title: rA1-dCas12a-BE:PD1, CDK  rep c; VEG-a, TET, S3, RAG, RAG, FAN, DYR rep b

value: rA1-dCas12a-BE and rA1-dCas12a-BE


title: SCN, HSD BEACON2 mouse embryo#1

status: Public on May 05 2020

type: SRA

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryos

growth_protocol: HEK293T and U2OS cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
For DNA, after 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) or the cells were lysed in 2× SDS loading buffer for western blot.
For DNA, DNA-seq libraries were prepared with NEB Next Ultra™ II  FS DNA Library Prep Kit. Targeted deep sequencing was performed on Illumina Hiseq X ten or NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, HEK293T and U2OS cells were seeded in a 24-well plate at a density of 1.6 × 105 per well and transfected with 200 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg dCpf1-BE expression vector (or hA3A-dCas12a-BE, hA3B-dCas12a-BE, hAID-dCas12a-BE, hA3AW98A-dCas12a-BE, hA3AW98Y-dCas12a-BE, hA3AW104A-dCas12a-BE, hA3AW104Y-dCas12a-BE, hA3AP134A-dCas12a-BE, hA3AP134Y-dCas12a-BE, hA3AW98Y/W104A-dCas12a-BE, hA3AW98Y/P134Y-dCas12a-BE, hA3AW104A/P134Y-dCas12a-BE, hA3AW98Y/W104A/P134Y-dCas12a-BE, hA3AW104A-dCas12a-BE-op, hA3AW104A/Y130F-dCas12a-BE-op, hA3AW104A/Y132D-dCas12a-BE-op, hA3AW98Y/W104A-dCas12a-BE-op, hA3AW98Y/W104A/Y130F-dCas12a-BE-op, hA3AW98Y/W104A/Y132D-dCas12a-BE-op, hA3AW104A/P134Y-dCas12a-BE-op, hA3AW104A/P134Y/Y130F-dCas12a-BE-op, hA3AW104A/P134Y/Y132D-dCas12a-BE-op and hA3AW98Y/W104A/Y130F/Y132D-dCas12a-BE-op expression vector) and 0.68 μg crRNA or sgRNA expression vector. After 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) or the cells were lysed in 2× SDS loading buffer for western blot.

tag: tissue

value: mouse embryos

tag: treatment

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: SCN, HSD BEACON2 mouse embryo#3


title: DN_21_USR17005265L

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

country: USA

institute: NorthShore University HealthSystem

library_source: transcriptomic

data_processing:
ATAC-Seq data: All raw sequence reads generated by Illumina HiSeq 2000 have been de-complexed at the University of Minnesota Genomic Center and provided as 2x50 bp pair-end fastq files (100 M reads per sample). Adapter remnants, low-quality reads, and low QSEQ short sequences near either end of reads were processed by Trimmomatic (ILLUMINACLIP:NexteraPE-PE.fa:2:30:7, SLIDINGWINDOW:3:18, MINLENGTH:26). The survived sequences were separated into pair-end and single-end fastq files per sample, respectively. The pair-end and single-end fastq files were individually mapped against the human genome reference file including decoy sequences (GRCh38p7/hg38, 1000 Genome Project) using bowtie2 (-x 2000, -mm --qc-filter –met 1 –sensitive –no-mixed -t) and subsequently merged and sorted as BAM-formatted files using samtools, only uniquely mapped reads (MAPQ > 30) were collected. Picard tools MarkDuplicate was then used to remove all PCR and optical duplicated reads from the BAM file.
RNA-Seq data: RNA sequencing files were provided in the format of 2x150 bp pair-end (25 M reads per sample) fastq files. Briefly, libraries were prepared using the NEB Nextera kit with customised adapters. Since the sequencing facility had performed pre-cleaning on raw reads, no Trimmomatic action was performed. The files were subsequently mapped to the human hg38 genome (GRCh38p7) using STAR v 2.6.0 (--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outBAMcompression 10 --outBAMsortingThreadN 20 --outBAMsortingBinsN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --outSJfilterReads Unique --limitBAMsortRAM 10000000000 --alignSoftClipAtReferenceEnds No --quantTranscriptomeBAMcompression 10 10 ).
Genome_build: GRCh38.p7

molecule: total RNA

organism: Homo sapiens

source_name: Dopaminergic, day-30 post induction

extract_protocol:
At the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well.
Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.
Reverse-transcription was performed using ThermoFisher High-capacity RNA-to-cDNA reverse transcription kit with random hexamers according to the manufacturer’s protocol. Briefly, 1 µg of total RNA was used for each 20 µl RT reaction. The reaction products were then diluted with 180 µl of RNase-free water for qPCR analysis. RNA quality control and gene expression quantification were performed by the qPCR method using gene-specific FAM-labelled TaqMan probes (ThermoFisher) against VPS45 with GAPDH as internal control on a Roche 480 II machine.

treatment_protocol: To prepare GABAergic neurons, NPCs were single-cell seeded in Virus-Neural Expansion Medium Cocktail onto laminin-coated (Sigma) plate at 200,000 cells per cm2 on Day 0. Virus-Neural Expansion Medium Cocktail was prepared as 7 ml Neural Expansion Media, 1 ml rtTA virus, 1 ml Ascl1-puro virus, 1 ml Dlx2-hygro virus and 5 µM ROCK inhibitor. On day 1, virus  were withdrawn and cells were fed with fresh Neural Expansion Media supplemented with 2µg/ml doxycycline (Sigma). From Day 2 to Day 6, cells were treated in Neural Expansion Media supplemented with 2 µg/ml doxycycline, 2 µg/ml puromycin (Thermofisher) and 100 µg/ml hygromycin (Thermofisher) to remove non-transduced cells. On day 7, switched media to conditioned NeuralbasalPlus Media and change media every 3 days. NeuralbasalPlus Media was conditioned using rat astrocyte (Thermofisher) 24 hr before media changing and BDNF, GDNF, NT-3. Doxycycline was withdrawn on Day 16 and 50 nM Ara-C was included in media if non-neuron cells were observed. On Day 28, neurons were harvested using Accutase for ATAC-seq or RNA isolation.

tag: cell type

value: iPS-derived GABAergic Neurons, 28 days post induction


title: GA_04_USR18003079L

source_name: GABergic , day-28 post induction


title: GA_05_USR18003080L


title: rA1-dCas12a-BE:S4, RAG, FAN  rep a; VEG-b, S6, RUN, DNM, CFT, CDK rep b

source_name: HEK293T cells

tag: cell line


title: DN_18_USR17005264L

treatment_protocol: The protocol for differentiation of dopaminergic neurons was adapted from Gonzalez et al. Briefly, NPCs were single-cell seeded in Neural Expansion Medium onto 6 well plate coated with Geltrex (Thermofisher). Dopaminergic priming media was added to the cells at 50% confluency on Day 0. Dopaminergic priming media was prepared by adding Neurobasal medium (Thermofisher) with the following components: N2 supplement (Thermofisher), B27 supplement (Thermofisher), 100 µg/ml Primocin (Invivogen), Glutamax (Thermofisher), 2 µM purmorphamine (Tocris), 100 ng/ml FGF8 (Thermofisher) and 0.25 µM SAG (R&D). Purmorphamine, FGF8 and SAG were added upon use. Media was changed on Day 2, 4 and 6. On Day 7 the cells were replated onto 6 well plate coated with Geltrex at 5x105 cells/well and media was switched to Dopaminergic differentiation media. Dopaminergic differentiation media was prepared by adding to Neurobasal medium the following components: B27 supplement, 100 µg/ml Primocin, Glutamax, 0.2 mM ascorbic acid (Sigma), 10 ng/µl BDNG (PeproTech), 10 ng/µl GDNF (PeproTech), 1 ng/µl TGFβ3 (PeproTech) and 0.1 mM cAMP (EMD). On Day 30 dopaminergic neurons were harvested using Accutase (Thermofisher) for ATAC-seq and RNA isolation.

value: iPS-derived Dopaminergic Neurons, 30 days post induction


title: ICM_rep2_ATACseq

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Raw sequencing reads were trimmed with Trim_Galore, a wrapper around Cutadapt (v0.4.0), to remove residual Illumina adapter sequences and low quality (q<20) ends, keeping unpaired reads and reads 10 bp or longer after trimming.
Trimmed reads were aligned to the genome using BWA (v0.7.17) aln (-q 15) and sampe.
PCR duplicates were removed with PicardTools (v2.8.1), and mitochondrial and low-quality alignments. (q<15) were removed with SAMtools (v1.7)
Processed alignments were converted to bigwig format using bamCoverage from the DeepTools suite, which binned the genome into 50 bp windows and calculated normalized signal (reads per kilobase million; RPKM) in each window.
Broad peaks were called with MACS2 (v2.1.1), using a q-value cutoff of 0.05, and settings --nomodel --shift -100 --extsize 200.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Bigwig files show genome-wide normalized ATAC-seq signal; BED files show regions of ATAC-seq enrichment (peaks).

organism: Bos taurus

source_name: In vitro produced embryo

growth_protocol: Follicles measuring 2-10 mm were aspirated to obtain cumulus oocyte complexes (COCs). Only COCs with healthy layers of cumulus cells were selected for maturation. These were washed in collection medium (6:4 M199 (Sigma M7653)): SOF-Hepes, supplemented with 2% fetal bovine serum (FBS; Hyclone/Thermo Scientific) and transferred to maturation medium (modified M199 medium (Sigma M2154)) supplemented with ALA-glutamine (0.1 mM), sodium pyruvate (0.2 mM), gentamicin (5 μg/ml), EGF (50 ng/ml), oFSH (50 ng/ml), bLH (3 μg/ml), cysteamine (0.1 mM), and 10% FBS. After COCs matured for 24 h, MII oocytes were washed in SOF-IVF medium (107.7 mM NaCl, 7.16 mM KCl, 1.19 mM KH2PO4, 0.49 mM, MgCl2, 1.17 mM CaCl2, 5.3 mM sodium lactate, 25.07 mM NaHCO3, 0.20 mM sodium pyruvate, 0.5 mM fructose, 1X non-essential amino acids, 5 μg/ml gentamicin, 10 μg/ml heparin, 6 mg/ml fatty acid-free (FFA) BSA) and transferred to drops of SOF-IVF medium under mineral oil. Frozen semen from a Holstein bull was thawed, and 106 sperm/ml were added to drops with MII oocytes, which were incubated at 38.5°C for 12-18 h. Zygotes were then removed from fertilization medium, and cumulus cells were removed by vortexing for 5 min in SOF-Hepes medium. Zygotes were then transferred to culture medium (KSOMaa supplemented with 4mg/mL BSA) under mineral oil, and incubated at 38.5°C in 5% CO2, 5% O2, and 90% N2. On day three, the culture medium was supplemented with 5% stem-cell qualified FBS (Gemini Bio 100-525). Blastocyst development was evaluated at 7 days post-insemination (dpi). CTFR-bESC lines (Bogliotti et al, 2018) were cultured in CTFR medium consisting in custom mTeSR1 (devoid of TGFb and FGF2) supplemented with 20 ng/mL human FGF2 (100-18B, Peprotech), 2.5 μM IWR-1 (I0161, Sigma Aldrich), and 100 U/mL penicillin - 100 μg/mL streptomycin (15140-122, Gibco) on irradiated mouse embryonic fibroblast (MEF) (A34180, Gibco) at 37°C and 5% CO2. Cells were sub-cultured every 4-5 days at 1:10 split ratio using TrypLE Express (12604-013, Gibco). Culture medium was changed daily between passages. To increase cell survival, bESC culture medium was supplemented with 10 μM ROCK inhibitor Y-27632 (ALX-270-333-M005, Enzo) at seeding.

extract_protocol:
Pools of oocytes and embryos were collected for ATAC-seq library preparation from three separate collections per developmental stage. Embryos intended for collection at the 2-cell, 4-cell, or 8-cell stages were divided into two groups, one of which was supplemented with α-amanitin, and cultured simultaneously. Germinal vesicle-stage oocytes were collected for ATAC-seq prior to maturation. Preimplantation embryos were collected at the 2-cell (30-32 h post-insemination), 4-cell (2 dpi), 8-cell (3 dpi), and morula stages (5 dpi). Oocytes or embryos (a minimum of 500 cells) were treated with pronase (10 mg/ml) to completely remove the zona pellucida and washed with SOF-Hepes on a warming plate. Cells were then transferred to 1 ml cold SOF-Hepes, and centrifuged at 500 rcf, 4°C, for 5 min. Morulae were subjected to additional vortexing for 3 min in cold ATAC-seq lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Cell pellets were then resuspended in 1 ml cold ATAC-seq cell lysis buffer and centrifuged at 500 rcf, 4°C, for 10 min, and supernatant was aspirated to isolate nuclear pellets, prior to library preparation.To isolate ICMs for ATAC-seq by immunosurgery, blastocysts were treated with pronase (10 mg/ml) and washed in SOF-Hepes medium, then washed in 20% anti-bovine whole serum (B8270-2ML SIGMA, dilute in SOF-Hepes medium), and transferred to individual drops of 20% anti-bovine whole serum solution under mineral oil (20 ul per drop). Blastocysts were incubated for 1 h at 38.5°C, washed in SOF-Hepes medium, then washed in 20% guinea pig complement (Innovative Grade US origin, IGP-COMPL-21249) and transferred to individual drops of 20% guinea pig complement solution under mineral oil (20 ul drop). Blastocysts were again incubated for 1 h at 38.5°C. ICM were isolated by pipetting, treated with trypsin for 2-3 min, and pipetted several times before adding 10% fetal bovine serum to stop trypsinization. ICM cells were then washed in 1 ml cold SOF-Hepes medium and centrifuged at 500 rcf, 4°C, for 5 min. Cell pellets were then resuspended in 1 ml cold ATAC-seq cell lysis buffer and centrifuged at 500 rcf, 4°C, for 10 min, and supernatant was aspirated to isolate nuclear pellets. Before cell lysis and library preparation, CTFR-bESCs were trypsinized and separated from MEF feeders by plating the cell suspension in CTFR culture medium supplemented with 10 μM ROCK inhibitor Y-27632 for 1 h in a 60 mm cell culture dish (430196, Corning) at 37°C and 5% CO2. After incubation, cells that did not adhere to the culture dish were recovered for downstream processing. For each library, 50,000 ESC were aliquoted and centrifuged at 500 rcf, 4°C, for 5 min, then washed with 50 ul cold 1xPBS buffer, then centrifuged at 500 rcf, 4°C, for 5 min, then resuspended in 50 ul cold ATAC-seq cell lysis buffer, then centrifuged at 500 rcf, 4°C, for 10 min to isolate nuclear pellets.
Nuclear pellets were resuspended in 50 μl transposition reaction mix (25 μl TD buffer (Nextera DNA Library Prep Kit, Illumina), 2.5 μl TDE1 enzyme (Nextera DNA Library Prep Kit, Illumina), 22.5 μl nuclease-free H2O) and incubated for 60 min at 37°C, shaking at 300 rpm. Transposed DNA was purified with the MinElute PCR purification kit (Qiagen, Hilden, Germany) and eluted in 10 μl buffer EB. Libraries were then PCR amplified. 50 μl reactions (25 μl SsoFast Evagreen supermix with low ROX (Bio-Rad, Hercules, CA), 0.6 μl 25 μM custom Nextera PCR primer 1, 0.6 μl 25 μM custom Nextera PCR primer 2 (for a list of primers, see Buenrostro et al (2015)), 13 μl nuclease-free H2O, and 10 μl eluted DNA) were cycled as follows: (1) 72°C for 5 min, 98°C for 30 s, then (2) thermocycled at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Libraries from GV oocytes, 2-cell, and 4-cell embryos were thermocycled for 13 cycles, and 8-cell and morulae libraries were thermocycled for 11 cycles. PCR-amplified libraries were again purified with the MinElute PCR purification kit and eluted in 10 μl buffer EB. The sub-nucleosomal length fraction of each library (150-250 bp) was size selected using the PippinHT system (Sage Science, Beverly, MA) with 3% agarose cassettes.

treatment_protocol: If embryos were to be transcriptionally inhibited, the culture medium was supplemented with α-amanitin (50 μg/ml) on day one.

tag: developmental stage

value: ICM

value: Control


title: SCN, HSD BEACON2 mouse embryo#4


title: Mor-3_ATACseq

growth_protocol: Follicles measuring 2-10 mm were aspirated to obtain cumulus oocyte complexes (COCs). Only COCs with healthy layers of cumulus cells were selected for maturation. These were washed in collection medium (6:4 M199 (Sigma M7653)): SOF-Hepes, supplemented with 2% fetal bovine serum (FBS; Hyclone/Thermo Scientific) and transferred to maturation medium (modified M199 medium (Sigma M2154)) supplemented with ALA-glutamine (0.1 mM), sodium pyruvate (0.2 mM), gentamicin (5 μg/ml), EGF (50 ng/ml), oFSH (50 ng/ml), bLH (3 μg/ml), cysteamine (0.1 mM), and 10% FBS. After COCs matured for 24 h, MII oocytes were washed in SOF-IVF medium (107.7 mM NaCl, 7.16 mM KCl, 1.19 mM KH2PO4, 0.49 mM, MgCl2, 1.17 mM CaCl2, 5.3 mM sodium lactate, 25.07 mM NaHCO3, 0.20 mM sodium pyruvate, 0.5 mM fructose, 1X non-essential amino acids, 5 μg/ml gentamicin, 10 μg/ml heparin, 6 mg/ml fatty acid-free (FFA) BSA) and transferred to drops of SOF-IVF medium under mineral oil. Frozen semen from a Holstein bull was thawed, and 106 sperm/ml were added to drops with MII oocytes, which were incubated at 38.5°C for 12-18 h. Zygotes were then removed from fertilization medium, and cumulus cells were removed by vortexing for 5 min in SOF-Hepes medium. Zygotes were then transferred to culture medium (KSOMaa supplemented with 4mg/mL BSA) under mineral oil, and incubated at 38.5°C in 5% CO2, 5% O2, and 90% N2. On day three, the culture medium was supplemented with 5% stem-cell qualified FBS (Gemini Bio 100-525). Blastocyst development was evaluated at 7 days post-insemination (dpi).

extract_protocol:
Oocytes and embryos were collected for ATAC-seq library preparation from three separate collections per developmental stage. Embryos intended for collection at the 2-cell, 4-cell, or 8-cell stages were divided into two groups, one of which was supplemented with α-amanitin, and cultured simultaneously. Germinal vesicle-stage oocytes were collected for ATAC-seq prior to maturation. Preimplantation embryos were collected at the 2-cell (30-32 h post-insemination), 4-cell (2 dpi), 8-cell (3 dpi), and morula stages (5 dpi). Oocytes or embryos (a minimum of 500 cells) were treated with pronase (10 mg/ml) to completely remove the zona pellucida and washed with SOF-Hepes on a warming plate. Cells were then transferred to 1 ml cold SOF-Hepes, and centrifuged at 500 rcf, 4°C, for 5 min. Morulae were subjected to additional vortexing for 3 min in cold ATAC-seq lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Cell pellets were then resuspended in 1 ml cold ATAC-seq cell lysis buffer and centrifuged at 500 rcf, 4°C, for 10 min, and supernatant was aspirated to isolate nuclear pellets.
Nuclear pellets were resuspended in 50 μl transposition reaction mix (25 μl TD buffer (Nextera DNA Library Prep Kit, Illumina), 2.5 μl TDE1 enzyme (Nextera DNA Library Prep Kit, Illumina), 22.5 μl nuclease-free H2O) and incubated for 60 min at 37°C, shaking at 300 rpm. Transposed DNA was purified with the MinElute PCR purification kit (Qiagen, Hilden, Germany) and eluted in 10 μl buffer EB. Libraries were then PCR amplified. 50 μl reactions (25 μl SsoFast Evagreen supermix with low ROX (Bio-Rad, Hercules, CA), 0.6 μl 25 μM custom Nextera PCR primer 1, 0.6 μl 25 μM custom Nextera PCR primer 2 (for a list of primers, see Buenrostro et al (2015)), 13 μl nuclease-free H2O, and 10 μl eluted DNA) were cycled as follows: (1) 72°C for 5 min, 98°C for 30 s, then (2) thermocycled at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Libraries from GV oocytes, 2-cell, and 4-cell embryos were thermocycled for 13 cycles, and 8-cell and morulae libraries were thermocycled for 11 cycles. PCR-amplified libraries were again purified with the MinElute PCR purification kit and eluted in 10 μl buffer EB. The sub-nucleosomal length fraction of each library (150-250 bp) was size selected using the PippinHT system (Sage Science, Beverly, MA) with 3% agarose cassettes.

value: Morula


title: WT, Aged uterus, replicate 7

city: Fukuoka

first: Teruhiko

last: Kawamura

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

department: Obstetrics and Gynecology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

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

source_name: 79 weeks of age WT mouse, uterus

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

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

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

tag: strain

tag: genotype

value: wild type

tag: age

value: 79 weeks

value: whole uterus


title: WT, Aged uterus, replicate 6


title: Mor-2_ATACseq


title: rA1-dCas12a-BE:VEG-b, TET, S6, S3, RUN, RAG, PD1, DYR, DNM, CFT, CDK rep a


title: DN_16_USR17005263L


title: Mor-1_ATACseq


title: WT, Aged uterus, replicate 5


title: NT rep 2

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
We developed a computational pipeline (RADAR, https://github.com/YangLab/RADAR) to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets. RADAR consists of three steps. STEP 1: RNA-seq read mapping. After quality control by FastQC (version 0.11.4, parameters: default), RNA-seq reads are trimmed by Trimmomatic (version 0.36, parameters: TruSeq3-PE-2.fa:2:30:10 TRAILING:25 MINLEN:30) (Bolger et al., 2014) to remove read sequences with low quality, and then mapped to ribosomal DNA (rDNA) sequences by BWA-MEM algorithm (version 0.7.9a, parameters: default) to remove reads mapped to redundant rRNAs. To capture more mismatches for RNA editing candidates, a two-round unique mapping strategy is then applied to align high-quality RNA-seq reads to human hg38 reference genome, sequentially by HISAT2 (version 2.1.0, parameters: --rna-strandness RF --no-mixed --secondary --no-temp-splicesite --known-splicesite-infile --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10 --dta -t -p 10) (Kim et al., 2019) with up to two mismatches and by BWA-MEM (version , parameters: -t 20 -A 1 -B 4) with up to six mismatches. After removing duplicate reads identified by Picard (version 2.7.1, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT) in the BAM file, uniquely-mapped reads that span exon-exon junctions are split into segments by the GATK (version 4.1.2.0) (McKenna et al., 2010) command, SplitNCigarReads (parameters: default). Base quality scores of all uniquely-mapped reads are recalibrated by two GATK (version 4.1.2.0) commands, BaseRecalibrator (parameters: default) and ApplyBQSR (parameters: default). STEP 2: RNA editing calling. RNA variants are determined from the BAM file with uniquely-mapped reads by the GATK (version 4.1.2.0) command HaplotypeCaller (parameters: --minimum-mapping-quality 0 --stand_call_conf 0 --dont-use-soft-clipped-bases true). After filtering out RNA variants overlapped with single nucleotide polymorphisms (SNPs) from dbSNP version 151 (http://www.ncbi.nlm.nih.gov/SNP/), the 1000 Genomes Project (https://www.internationalgenome.org/) and the University of Washington Exome Sequencing Project (http://evs.gs.washington.edu/EVS/), low-quality RNA variants with mapped read numbers < 2, hits per billion-mapped-bases (HPB, (Zhu et al., 2013)) < 3 or editing ratio < 0.05 were further removed. RNA variants for potential RNA editing events are classified into three groups according to their genomic locations as previously described (Ramaswami et al., 2013), including in Alu, non-Alu repetitive or non-repetitive regions. Different to those in Alu regions, RNA variants in non-Alu repetitive and non-repetitive regions are further filtered with a series of stringent cutoffs to remove false positive. In brief, RNA variants in simple repeats, in mononucleotide microsatellites ≥ 5 bp or within 4 bp of splice junctions are removed. In addition, BLAST-like alignment tool (BLAT, version 364, parameters: -repMatch=2253 -stepSize=5) (Kent, 2002) is used to remove RNA variants within highly similar regions. Finally, RNA variants within bidirectional transcription regions are also removed. All twelve types of RNA editing events in Alu, non-Alu repetitive and non-repetitive regions are eventually determined according to the strands of overlapped genes (Human: hg38 knownGene.txt updated at 2015/6/28).
Genome_build: hg38 for human samples
Supplementary_files_format_and_content: vcf for RNA-editing

growth_protocol: HEK293T cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
After 40hr after transfection, Cells in the first 15% of the fluorescence intensity were sorted by FACSAriaIII. Total RNAs of sorted cells were extracted by using the RNeasy Mini Kit (QIAGEN #74104).
For RNA, RNA-seq libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep Kit. Deep sequencing was performed on Illumina Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: HEK293T cells were seeded in a 24-well plate at a density of 1.6 × 105 per well and transfected with 200 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg BE expression vector (or BLANK, nCas9 BE3, AncBE4max, BEACON1 or BEACON2 expression vector) and 0.68 μg crRNA or sgRNA expression vector. After 40hr after transfection, Cells in the first 15% of the fluorescence intensity were sorted by FACSAriaIII. Total RNAs of sorted cells were extracted by using the RNeasy Mini Kit (QIAGEN #74104).

value: NT


title: DN_09_USR17005260L


title: DN_11_USR17005261L


title: NT rep 1


title: GV-3_ATACseq

source_name: Oocyte

value: Germinal vesicle


title: WT, Aged uterus, replicate 4


title: GV-2_ATACseq


title: ICM_rep1_ATACseq


title: WT, Aged uterus, replicate 3


title: DN_08_USR17005259L


title: GV-1_ATACseq


title: DN_07_USR17005258L


title: 8-cell_rep3_ATACseq


title: Cas9 rep 1


title: DN_12_USR17005262L


title: WT, 8 weeks of age uterus, replicate 6

source_name: 8 weeks of age WT mouse, uterus

value: 8 weeks


title: Cas9 rep 2


title: WT, 8 weeks of age uterus, replicate 5


title: rA1-dCas12a-BE:S4, PD1  rep b; S6, RUN, CFT rep c; VEG-a rep a

value: rA1-dCas12a-BE and rA1-dCas12a-BE and rA1-dCas12a-BE


title: AncBE4max rep 3


title: CN15_21_USR17005236L

source_name: Glutmatergic, day-15 post induction

treatment_protocol: To prepare cortical neurons, NPCs were single-cell seeded into Geltrex-coated plate at 40,000 cells per cm2 on Day 0. From Day 0 to Day 14, NPCs were cultured in NeuralbasalPlus media with every other day media change. NeuralbasalPlus media was prepared as 490ml NeuralBasal, 1x B27Plus Supplement (Thermofisher), 1x Glutamax, 10 ng/ml BDNF (PeproTech), 10ng/ml GDNF (PeproTech), 10ng/ml NT-3 (PeproTech). Cells were harvested at day 15 for ATAC-Seq or RNA isolation.

value: iPS-derived Glutamatergic Neurons, day-15 post induction


title: 8-cell_rep2_ATACseq


title: CN15_20_USR17005235L


title: AncBE4max rep 2


title: Cas9 rep 3


title: 8-cell_amanitin_rep3_ATACseq

value: Transcription inhibited


title: WT, 8 weeks of age uterus, replicate 3


title: CN15_18_USR17005233L


title: WT, 8 weeks of age uterus, replicate 4


title: 8-cell_rep1_ATACseq


title: WT, 5 weeks of age uterus, replicate 7

source_name: 5 weeks of age WT mouse, uterus

value: 5 weeks


title: WT, 8 weeks of age uterus, replicate 7


title: BE3 rep 3


title: AncBE4max rep 1


title: WT, 5 weeks of age uterus, replicate 6


title: 8-cell_amanitin_rep1_ATACseq


title: CN15_16_USR17005231L


title: NT:CDK rep c


title: CN15_19_USR17005234L


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


title: 8-cell_amanitin_rep2_ATACseq


title: CN15_14_USR17005230L


title: CN15_17_USR17005232L


title: BE3 rep 2


title: BEACON2 rep 2


title: WT, 5 weeks of age uterus, replicate 4


title: CN15_13_USR17005229L


title: WT, 5 weeks of age uterus, replicate 3


title: BE3 rep 1


title: 4-cell_rep3_ATACseq


title: BEACON2 rep 3


title: BEACON2 rep 1


title: CN15_12_USR17005228L


title: 4-cell_rep2_ATACseq


title: BEACON1 rep 3


title: 4-cell_amanitin_rep3_ATACseq


title: 4-cell_rep1_ATACseq


title: BEACON1 rep 2


title: 4-cell_amanitin_rep2_ATACseq


title: CN15_11_USR17005227L


title: single cell replicate 04

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
The final product was assessed for its size distribution and concentration using the BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl (pH 8.5) and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2 x 50 cycles according to the manufacturer's instructions.
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) was used to trim/filter low quality sequences using the “qtrim=lr trimq=10 maq=10” option.
Alignment of the filtered reads to the mouse reference genome (GRCm38) was performed using HISAT2 (version 2.1.0) and applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Gene expression values were calculated as transcripts per million (TPM) using custom R scripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file, gene expression values in TPM

source_name: CA1 neuron

extract_protocol:
Patch pipettes (1.5–2.0 MΩ) were filled with DEPC-treated internal solution containing (in mM): 140 K-methanesulfonate, 0.2 EGTA, 2 MgCl2 and 10 HEPES, pH-adjusted to 7.3 with KOH. RNase inhibitor (1U/μl, Ambion) was dissolved into the internal solution. Before filling the electrode with RNase inhibitor-containing solution (4.5 μl), the tip of the electrode was always loaded with a small volume of internal solution (~0.5 μl) to form a smooth seal. Immediately after establishing whole-cell mode, the cytosol of the recorded cell was aspirated into the patch pipette and immediately expelled into an RNase free 0.5-ml tube (Ambion).
The cDNA libraries were prepared using the SMART-Seq® HT Kit (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

treatment_protocol: The cytosol of single cell CA1 neuron was harvested using the whole cell patch-clamp technique.

value: postnatal 6- to 7-day-old

value: CA1 neuron


title: 4-cell_amanitin_rep1_ATACseq


title: single cell replicate 03


title: BEACON1 rep 1


title: single cell replicate 02


title: 2-cell_rep3_ATACseq


title: late_emb_GroSeq

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

description: nascent BrU-RNA

data_processing:
Nanopore reads were converted into FastQ using Guppy (Oxford Nanopore). Strand information of the sequenced cDNA was deduced by identifying known adapter sequences at each end of the sequence read using Last (Genome Res. 2011 21(3):487-93)
Adapter indexes were created for: ONT_VNP ACTTGCCTGTCGCTCTATCTTCTTTTT and ONT_SSP TTTCTGTTGGTGCTGATATTGCTGGG using the lastdb function. The indexes were than matched to the fastQ reads using: lastal -Q 1 -P10.
Reads with duplicated adapters and reads with adapters not within 80nt of end of sequence were discarded. The small fraction of reads matching splice leader sequences: CE_SL1, GGTTTAATTACCCAAGTTTGAG, CE_SL2 GGTTTTAACCCAGTTACTCAAG were also identified using Last and discarded. Strand-specific fastQ files were then mapped to the Ce10 genome using Minimap2 with standard parameters for nanopore data (-ax map-ont).
Read abundance for each gene was calculated using Bedtools with the WS235 reference genome.
Genome_build: WS235
Supplementary_files_format_and_content: wig file for respective Watson or Crick Gro-seq reads, representing gastrula or late stage embryos

organism: Caenorhabditis elegans

source_name: Embryonic cells

growth_protocol: Approximately 350,000 L1-stage egl-30(tg26) worms were grown to adulthood at 20°C on NGM plates until early embryos were detectable ex utero; embryos were bleached with sodium hypochlorite solution, washed with M9 buffer, and resuspended in aliquots of egg buffer

extract_protocol:
Staged embryos designated for Gro-seq analysis were prepared as described previously in Kruesi et al. 2013, with minor alterations.  First, we did not fragment nascent BrUTP-labeled RNA transcripts with sodium hydroxide, electing instead to keep full-length, nascent RNA molecules intact.  Second, we used the Ribo-Zero Gold rRNA Removal Kit (Illumina) to deplete rRNA transcripts from immunoprecipitated BrUTP-labeled nascent RNA in an effort to minimize noise and increase transcriptome coverage in our Gro-seq libraries
Sequencing libraries were prepared from BrUTP-labeled RNA using the PCR-cDNA sequencing kit from Oxford Nanopore Technologies (cat: SQK- PCS109).  Libraries were prepared using ~100 ng of input RNA according to the manufacturer’s specifications.  Briefly, full-length nascent RNAs are polyadenylated in vitro to initiate annealing of 3’ poly-T oligo and reverse transcription by SuperScript IV Reverse Transcriptase (cat: 118090010).  Double-stranded cDNAs were size-selected to a range of 300-1000 bp using SPRI beads (AmpureXP) and were amplified with low-cycle PCR prior to sequencing.  Following limited PCR amplification, cDNA libraries were primed with rapid sequencing adapters and loaded onto the MinION flow cell.  We sequenced independent, replicate cDNA libraries from gastrula and late stage embryos—we later merged reads from gastrula and late stage replicate libraries into single fastq files, representing ~15 million total reads for each developmental stage
Gro-Seq

treatment_protocol: Proper embryo synchrony and developmental staging were visually confirmed by microscopy during each time-course experiment—developmental timing was validated by comparing mRNA transcripts in staged embryo populations to expected gene expression patterns from single-embryo studies (Hashimony et al. 2015)

tag: affinity label

value: Br-UTP


title: CN15_10_USR17005226L


title: 2-cell_rep2_ATACseq


title: CN15_07_USR17005223L


title: 2-cell_rep1_ATACseq


title: gastrula_GroSeq

description: nascent BrU-RNA


title: 2-cell_amanitin_rep3_ATACseq


title: CN15_05_USR17005221L


title: CN15_04_USR17005220L


title: CN15_03_USR17005219L


title: zebrafish_disome_rep2

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

institute: Riken

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: GRCz11
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Danio rerio

source_name: whole embryo

growth_protocol:
cultured with standard system water at 28.5 degree
cultured with standard system water at 28.5 degree

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling

treatment_protocol: injected with sfGFP mRNAs at 1-cell stage

value: WT

value: 4 hpf embryo

value: AB strain


title: 2-cell_amanitin_rep2_ATACseq


title: zebrafish_monosome_rep1

description: Ribosome Profiling

value: injected with sfGFP mRNAs at 1-cell stage


title: neutrophil progenitor cells expressing K313-C/EBPα rep3

type: RNA

city: Freiburg

first: Mohamed

middle: Tarek

last: Badr

address: Hermann-Herder-Str. 11

department: Institute of Medical Microbiology and Hygiene

country: Germany

institute: University of Freiburg

description: Gene expression data from cells expressing K313-C/EBPα

hyb_protocol: Arrays were hybridized on the Clariom S mouse array with a constant temperature of 45° C for 16 hours while rotating at 60 rpm

scan_protocol: Standard Affymetrix Protocol

data_processing: Data were background adjusted, normalized and summarized by the SS-RMA method on the Transcriptome Analysis Console® 4.0 programm (Affymetrix).

label: biotin

source_name: Mouse HoxB8 neutrophil progenitor cells expressing K313-C/EBPα

label_protocol: biotin (The WT PLUS Reagent Kit is used to enable fragmented cDNA labelling by terminal deoxynucleotidyl transferase (TdT) using the  Affymetrix proprietary DNA Labeling Reagent that is linked to biotin

growth_protocol: Hoxb8 neutrophil progenitors were differentiated for 1 day in differentiation medium (Optimem Glutamax supplemented with 10 % FCS, 1 % Pen/Strep, 30 µM β-mercaptoethanol, and 1 % SCF supernatant). Cells were grown at 37°C, 5% CO2.

extract_protocol: RNA Purification was conducted by the TRIZOL method followed by RNA Cleanup with Roche High Pure RNA Isolation Kit.


title: 2-cell_amanitin_rep1_ATACseq


title: zebrafish_monosome_rep2

description: Ribosome Profiling


title: CN15_09_USR17005225L


title: neutrophil progenitor cells expressing K313-C/EBPα rep2


title: SCC6_PBS_REP2

status: Public on May 04 2020

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

state: MD

address: 1650 Orleans St - Rm 485

department: Oncology

institute: Johns Hopkins University

data_processing:
cellranger
Monocle 3 alpha
Genome_build: GRCh38

source_name: HNSCC cell line

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) and Ham’s F12 supplemented with 10% fetal bovine serum and maintained at 37°C and 5% carbon dioxide.

extract_protocol:
After cells were trypsinized, manual count and viability were checked using Trypan Blue in a brightfiled microscope. Cells were diluted to a final concentration of 1000 cells/uL.
Library construction from the single cell suspensions were performed using the 10X Genomics Chromium Single Cell 3' Reagent Kit v2, following manufacturer's instructions. Approximately, 8,000 cells were loaded for a final recovery of 5000 cells.
single cell RNA-seq

treatment_protocol: All cell lines were treated daily with cetuximab (100nM) or PBS (untreated) for 5 days starting 24 hours after seeding.

value: PBS

tag: replicate


title: CN15_08_USR17005224L


title: SCC25_PBS_ REP1


title: SCC1_PBS_REP2


title: SCC6_PBS_REP1


title: neutrophil progenitor cells expressing WT-C/EBPα rep3

description: Gene expression data from cells expressing wt C/EBPα

source_name: Mouse HoxB8 neutrophil progenitor cells expressing WT-C/EBPα

value: WT-C/EBP[alpha]


title: SCC25_PBS_REP2


title: SCC25_CTX_REP2

value: cetuximab


title: zebrafish_disome_rep1

description: Ribosome Profiling


title: SCC1_CTX_REP2


title: neutrophil progenitor cells expressing WT-C/EBPα rep1


title: SCC1_CTX_REP1


title: SCC1_PBS_REP1


title: SCC6 CTX 4d [HFTKCBCXY_1_GCCAAT]

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Transcript quantification with Salmon version 0.8.2
Estimation of gene level counts from transcript quantification with R/Bioconductor package tximport version 1.2.0 using the Gencode v26 gene annotations
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

molecule: polyA RNA

source_name: SCC6_100 nM cetuximab

growth_protocol: SCC25 and UM-SCC-1 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 0.4μg/mL (SCC25) or 1.0μg/mL hydrocortisone. UM-SCC-6 cells were cultured in DMEM high glucose supplemented with 10% and 1X NEAA. All cells were maintained at 37oC in a humidified incubator with 5% CO2

extract_protocol:
Total RNA was isolated from at least 1000 cells using the TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. The RNA concentration was determined by the spectrophotometer Nanodrop (Thermo Fisher Scientific, Waltham, MA) and quality was assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) system. An RNA Integrity Number (RIN) of 7.0 was considered as the minimum to be used in the subsequent steps for RNA-seq.
Library preparation was performed using the TrueSeq Stranded Total RNAseq Poly A1 Gold Kit (Illumina, San Diego, CA), according to manufacturer’s recommendations, followed by mRNA enrichment using poly(A) enrichment for ribosomal RNA (rRNA) removal.

treatment_protocol: For cetuximab treatment and proliferation assay, 12,500 cells (SCC25) or 25,000 (UM-SCC-1 and UM-SCC-6) were plated in quintuplicates in 6-well plates. Cetuximab (Bristol-Myers Squibb, Princeton, NJ) was purchased from Johns Hopkins Pharmacy. All cell lines were treated with cetuximab (100nM) or PBS (untreated control) for 5 days starting 24 hours after seeding. Media containing cetuximab or PBS was changed every day. Proliferation was measured using alamarBlue Cell Viability assay (Thermo Scientific), as described by the manufacturer. Briefly, 10% sample volume of alamarBlue reagent was added to each well and fluorescence (excitation 544nm, emission 590nm) was measured after 4 hours of incubation at 37oC. A media only well was used as blank control.

value: head and neck cancer cell line

value: 100 nM cetuximab

tag: time in days


title: CN15_02_USR17005218L


title: SCC6 CTX 5d [HFTKCBCXY_1_CTTGTA]


title: SCC25_CTX_REP1


title: SCC6 CTX 2d [HFTKTBCXY_2_GCCAAT]


title: SCC6 CTX 2d [HFTKTBCXY_2_ACAGTG]


title: SCC6 PBS 4d [HFTKTBCXY_1_CAGATC]


title: SCC6 PBS 3d [HFTKTBCXY_1_TGACCA]


title: SCC6 CTX 3d [HFTKTBCXY_2_ATGTCA]


title: SCC6_CTX_REP2


title: SCC6_CTX_REP1


title: SCC1 CTX 5d [HFKVNBCXY_2_GCCAAT]

source_name: SCC1_100 nM cetuximab


title: SCC6 PBS 5d [HFTKTBCXY_1_CCGTCC]


title: SCC6 PBS 0d [HFKVNBCXY_2_CTTGTA]


title: neutrophil progenitor cells expressing K313-C/EBPα rep1


title: SCC1 CTX 4d [HFKVNBCXY_2_ACAGTG]


title: SCC1 CTX 2d [HFKVNBCXY_1_CAGATC]


title: SCC6 PBS 1d [HFKVNBCXY_2_GTGAAA]


title: SCC1 CTX 3d [HFKVNBCXY_1_CCGTCC]


title: SCC1 PBS 1d [HFNWNBCXY_2_ACAGTG]


title: SCC25 CTX 5d [HFNWNBCXY_1_CAGATC]

source_name: SCC25_100 nM cetuximab


title: SCC1 PBS 4d [HFNWNBCXY_2_GTGAAA]


title: SCC1 PBS 3d [HFNWNBCXY_2_CTTGTA]


title: SCC25 CTX 2d [HFNYHBCXY_2_GTGAAA]


title: SCC1 PBS 5d [HFKVNBCXY_1_CGATGT]


title: SCC1 PBS 2d [HFNWNBCXY_2_GCCAAT]


title: SCC25 PBS 5d [HFNYHBCXY_2_GCCAAT]


title: neutrophil progenitor cells expressing WT-C/EBPα rep2


title: SCC25 PBS 2d [HFNYHBCXY_1_CAGATC]


title: SCC25 CTX 1d [HFNYHBCXY_2_CTTGTA]


title: SCC25 CTX 3d [HFNWNBCXY_1_CGATGT]


title: SCC25 CTX 4d [HFNWNBCXY_1_TGACCA]


title: SCC1 PBS 0d [HFNWNBCXY_1_CCGTCC]


title: SCC25 PBS 4d [HFNYHBCXY_2_ACAGTG]


title: SCC25 PBS 1d [HFNYHBCXY_1_TGACCA]


title: SCC6 PBS 2d [HFTKTBCXY_1_CGATGT]


title: SCC25 PBS 0d [HFNYHBCXY_1_CGATGT]


title: C. elegans 24h

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase v.22.0

source_name: in vitro culture media, secretions

growth_protocol: Synchronized C. elegans young adults (hermaphordites, strain N2) were cultured in M9 media for 5 h or 24 h

extract_protocol:
Total RNA purification using Trizol reagent
Illumina Truseq Small RNA Preparation

treatment_protocol: Collected culture media were sequentially spun at 1500 x g for 10 min at 4 °C, at 12,000 x g  for 45 min and ultracentrifuged as follows:  2 h at 100,000 x g, 4°C; the pellet was washed once with PBS, and centrifuged again for 2h at 100,000 x g, 4 °C.

value: young adult

value: in vitro culture media, secretions


title: HSF1_ZT14_INPUT

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: Input DNA

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (mm9) using BWA software
bigwig were produced using deeptools bamCoverage command with the following parameters: --centerReads --extendReads 37
HSF1peaks were analysed using Macs2 with default parameters with a p-value threshold below 0.001 and annotated with the closest gene using Chippeakanno R package.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, anannotated Macs2 peaks in txt format

source_name: liver

growth_protocol: Mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Animals were housed for 3 weeks under the indicated photoperiods.

extract_protocol:
For the HSF1 ChIP-Seq, chromatin preparation and chromatin immunoprecipitation were performed as in Rey et al., PLoS Biol 2011. The HSF1 polyclonal antibody is from Stressgen (Enzo Life Sciences). For each IP, 5ul of HSF1 antibody was used with 250ul of pre-cleared chromatin.
Libraries for ultra-high throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

value: liver

tag: chip antibody

tag: time point

value: ZT 14


title: C. elegans 5h


title: SCC25 PBS 3d [HFNYHBCXY_1_CCGTCC]


title: Calu3_totalRNA-untr-4h-B

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: Count File: Calu3_totalRNA_readcounts.txt.gz

data_processing:
PolyA-RNA and total-RNA sequencing reads were mapped to the hg38 version of the human genome using STAR (version 2.7.1a) combined with the GENCODE (v30) annotation and the non-standard parameters (--sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000).
Small-RNA sequencing reads were preprocessed using cutadapt (version 2.9) in two passes, first trimming i) the Illumina TruSeq adaptor at the 3’ end, ii) all 3’ end bases with mean Phred score below 30 and iii) the three 5’end overhang nucleotides associated with the Clonetech library preparation protocol. In the second pass, poly(A)-tails were trimmed. Trimmed reads were mapped to hg38 using bowtie (version 1.2.2) and the non-standard parameters (-q -n 1 -e 80 -l 18 -a -m 5 --best --strata). The expression of known miRNAs (miRBase 22 annotation) was estimated using mirdeep2 (version 2.0.0.7) and standard parameters. Gene expression was estimated using FeatureCounts (version 1.5.1) and the non-standard parameters (-F GTF -t exon -g gene_id -C -M --fraction -p -s 2 -O -T 16 -B -Q 4).
For scRNA-seq, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123). Genomes used were hg19, AY310120 (SARS-CoV-1) and MN908947 (SARS-CoV-2)
Genome_build: hg38, hg19
Supplementary_files_format_and_content: tab separated values

source_name: total RNA from Calu3 cells, untr infected 4hpi, replicate B

growth_protocol: H1299, Caco-2 and Calu-3 cells were grown in DMEM/10%FCS/PenStrep/non-essential amino acids/L-glutamine/pyruvate

extract_protocol:
For polyA/total/small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods. For single-cell RNA-sequencing, cells were fixed in methanol and stored at -80 degrees until further processing. Rehydration was done as described in Alles et al. 2017 (doi: 10.1186/s12915-017-0383-5)
PolyA and total RNA-seq libraries were constructed using the NEB Ultra II Directional RNA Library Prep Kit. SmallRNA-seq libraries were constructed using the Clontech SMARTer smRNA-Seq Kit. Single-cell libraries were constructed using a a Nadia device (Dolomite Bio) according to version 1.8 of the manufacturer's protocol, except that the second-strand synthesis step as described in Hughes et al. 2019 (doi: doi.org/10.1101/689273) was included after the exonuclease step.

treatment_protocol: Infections were done by adding the appropriate amount of virus stock solution (produced in Vero E6 cells) at an MOI of 0.3  directly to the cells. For mock infections, supernatant from non-infected Vero E6 cells was used.

tag: infection

value: untreated

tag: molecule subtype

value: total RNA extracted from whole cells


title: Calu3_totalRNA-untr-4h-A

source_name: total RNA from Calu3 cells, untr infected 4hpi, replicate A


title: Calu3_totalRNA-S2-12h-B

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 12hpi, replicate B


title: Calu3_totalRNA-S2-4h-B

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 4hpi, replicate B


title: Calu3_totalRNA-S2-24h-A

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 24hpi, replicate A


title: Calu3_totalRNA-S2-24h-B

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 24hpi, replicate B


title: Calu3_totalRNA-S1-4h-B

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 4hpi, replicate B


title: Calu3_totalRNA-S2-4h-A

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 4hpi, replicate A


title: Calu3_totalRNA-S1-4h-A

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 4hpi, replicate A


title: SCC1 CTX 1d [HFKVNBCXY_1_TGACCA]


title: Calu3_totalRNA-mock-4h-A

source_name: total RNA from Calu3 cells, mock infected 4hpi, replicate A

value: mock


title: Calu3_totalRNA-S2-12h-A

source_name: total RNA from Calu3 cells, SARS-CoV-2 infected 12hpi, replicate A


title: Calu3_totalRNA-mock-24h-A

source_name: total RNA from Calu3 cells, mock infected 24hpi, replicate A


title: Calu3_totalRNA-mock-24h-B

source_name: total RNA from Calu3 cells, mock infected 24hpi, replicate B


title: Calu3_totalRNA-S1-24h-B

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 24hpi, replicate B


title: NA19257 IP replicate

city: CHICAGO

first: Zijie

last: Zhang

department: Chemistry

institute: University of Chicago

description: jointPeakReadCount.txt

data_processing:
Seequencing reads were aligned to reference genome by Tophat2 using WASP pipeline to avoid mapping bias due to SNPs.
Read count of connected bins was quantified by R package MeRIPtools.
Joint peak calling and read count quntification by R package MeRIPtools.
QTL mapping using beta-binomial regression by R package MeRIPtools
Genome_build: hg19
Supplementary_files_format_and_content: (1) Joint m6A peaks across 60 thousand genome YRI individuals in BED12 file and associated read count of input and IP samples.   (2) summary statistics of beta-binomial regression

source_name: Lymphoblastoid cell line

growth_protocol: Standard LCL culture protocol according to instruction downloaded from Coriell institute.

extract_protocol:
TRIzol (Invitrogen) + polyT beads
Kapa RNA hyperPrep kit for Illumina

tag: batch

tag: molecule

value: m6A enriched mRNA


title: Calu3_totalRNA-S1-12h-A

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 12hpi, replicate A


title: Calu3_totalRNA-S1-24h-A

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 24hpi, replicate A


title: NA18907 IP replicate

description: jointPeakReadCount.txt


title: NA19192 IP replicate

description: jointPeakReadCount.txt


title: NA19159 IP replicate

description: jointPeakReadCount.txt


title: NA19239 IP replicate

description: jointPeakReadCount.txt


title: Calu3_totalRNA-mock-4h-B

source_name: total RNA from Calu3 cells, mock infected 4hpi, replicate B


title: single cell replicate 05

source_name: CA1 neuron

value: postnatal 6- to 7-day-old

value: CA1 neuron


title: NA18858 IP replicate

description: jointPeakReadCount.txt


title: NA18523 IP replicate

description: jointPeakReadCount.txt


title: NA18508 IP replicate

description: jointPeakReadCount.txt


title: NA18856 IP replicate

description: jointPeakReadCount.txt


title: NA19108 IP replicate

description: jointPeakReadCount.txt


title: Calu3_totalRNA-S1-12h-B

source_name: total RNA from Calu3 cells, SARS-CoV-1 infected 12hpi, replicate B


title: NA19209 IP replicate

description: jointPeakReadCount.txt


title: NA19200 IP replicate

description: jointPeakReadCount.txt


title: NA19092 IP replicate

description: jointPeakReadCount.txt


title: NA19222 IP replicate

description: jointPeakReadCount.txt


title: NA19193 IP replicate

description: jointPeakReadCount.txt


title: NA19204 IP replicate

description: jointPeakReadCount.txt


title: NA19153 IP replicate

description: jointPeakReadCount.txt


title: NA19152 IP replicate

description: jointPeakReadCount.txt


title: NA19144 IP replicate

description: jointPeakReadCount.txt


title: NA19147 IP replicate

description: jointPeakReadCount.txt


title: NA19160 IP replicate

description: jointPeakReadCount.txt


title: NA19138 IP replicate

description: jointPeakReadCount.txt


title: NA19137 IP replicate

description: jointPeakReadCount.txt


title: NA19140 IP replicate

description: jointPeakReadCount.txt


title: NA19143 IP replicate

description: jointPeakReadCount.txt


title: NA19130 IP replicate

description: jointPeakReadCount.txt


title: NA19131 IP replicate

description: jointPeakReadCount.txt


title: NA19127 IP replicate

description: jointPeakReadCount.txt


title: NA19128 IP replicate

description: jointPeakReadCount.txt


title: NA19119 IP replicate

description: jointPeakReadCount.txt


title: NA18486 IP replicate

description: jointPeakReadCount.txt


title: NA19116 IP replicate

description: jointPeakReadCount.txt


title: NA19101 IP replicate

description: jointPeakReadCount.txt


title: NA19093 IP replicate

description: jointPeakReadCount.txt


title: NA19102 IP replicate

description: jointPeakReadCount.txt


title: NA18916 IP replicate

description: jointPeakReadCount.txt


title: NA18870 IP replicate

description: jointPeakReadCount.txt


title: NA18913 IP replicate

description: jointPeakReadCount.txt


title: NA19098 IP replicate

description: jointPeakReadCount.txt


title: NA18861 IP replicate

description: jointPeakReadCount.txt


title: NA18862 IP replicate

description: jointPeakReadCount.txt


title: NA18912 IP replicate

description: jointPeakReadCount.txt


title: NA18852 IP replicate

description: jointPeakReadCount.txt


title: NA18855 IP replicate

description: jointPeakReadCount.txt


title: NA18516 IP replicate

description: jointPeakReadCount.txt


title: NA18501 IP replicate

description: jointPeakReadCount.txt


title: NA18511 IP replicate

description: jointPeakReadCount.txt


title: NA18522 IP replicate

description: jointPeakReadCount.txt


title: NA18499 IP replicate

description: jointPeakReadCount.txt


title: NA19257 Input replicate

description: jointPeakReadCount.txt

value: mRNA


title: NA19204 Input replicate

description: jointPeakReadCount.txt


title: NA19114 IP replicate

description: jointPeakReadCount.txt


title: NA18498 IP replicate

description: jointPeakReadCount.txt


title: NA18907 Input replicate

description: jointPeakReadCount.txt


title: NA19192 Input replicate

description: jointPeakReadCount.txt


title: NA18858 Input replicate

description: jointPeakReadCount.txt


title: NA19239 Input replicate

description: jointPeakReadCount.txt


title: NA19099 IP replicate

description: jointPeakReadCount.txt


title: NA19159 Input replicate

description: jointPeakReadCount.txt


title: NA18909 IP replicate

description: jointPeakReadCount.txt


title: NA18856 Input replicate

description: jointPeakReadCount.txt


title: NA18519 IP replicate

description: jointPeakReadCount.txt


title: NA19222 Input replicate

description: jointPeakReadCount.txt


title: NA19092 Input replicate

description: jointPeakReadCount.txt


title: NA18523 Input replicate

description: jointPeakReadCount.txt


title: NA18508 Input replicate

description: jointPeakReadCount.txt


title: NA18486 Input replicate

description: jointPeakReadCount.txt


title: NA19193 Input replicate

description: jointPeakReadCount.txt


title: NA19108 Input replicate

description: jointPeakReadCount.txt


title: NA19200 Input replicate

description: jointPeakReadCount.txt


title: NA19209 Input replicate

description: jointPeakReadCount.txt


title: NA19160 Input replicate

description: jointPeakReadCount.txt


title: NA19153 Input replicate

description: jointPeakReadCount.txt


title: NA19147 Input replicate

description: jointPeakReadCount.txt


title: NA19144 Input replicate

description: jointPeakReadCount.txt


title: NA19138 Input replicate

description: jointPeakReadCount.txt


title: NA19140 Input replicate

description: jointPeakReadCount.txt


title: NA19137 Input replicate

description: jointPeakReadCount.txt


title: NA19131 Input replicate

description: jointPeakReadCount.txt


title: NA19152 Input replicate

description: jointPeakReadCount.txt


title: NA19130 Input replicate

description: jointPeakReadCount.txt


title: NA19119 Input replicate

description: jointPeakReadCount.txt


title: NA19127 Input replicate

description: jointPeakReadCount.txt


title: NA19114 Input replicate

description: jointPeakReadCount.txt


title: NA19098 Input replicate

description: jointPeakReadCount.txt


title: NA19102 Input replicate

description: jointPeakReadCount.txt


title: NA19116 Input replicate

description: jointPeakReadCount.txt


title: NA18909 Input replicate

description: jointPeakReadCount.txt


title: NA19101 Input replicate

description: jointPeakReadCount.txt


title: NA19093 Input replicate

description: jointPeakReadCount.txt


title: NA18870 Input replicate

description: jointPeakReadCount.txt


title: NA19099 Input replicate

description: jointPeakReadCount.txt


title: NA18913 Input replicate

description: jointPeakReadCount.txt


title: NA18916 Input replicate

description: jointPeakReadCount.txt


title: NA19143 Input replicate

description: jointPeakReadCount.txt


title: NA18861 Input replicate

description: jointPeakReadCount.txt


title: NA19128 Input replicate

description: jointPeakReadCount.txt


title: NA18852 Input replicate

description: jointPeakReadCount.txt


title: NA19204 IP

description: jointPeakReadCount.txt


title: NA18519 Input replicate

description: jointPeakReadCount.txt


title: NA18522 Input replicate

description: jointPeakReadCount.txt


title: NA18855 Input replicate

description: jointPeakReadCount.txt


title: NA18501 Input replicate

description: jointPeakReadCount.txt


title: NA18499 Input replicate

description: jointPeakReadCount.txt


title: NA19239 IP

description: jointPeakReadCount.txt


title: NA18498 Input replicate

description: jointPeakReadCount.txt


title: NA18862 Input replicate

description: jointPeakReadCount.txt


title: NA19159 IP

description: jointPeakReadCount.txt


title: NA19257 IP

description: jointPeakReadCount.txt


title: NA18912 Input replicate

description: jointPeakReadCount.txt


title: NA18907 IP

description: jointPeakReadCount.txt


title: NA18856 IP

description: jointPeakReadCount.txt


title: NA18486 IP

description: jointPeakReadCount.txt


title: NA18523 IP

description: jointPeakReadCount.txt


title: NA18858 IP

description: jointPeakReadCount.txt


title: NA19108 IP

description: jointPeakReadCount.txt


title: NA19092 IP

description: jointPeakReadCount.txt


title: NA18508 IP

description: jointPeakReadCount.txt


title: NA18516 Input replicate

description: jointPeakReadCount.txt


title: NA19222 IP

description: jointPeakReadCount.txt


title: NA19200 IP

description: jointPeakReadCount.txt


title: NA19153 IP

description: jointPeakReadCount.txt


title: NA19152 IP

description: jointPeakReadCount.txt


title: NA19160 IP

description: jointPeakReadCount.txt


title: NA19144 IP

description: jointPeakReadCount.txt


title: NA19147 IP

description: jointPeakReadCount.txt


title: NA19193 IP

description: jointPeakReadCount.txt


title: NA19192 IP

description: jointPeakReadCount.txt


title: NA19130 IP

description: jointPeakReadCount.txt


title: NA19143 IP

description: jointPeakReadCount.txt


title: NA19137 IP

description: jointPeakReadCount.txt


title: NA19140 IP

description: jointPeakReadCount.txt


title: NA19131 IP

description: jointPeakReadCount.txt


title: NA19119 IP

description: jointPeakReadCount.txt


title: NA19128 IP

description: jointPeakReadCount.txt


title: NA19138 IP

description: jointPeakReadCount.txt


title: NA19127 IP

description: jointPeakReadCount.txt


title: NA19116 IP

description: jointPeakReadCount.txt


title: NA19209 IP

description: jointPeakReadCount.txt


title: NA19101 IP

description: jointPeakReadCount.txt


title: NA19098 IP

description: jointPeakReadCount.txt


title: NA18916 IP

description: jointPeakReadCount.txt


title: NA19102 IP

description: jointPeakReadCount.txt


title: NA19099 IP

description: jointPeakReadCount.txt


title: NA18913 IP

description: jointPeakReadCount.txt


title: NA19093 IP

description: jointPeakReadCount.txt


title: NA18909 IP

description: jointPeakReadCount.txt


title: NA18862 IP

description: jointPeakReadCount.txt


title: NA18861 IP

description: jointPeakReadCount.txt


title: NA18870 IP

description: jointPeakReadCount.txt


title: NA18519 IP

description: jointPeakReadCount.txt


title: NA18912 IP

description: jointPeakReadCount.txt


title: NA18852 IP

description: jointPeakReadCount.txt


title: NA18516 IP

description: jointPeakReadCount.txt


title: NA18499 IP

description: jointPeakReadCount.txt


title: NA18501 IP

description: jointPeakReadCount.txt


title: NA18522 IP

description: jointPeakReadCount.txt


title: NA19257 Input

description: jointPeakReadCount.txt


title: NA19192 Input

description: jointPeakReadCount.txt


title: NA19204 Input

description: jointPeakReadCount.txt


title: NA19159 Input

description: jointPeakReadCount.txt


title: NA19114 IP

description: jointPeakReadCount.txt


title: NA18907 Input

description: jointPeakReadCount.txt


title: NA18858 Input

description: jointPeakReadCount.txt


title: NA18508 Input

description: jointPeakReadCount.txt


title: NA18486 Input

description: jointPeakReadCount.txt


title: NA18523 Input

description: jointPeakReadCount.txt


title: NA18856 Input

description: jointPeakReadCount.txt


title: NA19108 Input

description: jointPeakReadCount.txt


title: NA18855 IP

description: jointPeakReadCount.txt


title: NA19092 Input

description: jointPeakReadCount.txt


title: NA19222 Input

description: jointPeakReadCount.txt


title: NA19160 Input

description: jointPeakReadCount.txt


title: NA19209 Input

description: jointPeakReadCount.txt


title: NA19193 Input

description: jointPeakReadCount.txt


title: NA19152 Input

description: jointPeakReadCount.txt


title: NA18511 IP

description: jointPeakReadCount.txt


title: NA19153 Input

description: jointPeakReadCount.txt


title: NA18498 IP

description: jointPeakReadCount.txt


title: NA19147 Input

description: jointPeakReadCount.txt


title: NA19200 Input

description: jointPeakReadCount.txt


title: NA19239 Input

description: jointPeakReadCount.txt


title: NA19144 Input

description: jointPeakReadCount.txt


title: NA19138 Input

description: jointPeakReadCount.txt


title: NA19137 Input

description: jointPeakReadCount.txt


title: NA19143 Input

description: jointPeakReadCount.txt


title: NA19131 Input

description: jointPeakReadCount.txt


title: NA19128 Input

description: jointPeakReadCount.txt


title: NA19130 Input

description: jointPeakReadCount.txt


title: NA19127 Input

description: jointPeakReadCount.txt


title: NA19119 Input

description: jointPeakReadCount.txt


title: NA19102 Input

description: jointPeakReadCount.txt


title: NA19114 Input

description: jointPeakReadCount.txt


title: NA19116 Input

description: jointPeakReadCount.txt


title: NA19099 Input

description: jointPeakReadCount.txt


title: NA18913 Input

description: jointPeakReadCount.txt


title: NA19098 Input

description: jointPeakReadCount.txt


title: NA18870 Input

description: jointPeakReadCount.txt


title: NA19093 Input

description: jointPeakReadCount.txt


title: NA18916 Input

description: jointPeakReadCount.txt


title: NA18912 Input

description: jointPeakReadCount.txt


title: NA18909 Input

description: jointPeakReadCount.txt


title: NA18855 Input

description: jointPeakReadCount.txt


title: NA19140 Input

description: jointPeakReadCount.txt


title: NA18861 Input

description: jointPeakReadCount.txt


title: NA18522 Input

description: jointPeakReadCount.txt


title: NA18519 Input

description: jointPeakReadCount.txt


title: NA18511 Input

description: jointPeakReadCount.txt


title: NA18862 Input

description: jointPeakReadCount.txt


title: NA18852 Input

description: jointPeakReadCount.txt


title: NA18516 Input

description: jointPeakReadCount.txt


title: NA18499 Input

description: jointPeakReadCount.txt


title: NA18501 Input

description: jointPeakReadCount.txt


title: NA18498 Input

description: jointPeakReadCount.txt


title: UF0616_brep1

city: Gainesville

first: Matias

last: Kirst

state: FL

address: Newin-Ziegler, Room 320

institute: University of Florida

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq FASTQ-files were quality and adapter trimmed using Trimmomatic v0.32
The pre-processed reads were aligned to v3.0 of the Populus thrichocarpa reference genome using STAR 2.5.2b
Picard v1.115 was used to remove duplicate reads and only unique alignments were kept for further analysis.
Three transcript assembly platforms were used to maximize the detection of novel genes: (1) Cufflinks version 2.2.1, (2) StringTie version 1.3.3 , and (3) Trinity version 2.3.2.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The master transcriptome was reformatted and annotated using gffcompare version 0.9.9c and subjected to expression filtering to remove artifacts generated by merging assemblies such that each transcript in the assembly was required to be expressed at FPKM >= 3 in at least two of the three biological replicates of at least three individuals and 50 observations.
Gene expression was measured using Cufflinks version 2.2.1
Supplementary_files_format_and_content: A single Comma separated (.csv) file includes a matirx with FPKM values for all samples (Matrix_fpkm_AllIndividuos.csv)

organism: Populus deltoides

source_name: Xylem

growth_protocol: Plants were clonally propagated from apical green cuttings in a glasshouse at University of Florida as previously described (Fahrenkrog et al., 2017). Half of the population was grown in 2015 and the other half in 2016 in the same greenhouse, same conditions and time of the year (from April to August). Both experiments were set with three biological replicates, using a row-column design.

extract_protocol:
Total RNA was extracted according to the CTAB-LiCl protocol (Chang et al., 1993).
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina  following the manufacturerÕs instructions.

value: 16 weeks


title: UF0616_brep3


title: UF0616_brep2


title: NA19101 Input

description: jointPeakReadCount.txt


title: UF0614_brep3


title: UF0598_brep3


title: UF0612_brep3


title: UF0613_brep2


title: UF0614_brep2


title: UF0614_brep1


title: UF0596_brep3


title: UF0612_brep2


title: UF0598_brep1


title: UF0613_brep1


title: UF0598_brep2


title: UF0596_brep2


title: NA18511 Input replicate

description: jointPeakReadCount.txt


title: UF0596_brep1


title: UF0593_brep2


title: UF0594_brep3


title: UF0593_brep3


title: UF0593_brep1


title: UF0594_brep1


title: UF0590_brep3


title: UF0590_brep2


title: UF0584_brep3


title: UF0590_brep1


title: UF0613_brep3


title: UF0583_brep2


title: UF0583_brep1


title: UF0583_brep3


title: UF0612_brep1


title: UF0594_brep2


title: UF0579_brep1


title: UF0582_brep2


title: UF0579_brep2


title: UF0582_brep3


title: UF0572_brep3


title: UF0572_brep2


title: UF0582_brep1


title: UF0565_brep2


title: UF0568_brep2


title: UF0579_brep3


title: UF0565_brep3


title: UF0566_brep1


title: UF0584_brep2


title: UF0565_brep1


title: UF0566_brep2


title: UF0563_brep3


title: UF0584_brep1


title: UF0562_brep3


title: UF0562_brep2


title: UF0562_brep1


title: UF0563_brep1


title: UF0563_brep2


title: UF0560_brep3


title: UF0560_brep2


title: UF0559_brep3


title: UF0572_brep1


title: UF0568_brep1


title: UF0568_brep3


title: UF0559_brep2


title: UF0559_brep1


title: UF0557_brep3


title: UF0557_brep2


title: UF0556_brep2


title: UF0556_brep3


title: UF0556_brep1


title: UF0557_brep1


title: UF0555_brep2


title: UF0554_brep3


title: UF0554_brep1


title: UF0555_brep1


title: UF0551_brep2


title: UF0555_brep3


title: UF0547_brep3


title: UF0554_brep2


title: UF0551_brep3


title: UF0551_brep1


title: UF0560_brep1


title: UF0544_brep3


title: UF0544_brep1


title: UF0547_brep1


title: UF0542_brep3


title: UF0544_brep2


title: UF0542_brep2


title: UF0539_brep3


title: UF0542_brep1


title: UF0538_brep3


title: UF0539_brep1


title: UF0539_brep2


title: UF0538_brep2


title: UF0536_brep3


title: UF0538_brep1


title: UF0536_brep1


title: UF0535_brep3


title: UF0535_brep2


title: UF0534_brep3


title: UF0532_brep1


title: UF0532_brep3


title: UF0534_brep1


title: UF0533_brep2


title: UF0533_brep3


title: UF0547_brep2


title: UF0535_brep1


title: UF0532_brep2


title: UF0534_brep2


title: UF0529_brep3


title: UF0533_brep1


title: UF0530_brep3


title: UF0529_brep2


title: UF0530_brep2


title: UF0530_brep1


title: UF0528_brep3


title: UF0528_brep1


title: UF0528_brep2


title: UF0525_brep1


title: UF0525_brep3


title: UF0536_brep2


title: UF0525_brep2


title: UF0523_brep3


title: UF0523_brep1


title: UF0523_brep2


title: UF0522_brep1


title: UF0521_brep3


title: UF0521_brep2


title: UF0529_brep1


title: UF0520_brep3


title: UF0520_brep1


title: UF0521_brep1


title: UF0518_brep1


title: UF0518_brep2


title: UF0520_brep2


title: UF0518_brep3


title: UF0517_brep3


title: UF0517_brep2


title: UF0516_brep2


title: UF0515_brep2


title: UF0516_brep3


title: UF0516_brep1


title: UF0515_brep1


title: UF0506_brep2


title: UF0505_brep3


title: UF0506_brep1


title: UF0504_brep3


title: UF0506_brep3


title: UF0505_brep2


title: UF0522_brep3


title: UF0505_brep1


title: UF0503_brep2


title: UF0503_brep1


title: UF0500_brep3


title: UF0517_brep1


title: UF0500_brep2


title: UF0499_brep3


title: UF0499_brep1


title: UF0499_brep2


title: UF0497_brep3


title: UF0497_brep2


title: UF0496_brep3


title: UF0500_brep1


title: UF0496_brep2


title: UF0497_brep1


title: UF0495_brep1


title: UF0495_brep2


title: UF0496_brep1


title: UF0493_brep3


title: UF0495_brep3


title: UF0488_brep3


title: UF0493_brep1


title: UF0504_brep2


title: UF0493_brep2


title: UF0485_brep2


title: UF0488_brep1


title: UF0485_brep1


title: UF0503_brep3


title: UF0485_brep3


title: UF0504_brep1


title: UF0488_brep2


title: UF0482_brep2


title: UF0482_brep3


title: UF0482_brep1


title: UF0481_brep3


title: UF0481_brep2


title: UF0481_brep1


title: UF0480_brep1


title: UF0479_brep3


title: UF0479_brep2


title: UF0477_brep3


title: UF0479_brep1


title: UF0477_brep2


title: UF0470_brep3


title: UF0470_brep2


title: UF0470_brep1


title: UF0466_brep3


title: UF0466_brep1


title: UF0477_brep1


title: UF0465_brep2


title: UF0466_brep2


title: UF0465_brep3


title: UF0464_brep1


title: UF0465_brep1


title: UF0464_brep2


title: UF0457_brep2


title: UF0464_brep3


title: UF0457_brep1


title: UF0457_brep3


title: UF0480_brep2


title: UF0456_brep2


title: UF0480_brep3


title: UF0456_brep3


title: UF0454_brep3


title: UF0456_brep1


title: UF0454_brep2


title: UF0452_brep3


title: UF0452_brep1


title: UF0451_brep3


title: UF0450_brep3


title: UF0451_brep1


title: UF0448_brep3


title: UF0450_brep2


title: UF0448_brep2


title: UF0446_brep1


title: UF0440_brep1


title: UF0440_brep3


title: UF0450_brep1


title: UF0439_brep2


title: UF0446_brep2


title: UF0446_brep3


title: UF0439_brep1


title: UF0431_brep2


title: UF0431_brep3


title: UF0448_brep1


title: UF0439_brep3


title: UF0454_brep1


title: UF0438_brep3


title: UF0452_brep2


title: UF0431_brep1


title: UF0430_brep3


title: UF0440_brep2


title: UF0430_brep2


title: UF0438_brep2


title: UF0430_brep1


title: UF0451_brep2


title: UF0425_brep3


title: UF0425_brep2


title: UF0425_brep1


title: UF0422_brep3


title: UF0422_brep1


title: UF0422_brep2


title: UF0419_brep3


title: UF0419_brep1


title: UF0419_brep2


title: UF0438_brep1


title: UF0416_brep3


title: UF0416_brep2


title: UF0413_brep1


title: UF0413_brep2


title: UF0412_brep2


title: UF0413_brep3


title: UF0412_brep1


title: UF0411_brep3


title: UF0404_brep3


title: UF0411_brep2


title: UF0403_brep2


title: UF0403_brep1


title: UF0411_brep1


title: UF0403_brep3


title: UF0402_brep2


title: UF0404_brep2


title: UF0402_brep3


title: UF0400_brep3


title: UF0400_brep2


title: UF0400_brep1


title: UF0399_brep3


title: UF0394_brep3


title: UF0399_brep1


title: UF0399_brep2


title: UF0416_brep1


title: UF0393_brep3


title: UF0394_brep1


title: UF0394_brep2


title: UF0412_brep3


title: UF0392_brep3


title: UF0393_brep1


title: UF0392_brep1


title: UF0391_brep2


title: UF0391_brep3


title: UF0402_brep1


title: UF0391_brep1


title: UF0390_brep1


title: UF0390_brep2


title: UF0388_brep1


title: UF0388_brep3


title: UF0388_brep2


title: UF0404_brep1


title: UF0385_brep3


title: UF0393_brep2


title: UF0385_brep2


title: UF0385_brep1


title: UF0380_brep2


title: UF0377_brep3


title: UF0380_brep1


title: UF0377_brep2


title: UF0377_brep1


title: RIC-seq_HeLa_Total_rep2

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Library strategy: RIC-seq
Illumina bcl2fastq conversion software (v.2.16) was used for base calling.
After the sequencing of RIC libraries, adapters and PCR duplicates were trimmed off using the Trimmomatic program (v.0.36) (Bolger et al., 2014) and homemade scripts, respectively. The poly(N) tails at the 3’ end were further clipped using the Cutadapt program (v.1.15) (Martin, 2011).
After filtering, the paired reads were first aligned to 45S pre-rRNA, and the unmapped reads were further aligned to the human reference genome (assembly version: hg19) using the STAR software (v.020201) (Dobin et al., 2013). The parameters used were as follows: STAR --runMode alignReads --genomeDir index --readFilesIn read.fq --outFileNamePrefix outprefix --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15. Three additional parameters were further applied (--alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5) to improve the mapping quality.
The low-quality and secondary mapping results were filtered using the SAMtools package (v.0.1.19).
Genome_build: hg19
Supplementary_files_format_and_content: genome-wide RNA-RNA interaction in hic format produced by Juicebox

source_name: human HeLa cells

growth_protocol: HeLa and 293T cells were grown in DMEM containing 10% fetal bovine serum plus 100 U/ml penicillin/streptomycin (Life Technologies; 15140) at 37 °C in 5% CO2. HT29 and HCT116 cells were cultured in modified McCoy’s 5A supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. GM12878 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. MCF-7 cells were maintained in MEM containing 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. IMR-90 cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 5 ng/ml fibroblast growth factor-basic (R&D), 1 μg/ml hydrocortisone hemisuccinate, 50 μg/ml ascorbic acid, 5 μg/ml rh Insulin, 2% fetal bovine serum and 100 U/ml penicillin/streptomycin. S2 cells were maintained in Schneider’s drosophila medium supplemented with 10% heat-inactivated fetal bovine serum and 100 U/ml penicillin/streptomycin.

extract_protocol:
After pCp-biotin labeling and proximity ligation, 200 μl of proteinase K buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 50 μl of proteinase K were applied to cell pellets and sequentially incubated at 37 °C for 60 min and 56 °C for 15 min. The RNA was extracted with 750 μl of TRIzol LS and 220 μl of chloroform following the manufacture’s instruction.
To remove the potential RNA-DNA ligation byproducts mediated by T4 RNA ligase, 20 μg of total RNA was treated with a mixture containing 10 μl of 10 × RQ1 DNase I buffer, 3 μl of RNAsin and 5 μl of DNase I at 37 °C for 20 min. RNA was then purified by acid Phenol: chloroform extraction and ethanol precipitation. The rRNA can be optionally removed using the Ribo-off rRNA Depletion Kit (Vazyme, N406-01) or one can directly proceed to the next step (to probe the rRNA structure and interactions). For fragmentation, 16 μl of total RNA was mixed with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2) and incubated at 94 °C for 5 min, and then quickly put on ice. To enrich pCp-biotin marked chimeric RNAs, 20 μl of pre-blocked MyOne Streptavidin C1 beads, 30 μl of NF-H2O and 50 μl of 2 × TWB buffer were applied to each RNA sample and incubated at room temperature for 30 min by rotating. After washing four times with 1× TWB buffer, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min (1000 rpm). The tube was quickly placed on a magnet stand for 1 min and the supernatant was transferred to a new EP tube. This elution process was repeated two more times. Finally, the enriched RNAs were extracted with acid Phenol: chloroform and precipitated at the final concentration of 300 mM NaCl, with 3 volumes of -20°C ethanol and 1 μl of glycoblue. RNA was pelleted at 13,000 rpm and washed twice with 75% ETOH before resuspending in 10 μl of nuclease-free water. To synthesis first-strand cDNA, 0.5 μl of N6 primer (0.1 μg/μl) was added to the mixture and incubated at 65 °C for 5 min, followed by rapid placement on ice for at least 2 min. Reverse transcription was performed by further addition of 5.5 μl of reverse transcription mix (3 μl of 5 × first-strand buffer, 1 μl of 10 mM dNTPs, 0.5 μl of 100 mM DTT, 0.5 μl of RNase inhibitor, 0.5 μl of Superscript II reverse transcriptase) to the mixture and incubation at 25 °C for 10 min, 42 °C for 40 min and then 70 °C for 15 min. We next created dUTP second strand cDNA by adding the following reaction mixture (10 μl of 5 × second-strand buffer, 0.8 μl of 25 mM dNTPs with 80% of the dTTP replaced by dUTP, 20.5 μl of RNase-free water, 0.2 μl of 5 U/μl RNase H and 2.5 μl of E. coli DNA polymerase I) to the first-strand cDNA mixture, and incubated at 16 °C for 2 h. The double-stranded (ds)DNA products were purified using 1.8 × AMPure beads following the manufacturer’s protocol and end-repaired with a mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The end-repaired DNA was then treated with Klenow exo- to add an adenine to the 3’ ends. For paired-end library construction, adaptors were ligated to dsDNA using quick T4 DNA ligase and incubated at 20 °C for 15 min. Subsequently, the ligated DNA product was purified twice with AMPure beads. The adaptor-ligated cDNA was mixed with 1 μl of 10 μM Illumina PE1.0, 1 μl of 10 μM index primer, 1 μl of 50 mM MgSO4, 2.5 μl of 10 × Pfx buffer, 0.4 μl of 25 mM dNTPs, 0.4 μl of 2.5 U/μl Platinum Pfx DNA polymerase (Thermo Fisher, 11708-013) and 3 μl of USER enzyme (NEB, M5505S). The mixture was incubated at 37 °C for 15 min to allow the USER enzyme to digest the dUTP strand, then at 94 °C for 2 min. PCR was performed with the following programme: 11 to 13 cycles of 94 °C for 15 s, 62 °C for 30 s and 72 °C for 30 s. The 200 to 450 bp of PCR products were purified from agarose gel by Qiaqucik mini Elute Kit. The DNA concentration was measured by Qubit and sequenced by Illumina paired-end sequencing.

treatment_protocol: Cells were fixed in 10 ml of PBS containing 1% formaldehyde at room temperature for 10 min and then quenched by addition of 1/20 volume of 2.5 M glycine. After washing three times with ice-cold PBS, cells were scraped into 15 ml tubes and collected by centrifugation at 2,500 rpm for 10 min at 4 °C. The cell pellet was resuspended in 1 ml of permeabilization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP-40, 0.3% Triton X-100, 0.1% Tween 20, 1× protease inhibitors, 2 U/ml SUPERase In RNase inhibitor), mixed briefly and incubated on ice for 15 min. The integrity of the cells was examined at this step under a microscope. Cells were spun down at 3,500 rpm for 5 min at 4 °C. After washing three times with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.2% NP-40), the cell pellet was briefly incubated with 200 μl of 1 × MN mixture (50 mM Tris-HCl pH 8.0, 5 mM CaCl2, 0.03 U/μl micrococcal nuclease) for 10 min at 37 °C. The reaction was stopped by washing twice with 1 × PNK + EGTA buffer (50 mM Tris- HCl pH7.4, 20 mM EGTA 0.5% NP-40) and twice with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.2% NP-40).

value: HeLa


title: RIC-seq_HeLa_Total_rep1


title: UF0392_brep2


title: IgG_control_for_hnRNPK_monomer_CLIP-seq_HeLa_rep1

data_processing:
Illumina bcl2fastq conversion software (v.2.16) was used for base calling.
After the sequencing of CLIP-seq libraries, adapters were trimmed off using the Cutadapt program (v.1.15) (Martin, 2011) and low-quality bases were removed by the Trimmomatic program (v.0.36) (Bolger et al., 2014).
After filtering, read 1 of the paired-end reads were first aligned to human 45S pre-rRNA, and the unmapped reads were further aligned to the human reference genome (assembly version: hg19) with the Bowtie software (v.1.2.3) (Langmead et al., 2009) by allowing two mismatches.
CLIP-seq peaks were identified by the Piranha tool (v.1.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated using bamCoverage software.

growth_protocol: HeLa cells were grown in DMEM containing 10% fetal bovine serum plus 100 U/ml penicillin/streptomycin at 37 °C in 5% CO2.

extract_protocol: The hnRNPK-RNA complexes were sequentially treated with micrococcal nuclease and alkaline phosphatase. After ligation with a 3' App modified DNA linker on beads, the protein-RNA complexes were fractionated on 4%-12% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The hnRNPK-specific monomer or dimer bands were cut and treated with proteinase K to extract respective RNA by phenol and chloroform. The extracted RNA was ligated with a 5' RNA linker and reverse transcribed using SuperScript III Reverse Transcriptase (Life Technologies, catalog# 18080-051). The PCR products were sequenced with the Illumina HiSeq X10 platform.

treatment_protocol: CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, 1×10^7 HeLa cells were irradiated at 400 mJ/cm2 with 254 nm UV light. The crosslinked cells were lysed and 15 μg of hnRNPK (Bethyl, A300-676A) or IgG (Cell Signaling Technology, #2729) specific antibody was applied to pull-down protein-RNA complexes.

tag: protocol

value: CLIP-seq

tag: antibody

value: Normal Rabbit IgG (Cell Signaling Technology, #2729)


title: IgG_control_for_hnRNPK_dimer_CLIP-seq_HeLa_rep1


title: UF0376_brep1


title: hnRNPK_monomer_CLIP-seq_HeLa_rep1

value: anti-hnRNPK (Bethyl, A300-676A)


title: RIC-seq_random_HeLa_rep2


title: IgG_control_for_hnRNPK_dimer_CLIP-seq_HeLa_rep2


title: hnRNPK_dimer_CLIP-seq_HeLa_rep2


title: hnRNPK_monomer_CLIP-seq_HeLa_rep2


title: UF0376_brep2


title: IgG_control_for_hnRNPK_monomer_CLIP-seq_HeLa_rep2


title: UF0376_brep3


title: hnRNPK_dimer_CLIP-seq_HeLa_rep1


title: UF0370_brep3


title: RIC-seq_HeLa_rRNA_depleted_rep2


title: RIC-seq_pcp_minus_HeLa_Total_rep2


title: RIC-seq_pcp_minus_HeLa_Total_rep1


title: RIC-seq_HeLa_rRNA_depleted_rep1


title: UF0370_brep2


title: UF0370_brep1


title: RIC-seq_random_HeLa_rep1


title: UF0390_brep3


title: UF0369_brep2


title: UF0369_brep3


title: UF0361_brep3


title: UF0361_brep1


title: UF0361_brep2


title: UF0355_brep2


title: UF0355_brep3


title: SCC25PBS_replicate2

data_processing:
adapters trimming with Trim Galore! version 0.5.0
alignment with Bowtie2 version 2.3.2
duplicated and mitochondrial DNA removal with Picard Tools version 2.18
unmapped and low quality reads removal with Samtools version 1.9
peaks calling with MACS2
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks

source_name: HNSCC cell line

extract_protocol:
For nuclei isolation, cells were scraped, washed in PBS and lysed (lysis buffer: 10mM Tris-Cl, pH7.4; 10mM NaCl; 3mM MgCl2; 0.05% IGEPAL).
Nuclei tagmentation and adapter ligation by Tn5 was performed using the Nextera DNA Sample Preparation kit (Illumina) and followed by purification with MinElute PCR Purification kit (QIagen), according to manufacturers’ instructions. Transposed DNA fragments were amplified for 5 cycles using the NEBNext Q5 HotStart HiFi PCR Master Mix with regular forward and reverse barcoded primers. Additional number of amplification cycles were determined by quantitative-PCR using the NEBNext HiFi Master Mix, SYBR Green I (Applied Biosystems) and Custom Nextera Primers. The final product was purified with MinElute PCR Purification kit (QIagen) and quality checked on 2100 Bioanalyzer (Agilent).

value: HNSCC cell line SCC25

tag: treatment

value: PBS


title: UF0355_brep1


title: UF0346_brep3


title: SCC25CTX_replicate3

tag: cell line

value: cetuximab


title: UF0346_brep1


title: UF0346_brep2


title: SCC25PBS_replicate3


title: UF0369_brep1


title: SCC25CTX_replicate2


title: UF0356_brep3


title: UF0356_brep2


title: UF0356_brep1


title: Islet_KO_rep3

city: Qingdao

first: Jie

last: Lu

address: 16 Jiangsu Rd

institute: Qingdao University

description: Gene expression in isolated islets of Uox-KO mice without any intervention

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (catalog no. 5188-5242; Agilent technologies) in Hybridization Oven.

scan_protocol: Microarray was performed on Aglient platform using Agilent SurePrint G3 Mouse Gene Expression Microarray 8×60K chips (Agilent technologies)

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). We used a cut off of normalized array values (log2-transformed values > 2.0 or < 0.5) for islet tissue transcripts. Raw data were normalized by quantile algorithm. Limma and agilp packages were loaded in R (version 3.4.1).

source_name: Islet, KO, replication3

label_protocol: Total RNA samples (100-1,000 ng) were polyA enriched and then reverse transcribed into double-stranded cDNA and then labelled by Low Input Quick Amp Labelling Kit (catalog no. 5190-2305; One-Color, Agilent technologies) following the manufacturer’s instructions.

growth_protocol: Hyperuricemic mice and their counterparts (Uox-KO and WT) were in basal condition. Diabetic mice (STZ-KO and STZ-WT) were treated with MLD-STZ for five days.

extract_protocol: Isolated islets from mice were prepared for the following RNA extraction. Briefly, total RNA was extracted and purified using RNeasy micro kit (catalog no. 74004; QIAGEN) following the manufacturer’s instructions and checked for a registrant identification number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Mice were euthanized with CO2 followed by cervical dislocation. The common bile duct close to the duodenum was ligated for the retrograde puncture of the common bile duct, followed by a slow perfusion of 3 mL pre-chilled collagenase IV at 0.5 mg/mL concentration (dissolved in Hanks’ balanced salt solution) to fully expand the pancreatic body and tail. The pancreas was then excised and digested at 37 °C for 11 minutes. Islets were purified in histopaque1077  by vortexing gently for several seconds.

tag: tissue

value: islets

tag: Sex

value: male

value: Uox-KO


title: Islet_STZ-KO_rep3

description: Gene expression in isolated islets of Uox-KO mice on the 16th day after the last multiple low dose of STZ injection (40mg/kg, i.p., 5 days)

source_name: Islet, STZ-KO, replication3

tag: genotype


title: Islet_STZ-WT_rep3

description: Gene expression in isolated islets of Uox-WT mice on the 16th day after the last multiple low dose of STZ injection (40mg/kg, i.p., 5 days)

source_name: Islet, STZ-WT, replication3

tag: age

value: WT


title: Islet_WT_rep2

description: Gene expression in isolated islets of Uox-WT mice without any intervention

source_name: Islet, WT, replication2


title: Islet_STZ-KO_rep1

source_name: Islet, STZ-KO, replication1


title: Islet_STZ-WT_rep1

source_name: Islet, STZ-WT, replication1


title: SCC25CTX_replicate1


title: SCC25PBS_replicate1


title: Islet_KO_rep1

source_name: Islet, KO, replication1


title: UF0344_brep2


title: SCC6PBS_replicate3

value: HNSCC cell line SCC6


title: Islet_STZ-KO_rep2

source_name: Islet, STZ-KO, replication2


title: Islet_WT_rep1

source_name: Islet, WT, replication1


title: Islet_STZ-WT_rep2

source_name: Islet, STZ-WT, replication2


title: SCC6CTX_replicate3


title: SCC6PBS_replicate1


title: Islet_KO_rep2

source_name: Islet, KO, replication2


title: UF0343_brep3


title: UF0343_brep2


title: UF0343_brep1


title: UF0344_brep1


title: UF0335_brep3


title: SCC6CTX_replicate2


title: SCC6CTX_replicate1


title: UF0335_brep2


title: SCC1PBS_replicate2

data_processing:
adapters trimming with Trim Galore! version 0.5.0
alignment with Bowtie2 version 2.3.2
duplicated and mitochondrial DNA removal with Picard Tools version 2.18
unmapped and low quality reads removal with Samtools version 1.9
peaks calling with MACS2
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks not provided for this sample because the processing of the fastq file did not result in good quality sequencing.

value: HNSCC cell line SCC1


title: UF0335_brep1


title: SCC1PBS_replicate1


title: SCC6PBS_replicate2


title: UF0344_brep3


title: Islet_WT_rep3

source_name: Islet, WT, replication3


title: UF0326_brep2


title: UF0324_brep3


title: SCC1CTX_replicate1


title: UF0326_brep1


title: SCC1PBS_replicate3


title: UF0324_brep1


title: UF0323_brep1


title: UF0322_brep3


title: UF0323_brep2


title: UF0322_brep1


title: UF0321_brep3


title: UF0321_brep2


title: SCC1CTX_replicate2


title: UF0322_brep2


title: UF0323_brep3


title: UF0321_brep1


title: SCC1CTX_replicate3


title: UF0324_brep2


title: UF0320_brep3


title: UF0320_brep2


title: UF0320_brep1


title: UF0317_brep2


title: UF0311_brep2


title: UF0311_brep3


title: UF0311_brep1


title: tumor 37

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

country: India

institute: CDFD

description: tumor 37

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

source_name: Surgically removed tongue

label_protocol: 2 μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Female

value: Squamous cell carcinoma of oral tongue

tag: Stage

tag: grade

value: I

tag: p53 status

value: NS-

source_name: pooled 11 cell line

tag: control type

value: Universal reference RNA


title: UF0317_brep3

source_name: Xylem

value: 16 weeks


title: tumor 27

description: tumor 27

value: Male