-seq


title: 1001200626_H9, pancreatic cells for patch-seq


title: Experiment 2 - Interferon-alpha condition (2h)


title: Experiment 1 - Interferon-alpha condition (2h)


title: HOC7 10nM trametinib-18hr

source_name: HOC7 10nM trametinib-18hr


title: 1001200626_H8, pancreatic cells for patch-seq


title: 1001200626_H6, pancreatic cells for patch-seq

value: not applicable


title: Experiment 4 - control condition (18h)

source_name: Pancretic human islets_control condition (18h)

value: control condition (18h)


title: 1001200626_H7, pancreatic cells for patch-seq


title: Experiment 5 - control condition (18h)


title: Experiment 6 - control condition (18h)


title: Experiment 6 - Interferon-alpha condition (2h)


title: 1001200626_H5, pancreatic cells for patch-seq


title: Experiment 2 - control condition (18h)


title: 1001200626_H11, pancreatic cells for patch-seq


title: 1001200626_H10, pancreatic cells for patch-seq


title: Experiment 6 - control condition (8h)

source_name: Pancretic human islets_control condition (8h)

value: control condition (8h)


title: 1001200626_H1, pancreatic cells for patch-seq


title: Experiment 3 - control condition (8h)

value: pancreatic human islets


title: 1001200626_H2, pancreatic cells for patch-seq


title: Experiment 5 - control condition (8h)


title: Experiment 1 - control condition (8h)


title: Experiment 6 - control condition (2h)

source_name: Pancretic human islets_control condition (2h)

value: control condition (2h)


title: 1001200626_G8, pancreatic cells for patch-seq


title: 1001200626_G5, pancreatic cells for patch-seq


title: Experiment 5 - control condition (2h)


title: 1001200626_G6, pancreatic cells for patch-seq


title: 1001200626_G7, pancreatic cells for patch-seq


title: 1001200626_G4, pancreatic cells for patch-seq


title: Experiment 4 - control condition (2h)


title: Experiment 3 - control condition (18h)


title: 1001200626_G2, pancreatic cells for patch-seq


title: Experiment 1 - control condition (18h)


title: 1001200626_H3, pancreatic cells for patch-seq


title: Experiment 2 - control condition (8h)


title: Experiment 4 - control condition (8h)


title: 1001200626_G9, pancreatic cells for patch-seq


title: 1001200626_G12, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 4 - Interferon-alpha condition (24h)

data_processing:
Bam files from different replicates were merged into a single one using samtools (version 1.8) (Li et al. 2009) and peaks were called from that merged file using MACS2 callpeak (version 2.1) (Zhang et al. 2008) using the parameters “-q 0.05 --nomodel --shift -100 --extsize 200”.
Differential analysis of ATAC-seq chromatin accessibility was performed using the R package DESeq2 (Love et al. 2014). A consensus peak set was generated for each timepoint by merging the called peaks. Then, reads were counted at each peak and the resulting matrix was used as input for DESeq2. Briefly, DESeq2 normalizes samples according to per-sample sequencing depth and accounting for intra-sample variability. Then, fits data to a negative binomial generalized linear model (GLM) and calculates the Wald statistic. Finally, raw p-values are FDR-corrected for multiple testing using the Benjamini-Hochberg method. Peaks with an absolute log2 fold change higher than 1 (|log2FC|>1) and an FDR < 0.05 were considered differentially accessible after the IFNα treatment.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Files in the BED (Browser Extensible Data) format displaying the regions of gained, lost and stable chromating accessibility at 2 and 24h. The annotation tracks include the following columns: chromosome, start, stop, name.

source_name: EndoC-BH1 cells

growth_protocol: The EndoC-βH1 cells were cultured in DMEM containing 5.6 mmol/l glucose (Gibco, Thermo-Fisher Scientific, Paisley, UK), 2% BSA fraction V, fatty acid free (Roche, Manheim, Germany), 50 μmol/l 2-mercaptoethanol (Sigma-Aldrich, Poole, UK), 10 mmol/l nicotinamide (Calbiochem, Darmstadt, Germany), 5.5 μg/ml transferrin (Sigma-Aldrich), 6.7 ng/ml selenite (Sigma-Aldrich), 100 units/ml penicillin and 100 μg/ml streptomycin (Lonza, Leusden, Netherlands) in Matrigel-fibronectin-coated plates

extract_protocol:
ATAC-seq assay was performed in 4 independent replicates for each time point (2 and 24 hours) as previously described in (Buenrostro, et  al. 2013). Briefly, 50,000 cells were isolated from their nuclei by incubating the cells in 300 μl cold lysis buffer for 25 min on ice and resuspending them after 5 and 15 min using a syringe with a 29G needle. The pellet was next washed in 100 μl of lysis buffer and centrifuged for 15 min at 500 g at 4°C.
The transposition reaction was carried out in a 25 μl reaction mix containing 2 μl of Tn5 transposase, 12.5 μl of TD buffer (Nextera DNA Library Prep Kit, 15028212, Illumina, San Diego, USA) and 10.5 μl DEPC-treated water. The transposition reaction mix was incubated at 37°C for 1 h following inactivation by incubating for 30 min at 40°C after addition of 5 μl of clean up buffer (900 mM NaCl, 300 mM EDTA), 2 μl of 5% SDS and 2 μl of Proteinase K. Isolation of the tagmented DNA was performed with 2x SPRI beads cleanup (Agencourt AMPure XP, Beckman Coulter) and was eluted in 20 μl DEPC treated water. Two sequential 9-cycle PCR were performed in order to enrich for small tagmented DNA fragments.

treatment_protocol: EndoC-BH1 cells were exposed or not to interferon-alpha (2.000U/ml) for 2 and  24h.

value: Interferon-alpha

tag: timepoint


title: ATAC-seq_Experiment 3 - Interferon-alpha condition (24h)


title: 1001200626_G1, pancreatic cells for patch-seq


title: Experiment 1 - control condition (2h)


title: 1001200626_G3, pancreatic cells for patch-seq


title: 1001200626_G11, pancreatic cells for patch-seq


title: Experiment 2 - control condition (2h)


title: ATAC-seq_Experiment 2 - Interferon-alpha condition (2h)


title: 1001200626_F9, pancreatic cells for patch-seq


title: 1001200626_F8, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 1 - Interferon-alpha condition (2h)


title: Experiment 3 - control condition (2h)


title: ATAC-seq_Experiment 1 - Interferon-alpha condition (24h)


title: ATAC-seq_Experiment 2 - Interferon-alpha condition (24h)


title: ATAC-seq_Experiment 4 - Interferon-alpha condition (2h)


title: ATAC-seq_Experiment 3 - Interferon-alpha condition (2h)


title: 1001200626_F4, pancreatic cells for patch-seq


title: 1001200626_F6, pancreatic cells for patch-seq


title: 1001200626_F5, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 4 - control condition (24h)

value: control


title: 1001200626_F3, pancreatic cells for patch-seq


title: 1001200626_H4, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 3 - control condition (24h)


title: ATAC-seq_Experiment 2 - control condition (24h)


title: 1001200626_F2, pancreatic cells for patch-seq


title: 1001200626_F12, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 4 - control condition (2h)


title: ATAC-seq_Experiment 1 - control condition (24h)


title: 1001200626_G10, pancreatic cells for patch-seq


title: 1001200626_F11, pancreatic cells for patch-seq


title: 1001200626_F7, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 3 - control condition (2h)


title: RNA-seq_Experiment 5 - Interferon-alpha condition (24h)

extract_protocol:
Total RNA was isolated from EndoC-Bh1 cells using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides. mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2500 system

treatment_protocol: EndoC-BH1 cells were exposed or not to interferon-alpha (2.000U/ml) for 2, 8 or 24h.


title: 1001200626_E9, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 1 - control condition (2h)


title: RNA-seq_Experiment 4 - Interferon-alpha condition (24h)


title: 1001200626_F1, pancreatic cells for patch-seq


title: ATAC-seq_Experiment 2 - control condition (2h)


title: 1001200626_E8, pancreatic cells for patch-seq


title: 1001200626_E7, pancreatic cells for patch-seq


title: RNA-seq_Experiment 3 - Interferon-alpha condition (24h)


title: 1001200626_E4, pancreatic cells for patch-seq


title: RNA-seq_Experiment 2 - Interferon-alpha condition (24h)


title: 1001200626_E5, pancreatic cells for patch-seq


title: RNA-seq_Experiment 5 - Interferon-alpha condition (8h)


title: RNA-seq_Experiment 4 - Interferon-alpha condition (8h)


title: 1001200626_E12, pancreatic cells for patch-seq


title: 1001200626_E6, pancreatic cells for patch-seq


title: 1001200626_E2, pancreatic cells for patch-seq


title: 1001200626_E11, pancreatic cells for patch-seq


title: RNA-seq_Experiment 1 - Interferon-alpha condition (8h)


title: RNA-seq_Experiment 2 - Interferon-alpha condition (8h)


title: 1001200626_E1, pancreatic cells for patch-seq


title: 1001200626_E10, pancreatic cells for patch-seq


title: RNA-seq_Experiment 3 - Interferon-alpha condition (8h)


title: RNA-seq_Experiment 4 - Interferon-alpha condition (2h)


title: 1001200626_F10, pancreatic cells for patch-seq


title: 1001200626_D9, pancreatic cells for patch-seq


title: RNA-seq_Experiment 5 - Interferon-alpha condition (2h)


title: RNA-seq_Experiment 3 - Interferon-alpha condition (2h)


title: 1001200626_D7, pancreatic cells for patch-seq


title: 1001200626_D6, pancreatic cells for patch-seq


title: 1001200626_D8, pancreatic cells for patch-seq


title: RNA-seq_Experiment 5 - control condition (24h)


title: RNA-seq_Experiment 4 - control condition (24h)


title: RNA-seq_Experiment 1 - Interferon-alpha condition (24h)


title: 1001200626_E3, pancreatic cells for patch-seq


title: RNA-seq_Experiment 2 - Interferon-alpha condition (2h)


title: RNA-seq_Experiment 2 - control condition (24h)


title: RNA-seq_Experiment 3 - control condition (24h)


title: RNA-seq_Experiment 1 - control condition (24h)


title: 1001200626_D12, pancreatic cells for patch-seq


title: 1001200626_D2, pancreatic cells for patch-seq


title: 1001200626_D11, pancreatic cells for patch-seq


title: 1001200626_D3, pancreatic cells for patch-seq


title: 1001200626_D4, pancreatic cells for patch-seq


title: 1001200626_D1, pancreatic cells for patch-seq


title: 1001200626_D10, pancreatic cells for patch-seq


title: RNA-seq_Experiment 3 - control condition (8h)


title: RNA-seq_Experiment 4 - control condition (8h)


title: 1001200626_C8, pancreatic cells for patch-seq


title: 1001200626_C9, pancreatic cells for patch-seq


title: RNA-seq_Experiment 1 - control condition (8h)


title: 1001200626_D5, pancreatic cells for patch-seq


title: RNA-seq_Experiment 5 - control condition (2h)


title: 1001200626_C7, pancreatic cells for patch-seq


title: RNA-seq_Experiment 4 - control condition (2h)


title: RNA-seq_Experiment 1 - Interferon-alpha condition (2h)


title: RNA-seq_Experiment 1 - control condition (2h)


title: RNA-seq_Experiment 2 - control condition (2h)


title: Nascent-RNA, Clone #19 DA

city: New York

first: Alan

last: Gerber

address: 1230 York Avenue

institute: The Rockefeller University

description:
nascent RNA
Clone #19 Dox and auxin treated
19_DA

data_processing:
Nascent RNA seq data were aligned to the human hg19 genome assembly using the Illumina RNA-Seq Alignment workflow version 1.1.1 with read mapping using TopHat 2 (Bowtie 2)
Alignment files were then uploaded to the Galaxy web platform and analyzed using the public server at usegalaxy.org (Afgan et al., 2018). Coverage files were generated using bamCoverage tool (Galaxy Version 3.0.2.0) with bin sizes of 1bp and RPKM Normalization method.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage files

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and Pen-Strep

extract_protocol:
Nuclei from two clones per condition were isolated by centrifugation through a sucrose cushion after NP-40 based cell lysis. Nuclei were extracted with 1X NUN (1% NP-40, 1M Urea and 300 mM NaCl). Chromatin was pelleted by centrifugation and washed twice with 1X NUN buffer. Nascent RNAs retained by elongating RNA polymerases were finally isolated by Trizol extraction of the pellets.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 12 hrs with water (vehicle, control condition) or doxycycline (Dox) 12 hrs followed by auxin for 2 hrs (DA).

value: HEK293-tagged RPB1

tag: clone

value: Dox and auxin treated


title: RNA-seq_Experiment 3 - control condition (2h)


title: 1001200626_C5, pancreatic cells for patch-seq


title: 1001200626_C3, pancreatic cells for patch-seq


title: 1001200626_C4, pancreatic cells for patch-seq


title: RNA-seq_Experiment 5 - control condition (8h)


title: 1001200626_C2, pancreatic cells for patch-seq


title: RNA-seq_Experiment 2 - control condition (8h)


title: 1001200626_C11, pancreatic cells for patch-seq


title: 1001200626_C12, pancreatic cells for patch-seq


title: Nascent-RNA, Clone #7 Ctl

description:
nascent RNA
Clone #7 control condition
7_Ctl

value: control condition


title: Nascent-RNA, Clone #7 DA

description:
nascent RNA
Clone #7 Dox and auxin treated
7_DA


title: 1001200626_C1, pancreatic cells for patch-seq


title: Nascent-RNA, Clone #19 Ctl

description:
nascent RNA
Clone #19 control condition
19_Ctl


title: RPC62 ChIP-seq, Clone #19 Ctl

description:
Clone #19, control condition
RPC62-19Ctl.bigwig

data_processing:
Sequencing data were uploaded to the Galaxy web platform (Afgan et al., 2018) and data quality was verified with the FastQC tool (Galaxy tool version 0.69). Reads were mapped on the hg19 genome assembly using Bowtie2 (Galaxy Tool Version 2.3.4.1)
Input subtracted coverage files were generated using bamCompare (Galaxy Tool Version 2.5.0.0) with signal extraction scaling (SES) option and normalization to 1x coverage.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage files

extract_protocol: Chromatin lysates were prepared by sonication and protein-DNA complexes were immunoprecipitated. ChIPseq libraries were prepared from 5-10 ng ChIP DNA following the instructions of Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012).

tag: chip antibody

value: RPC62 (rabbit anti-sera generated in-house. Original publication PMID:9171375.)


title: RPC62 ChIP-seq, Clone #19 DA

description:
Clone #19, Dox and auxin treated
RPC62-19DA.bigwig


title: 1001200626_B9, pancreatic cells for patch-seq

tag: cryopreserved


title: RPC62 ChIP-seq, Clone #7 DA

description:
Clone #7, Dox and auxin treated
RPC62-7DA.bigwig


title: 1001200626_B8, pancreatic cells for patch-seq

tag: diabetes


title: RPC62 ChIP-seq, Clone #7 Ctl

description:
Clone #7, control condition
RPC62-7Ctl.bigwig


title: Input, Clone #19 DA

description:
Clone #19, Dox and auxin treated, input
19DA_RPB3.bigwig
RPC62-19DA.bigwig


title: Input, Clone #19 Ctl

description:
Clone #19, control condition, input
19Ctl_RPB3.bigwig
RPC62-19Ctl.bigwig


title: 1001200626_B5, pancreatic cells for patch-seq

tag: Sex


title: 1001200626_B6, pancreatic cells for patch-seq

tag: patched


title: Input, Clone #7 DA

description:
Clone #7, Dox and auxin treated, input
7DA_RPB3.bigwig
RPC62-7DA.bigwig


title: 1001200626_B4, pancreatic cells for patch-seq


title: Input, Clone #7 Ctl

description:
Clone #7, control condition, input
7Ctl_RPB3.bigwig
RPC62-7Ctl.bigwig


title: 1001200626_B2, pancreatic cells for patch-seq


title: RPB3 ChIP-seq, Clone #19 DA

description:
Clone #19, Dox and auxin treated
19DA_RPB3
19DA_RPB3.bigwig

value: RPB3 (rabbit polyclonal antibody from Bethyl laboratories (RPB3 Antibody, A303-771A))


title: RPB3 ChIP-seq, Clone #19 Ctl

description:
Clone #19, control condition
19Ctl_RPB3
19Ctl_RPB3.bigwig


title: 1001200626_B12, pancreatic cells for patch-seq


title: 1001200626_C10, pancreatic cells for patch-seq


title: RPB3 ChIP-seq, Clone #7 DA

description:
Clone #7, Dox and auxin treated
7DA_RPB3
7DA_RPB3.bigwig


title: 1001200626_B3, pancreatic cells for patch-seq


title: RPB3 ChIP-seq, Clone #7 Ctl

description:
Clone #7, control condition
7Ctl_RPB3
7Ctl_RPB3.bigwig


title: E77_V1_0501

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

data_processing:
alignment, UMI counting were based on cellranger v3.10
cells were recovered via emptyDrops
doublets were removed via scrrublet
clusters were obtained via Seurat v3
Genome_build: Mmul10
Supplementary_files_format_and_content: tab-delimited text files including meta annotation for each cell and UMI counts for each gene and each cell

organism: Macaca mulatta

source_name: V1 cortex

extract_protocol:
After dissection of the telencephalon, V1 cortex  was incubated with papain for 30 min at 37C. Then cells were isolated by mechanical dissociation.
10X genomics single cell RNA-seq v2

tag: age

value: embryonic day (E) 77

tag: tissue

value: brain

tag: tissue region

value: Visual cortex V1


title: 1001200626_A9, pancreatic cells for patch-seq

value: Yes


title: 1001200626_A8, pancreatic cells for patch-seq

value: M


title: 1001200626_B1, pancreatic cells for patch-seq


title: E78_V1_0501

value: embryonic day (E) 78


title: 1001200626_A7, pancreatic cells for patch-seq


title: 1001200626_A6, pancreatic cells for patch-seq


title: 1001200626_A5, pancreatic cells for patch-seq


title: 1001200626_B7, pancreatic cells for patch-seq