title: Prostate_PND 30 Male_EB_Rep4

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

description: Total RNA from Prostate of  PND 30 male rats  exposed postnatally to EB was used for gene expression

hyb_protocol: Only the cRNAs with yields >1.65 µg and specific activities > 9.0 pmol of dye per µg cRNA were used for hybridization. Equal amounts (600 ng) of purified Cy3-labeled cRNA were hybridized to Agilent SurePrint G3 rat 8 × 60K microarrays (8 arrays per slide) following the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (V5.5, Agilent Technologies, Inc.) for 17 hours at 65°C in a hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%). The resulting images were analyzed by quantifying the Cy3 fluorescence intensity at each of the 62,976 spots (features) on each array using the Agilent Feature Extraction Software (Version 10.7.3)  with default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  The median fluorescence intensity of all the pixels within each feature was taken as the intensity value for that feature.

data_processing: A total of 33 raw data files for 33 samples (3-4 arrays for each control and treated rats) were obtained from the Agilent Feature Extraction Software. An excel spreadsheet containing  raw intensity data  for all 33 samples was used as an input file for further data preprocessing and normalization using SAS 9.4 (SAS institute Inc., Cary, NC).  There were 62,976 features (probes) on each array. Controls were removed and then data was normalized using 75th percentile scaling.

organism: Rattus norvegicus

source_name: Whole Prostate, male, PND 30, EB 2.5 mg/kg, replicate 4

label_protocol: Total RNAs (500ng) were labeled with cyanine dye (Cy3) using the Agilent One Color Low RNA Input Linear Amplification Kit according to the manufacturer’s protocol (Agilent Technologies, Inc.) followed by RNAeasy column purification (QIAGEN, Valencia, CA). For each reaction, cRNA yields and specific activities were determined using the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 11–13-week-old time-mated female SD rats were purchased from Envigo (Indianapolis, IN, USA) and were delivered to the National Center for Toxicological Research (NCTR) on GD 3 (day of birth=PND 0).  Pregnant dams were housed individually and maintained under a 12:12-h light-dark cycle with controlled room temperature (23°C ± 3°C) and humidity (50% ± 20%). Dams and male pups were fed with low phytoestrogen 5K96 chow (Purina Mills, St. Louis, MO) from gestation day (GD) 3. After birth, male offspring were also kept under same conditions.

extract_protocol: RNA samples from prostate of PNDs 30, 100 and 145 rats (N=3-4 litters/group) were extracted using the miRNeasy Kit (Qiagen, Valencia CA, USA). After extraction, the concentration of each RNA sample was determined using a NanoDrop 2000c spectrophotometer (version 3.0.1, Thermo Fisher Scientific Inc, Wilmington DE, USA). RNA samples with RNA Integrity Numbers (RINs) of 8.0 or above were used for gene expression measurements.

treatment_protocol: Sprague-Dawley (Hsd:SD) male rat offspring were administrated estradiol benzoate by subcutaneous injection at PND 1, 3 and 5 and subsequently, treated with  additional hormones (estradiol and testosterone) at PNDs 90-145.

tag: strain

value: Sprague-Dawley

value: Prostate

value: Male

value: Postnatal day (PND) 30

tag: treatment

value: EB


title: Prostate_PND 30 Male_EB_Rep2

status: Public on Aug 17 2020

type: RNA

country: USA

molecule: total RNA

source_name: Whole Prostate, male, PND 30, EB 2.5 mg/kg, replicate 2

tag: tissue

tag: gender

tag: age


title: Prostate_PND 145 Male_TE_Rep3

description: Total RNA from Prostate of  PND 145 male rats  exposed postnatally to T+E was used for gene expression

source_name: Whole Prostate, male, PND 145, T + E, replicate 3

value: Postnatal day (PND) 145

value: T+E


title: Prostate_PND 30 Male_EB_Rep3

source_name: Whole Prostate, male, PND 30, EB 2.5 mg/kg, replicate 3


title: Prostate_PND 30 Male_EB_Rep1

source_name: Whole Prostate, male, PND 30, EB 2.5 mg/kg, replicate 1


title: Mettl4-KO rep2 input

type: SRA

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

library_source: transcriptomic

data_processing:
m6ACE-seq analysis  Fastq sequences were first filtered for a quality score of 20, then trimmed of 5’ and 3’ adapter sequences and poly(A) tails using Cutadapt. The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed. Reads were mapped to the methylated spike-in (Table 1) using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates. Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR<0.1, padj<0.05). Identified sites that were 1-4 nucleotides upstream of another identified significant Rm6AC site or sites found within clustered read-starts were filtered out.   To calculate the RML of each site in each sample: The read-start counts at positions -4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions -51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions -21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition. A site was denoted as differentially methylated between METTL4WT-rescue and METTL4CD-rescue if the average RML differs between sample conditions with a log2fold-change cutoff of 2.0, as well as a one-tailed Student’s T-test p-value cutoff of <0.041 (false discovery rate, FDR < 0.1). Consensus motif analysis was performed using Meme-chip. Metagene analysis was performed using MetaPlotR.   RNAseq  10µg of RNA was treated with RQ1 RNase-Free DNase (Promega M6101) as per manufacturer’s protocol. 5µg of samples were then depleted of rRNA using the ribozero kit (Illumina MRZH11124). 50ng of each rRNA-depleted samples were then used for construct RNA-seq libraries using the ScriptSeq v2 RNASeq Library Preparation Kit (Illumina SSV21124). Libraries were sequenced on an Illumina PE151 platform.  RNAseq Splicing Analysis  WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations.   Alternative splicing differences were analysed by an in-house pipeline using replicate MATS (rMATS 3.2.5) and filtered based on cut-offs of FDR ≤ 0.05, an absolute change in percent spliced in (|ΔPSI|) ≥ 0.1. In addition, events with mean sample junction counts (IC_Sample + SC_Sample) < 20 were filtered out to reduce false positives arising from transcript dropout in low abundance isoforms. The validation of several differential alternative splicing events were performed using an RT-PCR assay.  Additional exon-level features were added to the data using databases constructed from the UCSC Table Browser, as well as in-house R scripts. Splice-site strengths were calculated using MaxEntScan. Comparisons were made between the exon features of the differentially spliced cassette exons and a transcriptome-wide background based on all known human internal exons. Cut-offs of 500nt and 30,000nt were applied on the exon and intron length datasets respectively to reduce data skewing caused by extreme outliers. Splice site strength values below 0 were also discarded from the analysis for similar reasons. The statistical significance of feature differences were calculated using Welch’s t-test and p-values were adjusted using Bonferroni correction when necessary.   The Jensen-Shannon Divergences of splice site sequence subsets and associated tests for statistical significance were calculated using DiffLogo. All other sequence logos were generated using ggseqlogo. The cassette exon sequences, as well as up to 200nt stretches up- and downstream of the exon (excluding the splice sites), were scanned for strand-specific 6-10nt motifs using MEME. The sequences generated by MEME were then fed into TOMTOM to search for RNA binding proteins with similar binding motifs. Functional annotation of the genes containing differentially spliced cassette exons was performed using DAVID.
RNAseq Analysis - WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations (33).
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of forward reads (m6ACE) or bedgraph files of transcript reads (RNA-seq).

organism: Homo sapiens

source_name: Human embryonic kidney cells

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37oC, and in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin, and used within passage number 3-20.

extract_protocol:
Total RNA was isolated using Trizol-LS.
Poly(A) RNA was purified using Poly(A)Purist Mag kit (Thermofisher AM1922) according to manufacturer’s instructions. Poly(A) RNA was fragmented using RNA fragmentation buffer (Ambion AM8740) and dephosphorylated at its 3’ end with T4 PNK (NEB M0201) for 30min at 37oC. 5’ phosphorylation was then initiated by adding 1mM ATP and incubating for 30min at 37oC. 3’ ligation was then performed as previously described 2, where 5’-adenylated,3-dideoxyC DNA adapters were ligated with truncated T4 RNA ligase 2 (NEB M0242) in 1X ATP-free T4 RNA ligase buffer [50mM Tris pH 7.5, 60µg/ml BSA, 10mM MgCl2, 10mM DTT, 12.5% PEG8000] for 2hr at 25oC. 3’-ligated methylated RNA spike-in (Table S1) was added to ligated Poly(A) RNA and the mixture was denatured for 5min at 65oC before incubating for 2min on ice. This denatured RNA mixture was incubated overnight at 4oC with anti-m6A antibody (Synaptic Systems 202003) in 1X IP buffer [150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL CA-630 (Sigma I8896)] supplemented with RNasin Plus (Promega N2611). In parallel, Protein-A-dynabeads (Life Technologies 10002D) was blocked overnight at 4oC in 1X IP buffer supplemented with 0.5mg/ml BSA (Sigma A7906). The iced antibody-RNA mixture was crosslinked with 0.15J/cm2 254nm UV radiation six times. 1% of the antibody-RNA mixture was set aside as “input” and the rest (designated as “m6ACE”) was mixed with decanted BSA-blocked Protein-A-dynabeads for 1.5hr at 4oC. Beads bound with crosslinked RNA were then washed with the following cold buffers in this order: Wash buffer 1 [1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 2 [0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 3 [1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA], TE [10mM Tris pH 8, 1mM EDTA] and finally 10mM Tris pH 8. m6ACE RNA was subjected to 5’ to 3’ exonuclease treatment with XRN-1 (NEB M0338) for 1hr at 37oC. The m6ACE RNA-bead mixture was then washed with Wash buffer 1, Wash buffer 2, Wash buffer 3, TE and 10mM Tris pH 8. Both input and m6ACE RNAs were reverse crosslinked in elution buffer [1%SDS, 200mM NaCl, 25mM Tris pH 8, 2mM EDTA, 1mg/ml Proteinase K (Thermo Scientific EO0491)] for 1.5hr at 50oC. RNAs were ethanol-precipitated and ligated to 5’adapters (Table S1) with T4 RNA ligase (Ambion AM2140) for 16hr at 16oC. Reverse transcription primer (Table S1) was annealed (72oC 2min, ice 2min) and reverse transcription was performed with SuperscriptIII (Invitrogen 18080) for 1hr at 50oC, with the reaction stopped by incubating for 15min at 70oC. The cDNA was used for PCR amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and Truseq PCR primers. Finally, primer-dimer and adapter-dimers were removed with AMpure XP beads before undergoing PE75 sequencing on the Illumina Nextseq platforms.

tag: cell line

tag: m6a antibody

value: Synaptic Systems 202003

tag: passage number

tag: genotype


title: 1-ca: patient 1 cancer

city: Jinan

first: Jinghui

last: Liang

address: Wenhuaxi street

institute: Shandong University

description: Gene expression from lung adenocarcinoma

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 14 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: fresh lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol following the manufacturer's recommendations.  RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

value: lung adenocarcinoma

value: female


title: Prostate_PND 100 Male_TE_Rep3

description: Total RNA from Prostate of  PND 100 male rats  exposed postnatally to T+E was used for gene expression

source_name: Whole Prostate, male, PND 100, T + E, replicate 3

value: Postnatal day (PND) 100


title: Control_ZT0_repl_B

city: Liverpool

first: Mirko

last: Pegoraro

state: Liverpool

address: Byrom Street

department: School of Natural Science and Psychology

country: United Kingdom

institute: Liverpool John Moores University

description:
cuffdiff output ZT0
PJN0B

data_processing:
The data were then processed using trimmomatic (version 0.32) to remove the adapters.
The library were quality checked using fastQC (version 0.11.2).
The RNA-seq was aligned to the Drosophila melanogaster transcriptome (NCBI_build5.41) using TopHat (version 2.1.0) with these options: -i 50 -I 5000 --transcriptome-index NCBI_genes --coverage-search -p 8 Bowtie2Index/genome -G genes.gtf (from NCBI_build5.41) as genome annotation reference.
Cufflinks and cuffmerge (version 2.2.1) were used to quantify the expression of the transcripts isoforms of the TopHat aligned RNA with the following options: –u multi-reads correction, -g genes.gtf (from NCBI_build5.41) as gene annotation reference –b genome.fa (from NCBI_build5.41/Bowtie2Index) as reference genome –M Mask_sequences.fa (including mitochondrial and ribosomal RNA as well polyA, polyC sequences).
To calculate difference of expressions between samples we used cuffdiff. As for cuffmerge we used –b genome.fa –M Mask_sequences.fa. In addition we used -u multi-read correction, merged.gtf (the transcript annotation file produced by cuffmerge) and a geometric method for library normalization
Genome_build: Drosophila melanogaster transcriptome (NCBI_build5.41)
Supplementary_files_format_and_content: the process data are the output of cuffdiff analysis. We ran the analysis for ZT0 and ZT12 separetelly.

organism: Drosophila melanogaster

growth_protocol: 12 hour of dark:12 hours of darknes, 25C, standart yeast rich drosophila food.

extract_protocol:
Flies (3-4 days old) were entrained for 3 days in LD12:12 at 25°C and then male heads were collected in liquid nitrogen at ZT0 and 12. RNA was extracted using the Maxwell®16 MDx Research Instrument (Promega) combine with the Maxwell®16 Tissue Total RNA pufication kit (AS1220, Promega).
The RNAseq library preparation and sequencing was carried by Glasgow Polyomics using an IlluminaNextseq500 platform.Two independent libraries paired-end were generated per time point per line

treatment_protocol: Samples where keep at 12:12LD and 25C until the collection time. Lines were generated from selected lines for nocturnal/diurnal behavior, via crossing with balancers lines.

tag: line/diurnal preference

value: control intermidiate (PJN)

tag: dev stage

value: Adults

tag: time point

value: Heads


title: Prostate_PND 145 Male_TE_Rep1

source_name: Whole Prostate, male, PND 145, T + E, replicate 1


title: Prostate_PND 145 Male_TE_Rep2

source_name: Whole Prostate, male, PND 145, T + E, replicate 2


title: LS180_FOXA1_rep2

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

library_source: genomic

data_processing:
Reads were trimmed with Trimmomatic software
Trimmed reads were aligned to the hg19 human genome using the bwa mem aligner.
Aligned reads were indexed with samtools
Sequencing coverage track was created with BAMscale.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale

molecule: genomic DNA

source_name: Colon

growth_protocol: All cell lines were maintained in Dulbecco's modified Eagle's (DMEM) (Thermo Fisher Scientific, Invitrogen) medium containing 10% (v/v) fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed using the Active Motif ChIP kit (Active Motif, Carlsbad, CA, USA) According the instruction by the manufacturer. Briefly, 5 × 107 LS180 cells grown in 15-cm plates were cross-linked with 1% formaldehyde, and cells were lysed and sonicated. Protein–DNA complexes were immunoprecipitated with control IgG (Santa cruz, Cat#2028) or anti-FOXA1 (Santa Cruz, Cat# sc-6553) antibody. The IP material was washed and heated at 65°C overnight to reverse crosslinks.

treatment_protocol: untreated cells

tag: cell type

value: colon epithelial

tag: antibody


title: Prostate_PND 100 Male_TE_Rep2

source_name: Whole Prostate, male, PND 100, T + E, replicate 2


title: Prostate_PND 100 Male_TE_Rep1

source_name: Whole Prostate, male, PND 100, T + E, replicate 1


title: 1-n: patient 1 normal

description: Gene expression from normal tissues

value: lung  normal tissue


title: Prostate_PND 145 Male_EBTE_Rep2

description: Total RNA from Prostate of  PND 145 male rats  exposed postnatally to EB+T+E was used for gene expression

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg + T + E, replicate 2

value: EB+T+E


title: Prostate_PND 145 Male_EBTE_Rep3

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg + T + E, replicate 3

value: Sprague-Dawley


title: LS180_FOXA1_rep1


title: LS180_genomic_rep1


title: Nocturnal_ZT12_repl_B

description:
cuffdiff output ZT12
NDN12B

value: Nocturnal (NDN)


title: LS180_IgG_rep2

value: IgG


title: Control_ZT0_repl_A

description:
cuffdiff output ZT0
PJN0A


title: LS180_IgG_rep1


title: Nocturnal_ZT12_repl_A

description:
cuffdiff output ZT12
NDN12A


title: Nocturnal_ZT0_repl_B

description:
cuffdiff output ZT0
NDN0B


title: Nocturnal_ZT0_repl_A

description:
cuffdiff output ZT0
NDN0A


title: D16+_10X

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: UMI.csv

data_processing:
Fastq files were generated using mkfastq of cellranger v2.1.0. Gene counting was performed using ‘count’ module of cellranger (v2.1.0).
All librariers were then merged using ‘aggr’ function of cellranger without normalization. The output of ‘aggr’ was used for further analysis with Seurat and Monocle.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited table containing the UMI values of the genes in each single-cell library and Tab-delimited text file containing time-point annotation of the cells.

molecule: polyA RNA

source_name: BJ Fibroblasts

growth_protocol: BJ fibroblasts were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies).

extract_protocol:
cDNA was harvested as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E
Libraries were constructed as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E

value: BJ Fibroblasts

value: BJ fibroblasts 16 days post induced viral expression of OSKM

tag: time

tag: tra-1-60 staining

value: Positive


title: D8_10X

description: UMI.csv

value: BJ fibroblasts 8 days post induced viral expression of OSKM


title: WT2: Lung_virus-3 infected_3d_rep2

city: Nanjing

first: Yanna

last: Guo

address: No.6 Tongwei Road

department: Institute of Immunology

institute: Nanjing Agriculture university

description: Gene expression after 3 day in virus-3-infected mouse

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Mus musculus

source_name: Balb/c mouse lung, virus-3 infected, day 3 post-infection,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice lung tissues infected by H7N9 and its mutant viruses with  with 5x105 EID50 were collected 3 days post-infection and were homogenized using a tissue homogenizer to collect tissue supernatant .

extract_protocol: Mice lung tissue supernatant was collected, lysis/binding buffer was added into the supernatant (1ml Lysis/binding buffer per 0.1g tissue) to lysate cells. The total RNA was extracted using an mirVanaTM RNA isolation kit (Ambion) following the manufacturer's instructions

treatment_protocol: Specific pathogen-free 4- to 6-week-old female Balb/c mice were treated with PBS as a negative control, H7N9/AH1-PB2-627K(WT)、H7N9/AH1-PB2-627E and H7N9/AH1-PB2-627E/701N respectively，each group have three mice.

value: Balb/c

value: lung


title: WT3: Lung_virus-3 infected_3d_rep3

source_name: Balb/c mouse lung, virus-3 infected, day 3 post-infection,replicate 3

value: female


title: WT1: Lung_virus-3 infected_3d_rep1

source_name: Balb/c mouse lung, virus-3 infected, day 3 post-infection,replicate 1


title: D12_10X

description: UMI.csv

value: BJ fibroblasts 12 days post induced viral expression of OSKM


title: EN4: Lung_virus-2 infected_3d_rep3

description: Gene expression after 3 day in virus-2-infected mouse

source_name: Balb/c mouse lung, virus-2 infected, day 3 post-infection,replicate 3


title: EN2: Lung_virus-2 infected_3d_rep2

source_name: Balb/c mouse lung, virus-2 infected, day 3 post-infection,replicate 2


title: Prostate_PND 100 Male_EBTE_Rep3

description: Total RNA from Prostate of  PND 100 male rats  exposed postnatally to EB+T+E was used for gene expression

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg + T + E, replicate 3

value: Prostate

value: Male

value: Postnatal day (PND) 100


title: Prostate_PND 145 Male_EBTE_Rep1

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg + T + E, replicate 1

value: Postnatal day (PND) 145


title: Prostate_PND 145 Male_EB_Rep4

description: Total RNA from Prostate of  PND 145 male rats  exposed postnatally to EB was used for gene expression

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg, replicate 4

value: EB


title: Prostate_PND 100 Male_EBTE_Rep1

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg + T + E, replicate 1

value: EB+T+E


title: Prostate_PND 145 Male_EB_Rep3

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg, replicate 3

value: Sprague-Dawley


title: E4: Lung_virus-1 infected_3d_rep2

description: Gene expression after 3 day in virus-1-infected mouse

source_name: Balb/c mouse lung, virus-1 infected, day 3 post-infection,replicate 2


title: D2_10X

description: UMI.csv

value: BJ fibroblasts 2 days post induced viral expression of OSKM


title: EN1: Lung_virus-2 infected_3d_rep1

source_name: Balb/c mouse lung, virus-2 infected, day 3 post-infection,replicate 1


title: Prostate_PND 145 Male_EB_Rep1

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg, replicate 1


title: Control_ZT12_repl_A

description:
cuffdiff output ZT12
PJN12A

value: control intermidiate (PJN)

value: Adults

value: Heads


title: Prostate_PND 100 Male_EB_Rep3

description: Total RNA from Prostate of  PND 100 male rats  exposed postnatally to EB was used for gene expression

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg, replicate 3


title: Prostate_PND 145 Male_EB_Rep2

source_name: Whole Prostate, male, PND 145, EB 2.5 mg/kg, replicate 2


title: D0_10X

description: UMI.csv

value: BJ Fibroblasts

value: WT


title: D16-_10X

description: UMI.csv

value: BJ fibroblasts 16 days post induced viral expression of OSKM

value: Negative


title: C4: Lung_PBS control_3d_rep3

description: Gene expression after 3 day in PBS-infected mouse

source_name: Balb/c mouse lung, PBS treated, day 3 post-infection,replicate 3

value: Balb/c

value: female

value: PBS control

value: lung


title: D1/8 KLY194 Rep2_Total_Run2

first: Katherine

last: Larrimore

address: 1 Research Link

department: Cell Biology

institute: Temasek Life Sciences Laboratory

data_processing:
Sequencing adapters were trimmed using Cutadapt (Martin, 2011)
Reads were then mapped to S. cerevisiae mRNAs using Bowtie (Langmead et al., 2009) allowing for no mismatches.
Abundance of each mRNA and its translation was then quantified as reads per kilobase of coding sequences per million mapped reads in the library (RPKM).
All RPKM values were subsequently normalized such that the median mRNA in a non-duplicated chromosome in an aneuploid strain was equal to the RPKM of that mRNA in a euploid strain.
This was accomplished by calculating the median of RPKM (aneuploid)/RPKM(euploid) for all genes on non-duplicated chromosomes, then dividing all RPKM values in the aneuploid strain by this ratio
Genome_build: S288c reference genome version 64 (UCSC sacCer3)
Supplementary_files_format_and_content: tab-delimited text (.txt) files include RPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae

growth_protocol: Strains were cultured in YPD at 25°C.

extract_protocol:
750ml of yeast cultures were grown to OD600 0.6-0.7 un/ml at 25°C. Cycloheximide was added to final concentration of 0.1 mg/ml, and the cultures were put back to incubate for the additional two minutes. Treated cells were harvested by centrifugation at 4°C. Pellets were homogenized in the ice-cold lysis buffer (1X Yeast Polysome Buffer, 1% Triton X-100, 0.1 mg/ml Cycloheximide). For that, 1.5 ml of lysis buffer and 5 g of glass beads were added for each gram of pellet. Cells were lysed by vortexing 6x 20 seconds and incubated on ice between cycles. Crude extract was spun at 3,000 x g for 5 min, the supernatant was collected to chilled 1.5 ml tubes on ice, and the lysate was clarified by centrifugation for 10 minutes at 20,000 x g in a 4°C centrifuge. The supernatant was recovered avoiding both the pellet and the lipid layer at the top of the tube. DNase UI was added to a final concentration of 10 U/ml. For each lysis, A260 was adjusted to 200, and the 100 µl aliquot was kept for the Total RNA extraction and 200µl aliquot was used for the Ribosome Protected Fragment RNA preparation. 10µl of 10% SDS was added to the 100µl aliquot, and the sample was snap frozen in liquid nitrogen and kept at -80oC until ready for use. 0.3 units of Truseq Nuclease per A260 of lysate was added to the 200µl aliquot of clarified lysate. Reaction was incubated at room temperature for 60 minutes with gentle mixing. Nuclease digestion was stopped with 10 µl of SUPERaseIn RNase Inhibitor (Life Technologies, cat. No. AM2696) and chilled on ice.
Truseq™ Ribosome Profiling kit (Illumina, formerly ArtSeq) was used for obtaining ribosome-protected RNA fragments using size-exclusion chromatography columns.  Both RPF and total mRNA input fragments were cloned according to the manufacturer protocol.

tag: run

tag: fraction

value: Total RNA


title: D1/8 KLY194 Rep2_RPF_Run2

tag: strain

value: Ribosome Protected Fragments


title: D1/8 KLY194 Rep1_Total_Run2


title: E3: Lung_virus-1 infected_3d_rep1

source_name: Balb/c mouse lung, virus-1 infected, day 3 post-infection,replicate 1

tag: tissue


title: E8: Lung_virus-1 infected_3d_rep3

source_name: Balb/c mouse lung, virus-1 infected, day 3 post-infection,replicate 3

tag: gender


title: D1/8 KLY194 Rep1_RPF_Run2


title: C3: Lung_PBS control_3d_rep2

source_name: Balb/c mouse lung, PBS treated, day 3 post-infection,replicate 2


title: D13 KLY195 Rep2_Total_Run2


title: Prostate_PND 100 Male_EB_Rep2

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg, replicate 2

value: Prostate

value: Male

tag: age

value: Postnatal day (PND) 100

tag: treatment

value: EB


title: Prostate_PND 100 Male_EB_Rep1

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg, replicate 1

value: Sprague-Dawley


title: D13 KLY195 Rep2_RPF_Run2


title: Prostate_PND 145 Male_Control_Rep3

description: Total RNA from Prostate of  PND 145 male rats  exposed postnatally to vehicle was used for gene expression

source_name: Whole Prostate, male, PND 145, untreated, replicate 3

value: Postnatal day (PND) 145

value: vehicle


title: D13 KLY195 Rep1_Total_Run2


title: 180_FS_M1

city: Milwaukee

first: Michele

middle: A

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

data_processing:
RNA seq reads were aligned to the mm9 genome assembly using STARR in Base Pair Tech using default paramenters and normalized using ERCC spike-ins.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx and FPKM

source_name: GATA4 knock in E14.5 forestomach epithelial cells

growth_protocol: epithelial cells isolated from E14.5 embryonic stomachs

extract_protocol:
RNA was isolated using Xsmall nucleospin columns and quanitifed on a QuBit and tapestation checked for quality
Libraries were prepared acccording to NEB instructions accompanying the NEBnext Ultra II Directional RNA library prep kit

value: G4 cKI mutant

value: forestomach epithelial cells

tag: developmental stage


title: D13 KLY195 Rep1_RPF_Run2


title: 251_FS_C5

source_name: wild type E14.5 forestomach epithelial cells

value: G4 cKI control


title: Prostate_PND 145 Male_Control_Rep2

source_name: Whole Prostate, male, PND 145, untreated, replicate 2


title: Prostate_PND 100 Male_EBTE_Rep2

source_name: Whole Prostate, male, PND 100, EB 2.5 mg/kg + T + E, replicate 2

value: EB+T+E


title: 221_FS_C3


title: Prostate_PND 100 Male_Control_Rep3

description: Total RNA from Prostate of  PND 100 male rats  exposed postnatally to vehicle was used for gene expression

source_name: Whole Prostate, male, PND 100, untreated, replicate 3


title: 220_FS_C2


title: 223_FS_M4


title: D13 KLY196 Rep1_RPF_Run2


title: D13 KLY196 Rep1_Total_Run2


title: 48hr Vehicle Treatment (B)

city: South San Francisco

first: Gene

last: Cutler

state: CA

address: 561 Eccles Ave

institute: RAPT Therapeutics

data_processing:
Sequencing results were processed on the Seven Bridges Genomics platform.
Kallisto Quant (version 0.43.1) was used to align reads to the gencode.v27 transcript reference.
Genome_build: gencode.v27

source_name: variant small cell lung cancer cell line

extract_protocol:
RNA was extracted from approximately 1 million cells using the Allprep DNA/RNA Mini Kit (Qiagen)
Whole transcriptome non-stranded libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina)

tag: cell line

tag: treatment time


title: 29_HS_M5

source_name: GATA4 knock out E14.5 hindstomach epithelial cells

tag: genotype

value: G4 cKO mutant

value: hindstomach epithelial cells


title: 182_FS_M2


title: D1/2/8/11 KLY193 Rep2_Total_Run2


title: 48hr Vehicle Treatment (A)


title: 27_HS_M4


title: 48hr USP7-797 Treatment (B)


title: D1/2/8/11 KLY193 Rep2_RPF_Run2


title: C2: Lung_PBS control_3d_rep1

source_name: Balb/c mouse lung, PBS treated, day 3 post-infection,replicate 1

value: Balb/c

value: female

value: PBS control


title: 20_HS_M3


title: 24hr Vehicle Treatment (B)


title: D1/2/8/11 KLY193 Rep1_Total_Run2

value: Total RNA


title: Prostate_PND 100 Male_Control_Rep2

source_name: Whole Prostate, male, PND 100, untreated, replicate 2

value: Prostate


title: 48hr USP7-797 Treatment (A)


title: Prostate_PND 145 Male_Control_Rep1

source_name: Whole Prostate, male, PND 145, untreated, replicate 1

value: Male


title: 7_HS_M2


title: D1/2/8/11 KLY193 Rep1 _RPF_Run2

source_name: saccharomyces cerevisiae

value: Ribosome Protected Fragments


title: 6_HS_M1


title: Prostate_PND 100 Male_Control_Rep1

source_name: Whole Prostate, male, PND 100, untreated, replicate 1

value: Postnatal day (PND) 100


title: Prostate_PND 30 Male_Control_Rep4

description: Total RNA from Prostate of  PND 30 male rats  exposed postnatally to vehicle was used for gene expression

source_name: Whole Prostate, male, PND 30, untreated, replicate 4

value: Sprague-Dawley

value: Postnatal day (PND) 30


title: Prostate_PND 30 Male_Control_Rep3

source_name: Whole Prostate, male, PND 30, untreated, replicate 3

value: vehicle


title: Prostate_PND 30 Male_Control_Rep2

source_name: Whole Prostate, male, PND 30, untreated, replicate 2


title: Prostate_PND 30 Male_Control_Rep1

source_name: Whole Prostate, male, PND 30, untreated, replicate 1


title: D1/2/8 NVY3_Total_Run2


title: 24hr Vehicle Treatment (A)


title: D1/2/8 NVY3_RPF_Run2


title: 16_HS_C3

source_name: wild type E14.5 hindstomach epithelial cells

value: G4 cKO control


title: 24hr USP7-797 Treatment (A)


title: WT_Total_Run2

value: WT


title: Normal iPSC-CMs co-cultured with Hypoplastic left heart syndrome (HLHS) iPSC-ECs 3

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

description:
gene.count.txt.gz
HLHS3

data_processing:
10X Genomics: Barcodes and UMI are in the R1 file: 1-16 (barcode), 17-26 (UMI)
Cell Ranger
Seurat
TrimGalore
STAR
featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: raw read counts

source_name: Peripheral blood mononuclear cells (PBMCs)

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol: Total RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research) in accordance to manufacturer’s instructions, followed by DNAse treatment.

value: Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs)


title: 24hr USP7-797 Treatment (B)


title: 3_HS_C2


title: WT_RPF_Run2


title: D1/2 NVY2_Total_Run1

value: D1/2 NVY2


title: Rbx2cKO-Nes_2

city: Davis

first: Sergi

last: Simo

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: Rbx2 flox/flox; Nestin-Cre/+

data_processing:
Base-calling software HCS 1.5/RTA 1.13
The fastq files were processed with expHTS (see https://dl.acm.org/citation.cfm?id=2811442) to remove PCR duplicates, and to trim low quality sequences and adapter contamination, keeping reads of minimum length 30 bases.
Trimmed reads were aligned to the GrCm38 primary assembly using the gencode vM10 annotation with STAR v.2.5.1b (parameters as recommended for ENCODE in STAR manual).  STAR also generated the read counts per gene.
Raw counts per gene were normalized using the cpm command in edgeR
Genome_build: GrCm38
Supplementary_files_format_and_content: Processed data file format: excel; Content: Counts per milion (CPM)

source_name: Telencephalon

extract_protocol:
Telencephalons were removed and stored in RNAlater (Qiagen). RNA was purified with Total RNA purification Plus Micro kit (Norgen Biotek Corp.) following manufacter instructions. Poly-A enrichment using the Kapa Stranded mRNA-seq kit (KapaBiosystems) was done and sequenced on 1 high output flowcell of an Illumina NextSeq 500 (Illumina) with paired-end 40bp reads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6J and 129 (mix background)

value: Telencephalon

value: Rbx2 flox/flox; Nestin-Cre/+


title: Normal iPSC-CMs co-cultured with Hypoplastic left heart syndrome (HLHS) iPSC-ECs 2

description:
gene.count.txt.gz
HLHS2

value: Peripheral blood mononuclear cells (PBMCs)


title: D1/2 NVY2_RPF_Run1


title: Rbx2cKO-Nes_1

description: Rbx2 flox/flox; Nestin-Cre/+


title: Normal iPSC-CMs co-cultured with Hypoplastic left heart syndrome (HLHS) iPSC-ECs 1

description:
gene.count.txt.gz
HLHS1


title: D2 NVY1_Total_Run1

value: D2 NVY1


title: Normal iPSC-CMs co-cultured with normal iPSC-ECs 2

description:
gene.count.txt.gz
Control2


title: 19_HS_C4

value: hindstomach epithelial cells


title: Normal iPSC-CMs co-cultured with normal iPSC-ECs 1

description:
gene.count.txt.gz
Control1


title: WT_Total_Run1

value: Total RNA


title: Control_2

description: Rbx2 flox/flox

value: Rbx2 flox/flox


title: Control_1

description: Rbx2 flox/flox


title: 28 d exposure to lindane aging for 30 d [control-2]

status: Public on Aug 16 2020

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
The raw data were merged into pool reads, and the scaffolding contig algorithm from CLC Genomics Workbench( version 6.0.4) were applied for de novo assembly.
The primary unigenes were assembled again using CAP3 software, and a sequence set of final unigenes were obtained.
The reads of each samples were mapping regarding unigenes as reference, and then the coverage of each read in each sample could be obtained. The expression levels of unigenes were normalized to convert reads into FPKMs using eXpress software.
Supplementary_files_format_and_content: contig assembly and FPKM values for each Sample

organism: Eisenia fetida

source_name: 28 d exposure to lindane aging for 30 d

extract_protocol:
Total RNA of earthworms was extracted using RNAiso Plus Total RNA extraction reagent (Cat# 9109, TAKARA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nominal 2.4 mg/kg of lindane was half freshly spiked and half preaged for 30 d in soil. Then two kinds of soils containing lindane were used to treat adult earthworm for 7 d and 28 d, respectively. An additional group of earthworm at 0 d (without exposure) was also sampled.

value: sections from whole body

value: 28 d exposure to lindane aging for 30 d


title: 28 d exposure to lindane aging for 30 d [control-3]


title: 7 d exposure to lindane aging for 30 d [30d-28d-3]

source_name: 7 d exposure to lindane aging for 30 d

value: 7 d exposure to lindane aging for 30 d


title: 28 d exposure to lindane aging for 30 d [control-1]


title: 7 d exposure to lindane aging for 30 d [30d-28d-1]


title: 28 d exposure to lindane aging for 0 d [30d-7d-1]

source_name: 28 d exposure to lindane aging for 0 d

value: 28 d exposure to lindane aging for 0 d


title: 28 d exposure to lindane aging for 0 d [30d-7d-3]


title: 7 d exposure to lindane aging for 0 d [0d-28d-3]

source_name: 7 d exposure to lindane aging for 0 d

value: 7 d exposure to lindane aging for 0 d


title: 7 d exposure to lindane aging for 0 d [0d-28d-2]


title: 0 d exposure [0d-7d-2]

source_name: 0 d exposure

value: 0 d exposure


title: 0 d exposure [0d-7d-3]


title: 7 d exposure to lindane aging for 0 d [0d-28d-1]


title: scRNAseq_Celseq2_2iL_Zic3_KO_rep2

city: Utrecht

first: Wout

last: Megchelenbrink

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Centre for Pediatric Oncology

data_processing:
scRNA-seq libraries were mapped to the Gencode M1-NCBIM37 (mm9) reference genome using STAR (v2.5.2b). UMI counts for a whitelist of 384 cell barcodes were determined using a custom R-script.
Diagnostics (non-mito read counts, mito-read counts and ERCC counts) were plotted per plate and low quality cells (< 2,000 genes or < 10,000 reads or >=25% mitochondrial) were omitted
Count matrices were concatenated and downstream analysis was performed with Seurat (v3.1.2)
Genome_build: mm9
Supplementary_files_format_and_content: Abundance measurements (tab delimited and gzipped) contain the raw read counts per gene per cell (counts matrix). Samples were concatenated and annotated in the column header
Supplementary_files_format_and_content: Bigwig files are derived from all the cells (384) merged per sample

source_name: Embryonic stem cell

growth_protocol: Mouse embryonic stem cells E14Tg2a (E14) were purchased from ATCC and cultured without feeders in the presence of LIF. SL-ESCs were maintained in DMEM with 15% ES grade fetal calf/bovine serum. 2iL-ESCs were maintained in Ndiff227 (Takara Bio, lnc.) medium supplemented with 1μM MEK inhibitor PD0325901 and 3μM GSK inhibitor CHIR99021.

extract_protocol:
Single cells were sorted to 384-well plates which already contained primers and oil
Libraries were constructed following the Celseq2 protocol from Hashimshony (2016). In brief, each cell was lysed and reverse transcribed to first strand cDNA and synthesised second strand together with ERCC-spike-in control in each well of 384-well plates. Double stranded cDNA was pooled together and purifed with Ampure XP beads. The purified cDNA pool was transribed using the IVT procedure overnight, treated with EXOI-rSAP and fragmented. RNA was purified with AMPure XP beads, reverse transcibed and amplified with indexed Illumina primers and purifed with AMPure XP beads for sequencing.

tag: culture medium


title: 0 d exposure [0d-7d-1]


title: scRNAseq_Celseq2_SL_Zic3_KO_rep1

value: ser+LIF


title: scRNAseq_Celseq2_2iL_Zic3_KO_rep1


title: scRNAseq_Celseq2_SL_Zic3_KO_rep2


title: Control_3

description: Rbx2 flox/flox


title: Normal iPSC-CMs co-cultured with normal iPSC-ECs 3

description:
gene.count.txt.gz
Control3

value: Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs)


title: D2 NVY1 _RPF_Run1

value: Ribosome Protected Fragments


title: WT_RPF_Run1

value: WT


title: STARRseq_input_DNA_2iL_rep2

data_processing:
STARR-seq libraries were sequenced on an Illumina Nextseq 500 (43 bp) or Illumina Miseq (76 bp). Paired-end FASTQ files were mapped to the mm9 genome with BWA MEM (v0.7.10-r789) using standard settings. Low quality (MAPQ < 10) reads and non-properly paired reads were discarded.
Library complexity, GC bias, insert size metrics and PCR duplication were estimated by PICARD Tools (v2.8.1). Genome coverage was computed with bedtools (v2.27.1)
Putative enhancer peaks were identified using MACS2 (v2.1.1.20160309) with parameter p=1e-5 using the matching input DNA file as control. Next, peaks were refined using a binomial model. Peaks differential between 2iL and SL were called with DESeq2 while correcting for input coverage (see methods section of the manuscript)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files contain the RPKM values of STARR-seq RNA, input DNA and the Empirical Bayes shrunken enrichment (EBSE) of STARR-seq over input in bins of 50bp. Abundance measurements contain the normalized reads per enhancer per library, fold changes and p-values

extract_protocol:
Total RNA were extracted with RNeasy maxi prep kit (Qiagen, #75162) then polyA RNA were isolated with Dynabeads Oligo-dT25 (Invitrogen, #61002) and concentrated according to the RNeasy Mini kit (Qiagen, #74106) clean-up procedure. Input DNA were extracted with Plasmid Maxi Kit (Qiagen, #12165)
All the polyA RNA were transcribed to STARR-seq cDNA in 25 reactions with reporter-RNA specific primer and the cDNA were amplified with reporter-specific primers for 15 cycles. Amplified cDNA was purified with 0.8x AMpureXP beads. Illumina sequencing indexes were added to the amplified cDNA according to PCR for 8 cycles with NEBNext Multiplex Oligos for Illumina (NEB, #E7335L and #E7500L) in 25 reactions. The indexed library was size-selected on 1% agarose gel to eliminate all small fragments.  For input library, every 100ng of input was amplified using input-specific primers (GATTTGATATTCACCTGGCCCGC & CTTATCATGTCTGCTCGA*A*G*C; where * indicates phosphonothioate bonds) and size-selected for a range of 1600-2200bp on 1% agarose gel. 10 reactions were performed in total. Indexes were added to purified input DNA following the same indexing procedure as for STARR-seq cDNA in 10 reactions and purified/size-selected again on 1% agarose gel.

treatment_protocol: STARR-seq plasmids pool constructed following the protocol described by Arnold et al., Science (2013) were transfected to mESCs cultured in 2iL or SL using Lipo3000. Cells were refreshed after 12 hours and harvested after 24 hours for RNA and DNA extraction.


title: STARRseq_input_DNA_SL_rep1


title: STARRseq_input_DNA_SL_rep2


title: scRNAseq_Celseq2_SL_WT


title: STARRseq_input_DNA_2iL_rep1


title: scRNAseq_Celseq2_2iL_WT


title: STARRseq_RNA_SL_rep2


title: STARRseq_RNA_SL_rep1


title: STARRseq_RNA_2iL_rep2


title: 28 d exposure to lindane aging for 0 d [30d-7d-2]


title: 7 d exposure to lindane aging for 30 d [30d-28d-2]


title: STARRseq_RNA_2iL_rep1


title: RNAseq_SL_Zic3_KO_rep2

data_processing:
RNA-seq libraries were mapped to the Gencode M1-NCBIM37 (mm9) reference genome using STAR (v2.5.2b).
Read normalization and differential analysis was performed using DESeq2 (v.1.22.2) with default settings.
Bigwig files were created using deeptools “bamCoverage” (v3.0.2-1-ac193610) using parameters "--binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2620345972 --ignoreForNormalization chrX -p 30"
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurement contain normalized read counts, fold changes and p-values per gene in P53KO and ZIC3KO ESCs compared to WT ESCs

growth_protocol: Mouse embryonic stem cells E14Tg2a (E14) were purchased from ATCC. R1 cells with FUCCI reporter were received from Stephen Dalton for making P53-/- by Menno ter Huurne. EB5 P53-/- cells were received from Hitoshi Niwa. The mESCs were cultured without feeders in the presence of LIF. SL-ESCs were maintained in DMEM with 15% ES grade fetal calf/bovine serum. 2iL-ESCs were maintained in Ndiff227 (Takara Bio, lnc.) medium supplemented with 1μM MEK inhibitor PD0325901 and 3μM GSK inhibitor CHIR99021.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106).
1μg of RNA was used for library construction using the KAPA RNA HyperPrep Kit with RiboErase (KAPABiosystems #KK8560).


title: vargas11_FIB-3

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

description:
positive controls
RNAs identified by CLIP and data normalization.txt

data_processing:
Sequence files generation using CASAVA 1.8.2 (Illumina), 3' adapter sequence were trimmed using Cutadapt and reads shorter than 5 nucleotides were removed.
Sequence reads were assembled de novo and mapped to the E. histolytica genome assembly (AmoebaDB v1.7) using Trinity and Tophat version 2.0.6 with default parameters, respectively.
Visualization of mapped reads was done with the Integrative Genomics Viewer (IGV). A heatmap was constructed with the sequence reads from the different CLIP assays, and the 214,672 EhArpv2-specific reads were retrieved.
Contigs of the unmapped reads were assembled with the highest copy-number sequences using the PRABI (Paôle Rhône-Alpes de Bioinformatique-Doua Site http://www.prabi.fr/) and compared to the available databases using Megablast
Genome_build: Entamoeba histolytica HM1:IMSS (AmoebaDB v1.7)

organism: Entamoeba histolytica HM-1:IMSS

source_name: Trophozoites

growth_protocol: E. histolytica trophozoites from pathogenic HM1:IMSS strain were axenically grown at 37°C in TYI-S-33 medium.

extract_protocol:
RNA molecules were released by protein digestion adding SDS (0.5% to 1%) and proteinase K (1.2mg/mL) for 1h at 55°C and purified by homogenization in 3 vols of TRIzol and filtering through RNA purification Direct-zol™ RNA Miniprep Kit (Zymo Research) columns
Purified RNA was fragmented for 5 min with Ambion reagent at 70°C (Ambion, #AM8740), recovered with the RNeasy MinElute Cleanup Kit (Qiagen #74204), dephosporylated with Antartic phosphatase at 37°C for 30 min (NEB #M0289S) and phosphorylated with T4 Polynucleotide Kinase (NEB #M0201S). Libraries were constructed according to manufacter's recommendations using TruSeq Small RNA Sample Prep Kit (Illumina, #RS-200-0012) and were purified with AMPure XP beads (Agencourt, #A63880). Then, sequencing was performed using HiSeq 2500 platform (Illumina) in a multiplexed 51+7 bases single read using a TruSeq SR Cluster kit v3-cBot-HS (Illumina, #GD-401-3002) and a TruSeq SBS kit v3-HS 50 cycles (Illumina, #FC-401-3002).

treatment_protocol: To identify RNA-protein complexes CLIP assays were done as follows. 1.2x107 trophozoites in logarithmic growth phase were exposed to UV light in a Stratalinker "UVP CL-1000" (energy X100uJ/cm2) for 30min.

tag: growth

value: Trophozoites in logarithmic growth phase

tag: clip antibody

value: α-EhFibrillarin


title: RNAseq_2iL_Zic3_KO_rep2


title: vargas12_ABP34-3

description:
negative control
RNAs identified by CLIP and data normalization.txt


title: vargas10_Nop58-3


title: vargas9_Arpv2-3

description:
sample of interest
RNAs identified by CLIP and data normalization.txt


title: RNAseq_2iL_Zic3_KO_rep1


title: Rbx2cKO-Nes_3

description: Rbx2 flox/flox; Nestin-Cre/+

value: C57BL/6J and 129 (mix background)

value: Telencephalon

value: Rbx2 flox/flox; Nestin-Cre/+


title: vargas8_ABP34-2


title: vargas7_FIB-2


title: RNAseq_SL_Trp53_KO_rep1


title: RNAseq_SL_Trp53_KO_rep2


title: vargas4_ABP34-1


title: vargas6_Nop58-2


title: vargas3_FIB-1


title: vargas5_Arpv2-2


title: RNAseq_2iL_Trp53_KO_rep2


title: Test_15_CCC

city: Beijing

first: Fan

last: Yang

address: No.2 Anzhen Street

institute: Beijing Anzhen Hospital, Capital Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by stringtie v1.3.3
Genome_build: hg38
Supplementary_files_format_and_content: files include FPKM values for each sample

source_name: Thyroid

extract_protocol:
PTC tissue and normal thyroid tissue were collected during surgery and  flash frozen by  liquid nitrogen. Total RNA of tissue sample was extracted using Trizol, according to manufacturer’s procedure, quantified and quality controlled using a 2100 Bioanalyzer (Agilent). RNA samples with RNA Integrity Number (RIN) above 7 were depleted for ribosomal RNA and converted into cDNA library using a TruSeq Stranded Total Library Preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: papillary thyroid carcinoma

tag: tumor extension (ajcc8th standard)

value: within gland

tag: lymph node metastasis

value: regional lymph node metastasis

tag: distant metastasis

tag: mulitfocal/unifocal

value: unifocal

tag: max tumor size (centimeter)

tag: year of diagnosis

tag: age at diagnosis

value: female

tag: vital status when data upload

value: alive


title: Test_14_ZSM

value: gross extrathyroidal extension

tag: gender


title: Test_13_TGZ


title: vargas2_Nop58-1

tag: strain


title: RNAseq_SL_WT_rep2

tag: cell line


title: Test_12_XHL


title: RNAseq_SL_Zic3_KO_rep1


title: Test_11_YXQ


title: RNAseq_SL_WT_rep1


title: Test_10_WJ

value: male


title: RNAseq_2iL_WT_rep2


title: RNAseq_2iL_WT_rep1


title: Test_9_WXF


title: ChIPseq_Zic3_SL_rep2

data_processing:
ChIP-seq libraries were mapped using Bowtie2 (v2.1.0) with default settings
Bigwig files were created using deeptools “bamCoverage” (v3.0.2-1-ac193610) using parameters "--binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2620345972 --ignoreForNormalization chrX -e -p 30"
Narrow peaks were generated by MACS2 (v2.1.1.20160309)  with p-value = 0.1 using GSM4196597 as input. Next, we applied the Irreproducible Discovery Rate (IDR; v2.03) with a threshold of 0.03 to the narrowPeak files of both replicates. Read counts were determined using featureCounts (v1.6.3) in paired-end mode using a bedfile that contains the union of 2iL- and SL peaks
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files contain RPKM scaled abundance in bins of 50bp. Abundance measurements contain normalized reads and differential analysis results from DESeq2

extract_protocol:
ESCs were fixed using 1% formaldehyde (Millipore #344198) for 10 min at room temperature then quenched by adding 1.25M glycine to a final concentration of 0.125M. Cell pellets were snap frozen and stored in -80℃. Every 10 million cells were lysed by 300μL 1% SDS include freshly made Protease Inhibitor (PI) cocktail (Roche #4693132001), sonicated with Diagenode Bioruptor Pico and diluted with 2.7mL PBA (1x PBS + 0.5% BSA) with fresh added PI cocktail. Dynabeads protein A+G (Invitrogen #10008D, 10009D) were washed and pre-blocked with cold PBA for 30 minutes. Diluted chromatin containing 30μg DNA was incubated with 15μg P53 antibody (Novocastra #CM5P) and 60μL pre-blocked beads and rotated at 4℃ overnight. After incubation, beads were washed subsequently with High-NaCl, Low-NaCl, LiCl, TE and TE washing buffers for 10 minutes and transferred to new eppendorf tube. Beads were eluted with 200µL elution buffer (1%SDS, 0.2M NaCl, 0.1μg/μL Proteinase K) at 65°C thermo shaker 1000rpm for 20 minutes. Supernatants were purified with MinElute PCR Purification Kit (QIAGEN #28006).
1-5ng of DNA was used for library construction with KAPA Hyper Prep Kit (KAPA #KK8504).

value: ser+LIF

tag: chip antibody


title: Test_5_LYQ


title: Test_4_CSX


title: Test_6_YLL

value: multifocal


title: Test_7_XBH


title: Test_8_LYY


title: Test_1_GCL


title: ChIPseq_Zic3_SL_rep1


title: Test_2_RL


title: ChIPseq_Zic3_2iL_rep1


title: ChIPseq_Zic3_2iL_rep2


title: Con2_7_YXM

value: normal thyroid tissue


title: Test_3_GCJ


title: Con2_6_LYQ


title: RNAseq_2iL_Trp53_KO_rep1


title: vargas1_Arpv2-1


title: Con2_5_WFQ


title: Con2_3_RL


title: Con2_2_GCL


title: 455-1 [201814487-01]

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the hg19 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE v19 GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: Processed files is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: bronchial epithelial cells_saline

growth_protocol: 5x10^5 NHBE cells were cultured on top of the membrane in bronchial epithelial cell growth medium (BEGM) until cells were confluent.

extract_protocol:
Total RNA was extracted using a Direct-zol™ RNA MicroPrep kit
Total RNA was prepped for sequencing with the KAPA RNA HyperPrep Kits with RiboErase (HMR) according to manufacturer's protocols

treatment_protocol: Treated samples were exposed to MAB microparticles diluted in 100μL at a concentration equal to a multiplicity of infection (whole bacterium) of 10:1. Bronchial epithelial cells were harvested at day 3.

tag: cell type

value: bronchial epithelial cells

tag: treatment

value: saline


title: 455-2 [201814488-01]

value: Mycobacterium abscessus microparticle


title: 270-2 [201814484-01]


title: Con2_1_SSJ


title: Con1_9_JLM


title: Con1_8_GJ


title: 270-1 [201814483-01]


title: P4

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the Ensembl GRCm38.91 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

growth_protocol: 6-week-old C57Bl/6 male mice were used for the study approved by the Animal Studies Subcommittee (IACUC) at Miami VA Health

extract_protocol:
Lung was homogenized in TRI reagent and total RNA extraction was performed with the Direct–zol RNA extraction kit
Total RNA was prepped for sequencing with the KAPA RNA HyperPrep Kits with RiboErase (HMR) according to manufacturer's protocols

treatment_protocol: Treated mice received intra-tracheal challenges with Mycobacterium abscessus cell wall particles at day 1,  then subsequent challenges with intranasal particles every other day for total 7 times.   Mice were sacrificed at day 21.

tag: age

value: 6 weeks

tag: Sex

value: intra-tracheal Mycobacterium abscessus cell wall particle

tag: tissue

value: lung


title: 422-1 [201814479-01]


title: Con1_6_LCL

tag: sample type

value: papillary thyroid carcinoma

tag: tumor extension (ajcc8th standard)


title: P3


title: 422-2 [201814480-01]


title: 803-2 [201814476-01]


title: P2


title: P1


title: Myc_c2

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Single-stranded DNA libraries containing transcription factor binding site sequences and all possible single base variants were commercially synthesized on microarray chips (Agilent). Double-stranded DNA was generated on the chip by hybridization with the wild-type reverse complement oligonucleotides in solution (variant complements were absent from the hybridization solution). For each wild-type sequence, the solution contained ~2.5 μM (large excess) unlabeled HPLC-purified oligonucleotides and ~0.25 μM FAM/Cy3-labelled HPLC-purified oligonucleotides (Integrated DNA Technologies). The reaction buffer mixture for the hybridization step was 100 μl 10x reaction buffer (260 mM Tris-HCl, pH 9.5, 65 mM MgCl2) in a total volume of 1000 μl, similarly to 20. The chip was incubated with reaction mixture in a hybridization oven using a pre-warmed stainless-steel chamber and gasket cover slip. After a 5-hour incubation (85 °C for 10 min, 75 °C for 10 min, 65 °C for 60 min, 60 °C for 120 min, and 55 °C for 100 min), the hybridization chamber was disassembled in a glass staining dish in 500 ml phosphate buffered saline (PBS) / 0.01% Triton X-100 at 37°C. The chip was transferred to a second staining dish, washed for 10 min in PBS / 0.01% Triton X-100 at 37°C, washed once more for 3 min in PBS at room temperature, similarly to 20. The fluorescent signal (Cy3/FAM) of hybridized oligonucleotides was measured using a GenePix 4400A microarray scanner to confirm that the hybridization was successful and reproducible, and that no significant cross-hybridization occurred. Protein binding and antibody steps were performed similarly to protein-binding microarray (PBM) assays (Berger et al., Nature Biotechnology 2006). The fluorescent signal of bound transcription factor for each DNA spot was measured using a GenePix 4400A microarray scanner.

scan_protocol: Protein-bound arrays were scanned to detect Alexa-488-conjugated or Alexa-647-conjugated (detected at 635nm wavelength) antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots of interest. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescent signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots.

label: Alexa 647

molecule: protein

organism: synthetic construct

source_name: Human Myc

label_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manuscript, for each tested protein.

tag: transcription factor

value: Myc

tag: protein concentration


title: Con2_4_GCJ

value: within gland

tag: lymph node metastasis

tag: distant metastasis

tag: mulitfocal/unifocal

tag: max tumor size (centimeter)


title: 803-1 [201814475-01]


title: Con1_4_WFQ

value: unifocal

tag: year of diagnosis

tag: age at diagnosis

tag: gender

tag: vital status when data upload


title: Con1_5_DMM

value: female


title: C3

tag: strain


title: Con1_3_XYC

value: alive


title: C2

tag: treatment


title: Gabpa

source_name: Human Gabpa

growth_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manuscript, for each tested protein.

value: Gabpa


title: Gata1

source_name: Human Gata1

extract_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manuscript, for each tested protein.


title: Con1_2_YYL


title: 558-2 [201814472-01]

tag: cell type


title: 558-1 [201814471-01]


title: C1

tag: age

tag: Sex

value: male


title: Con1_1_SSJ

tag: sample type


title: Con1_7_ZLY

tag: tumor extension (ajcc8th standard)


title: Mad

source_name: Human Mad

tag: transcription factor

value: Mad


title: Cbf1

source_name: Yeast Cbf1

tag: protein concentration


title: Ets1_replicate2

source_name: Human Ets1


title: Ets1_replicate1


title: HAP1_WT-T0-A

status: Public on Aug 15 2020

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: gRNA amplicon

data_processing:
Library strategy: CRISPR-seq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

source_name: HAP1 cell line

growth_protocol:
During generation and clonal expansion, H1-iCas9 cells were cultured on Matrigel (Corning; 0.5mg per 6-well plate) in E8 medium (Life Technologies), passaged using GCDR (STEMCELL) and cryopreserved in mFreSR medium (STEMCELL)
MEF culture: culture on irradiated mouse embryonic fibroblasts (MEFs) in human embryonic stem cell (hESC) medium as described (Ditadi and Sturgeon, 2016). hESC medium consists of DMEM/F12 (50:50; ThermoFisher) supplemented with 20% knockout serum replacement (KOSR) (GIBCO), 1% penicillin/streptomycin (ThermoFisher). 2mM L-glutamine (ThermoFisher), 1% non-essential amino acids (NEAA) (ThermoFisher) and 55uM beta-mercaptoethanol (Sigma). Immediately prior to use, hESC media was supplemented with 15ng/ml human basic fibroblast growth factor (hbFGF) (R&D Systems). Cells were passaged every 4-5 days using TrypLE Express (GIBCO), and plated in presence of 10uM ROCK inhibitor Y-27632 (ROCKi) (Tocris) for 24 hours. Cells were cryopreserved in freezing medium containing 50% hESC medium plus 40% FCS plus 10% DMSO.
Feeder-free conditions: H1-iCas9 cells were maintained on tissue culture plates coated with recombinant human laminin at a concentration of 0.5ug/cm^2 (rhLaminin-521, ThermoFisher; doluted in DBPS with Ca^2+ and Mg^2+, GIBCO) or vitronectin at a concentration of 1.05ug/cm^2 (STEMCELL, diluted in PBS) in mTeSR1 complete medium (STEMCELL). Cells were passaged every 4-5 days using ReLeSR enzyme-free dissociation reagent (STEMCELL) in the absence of ROCKi (only used for thawing and transduction), and cryopreserved in mFreSR medium (STEMCELL). H1 and H1-iCas9 cells were maintained in culture plates of 24-well to 10-cm size at individually optimized cell numbers. Growth media were changed daily with occasional "double-feeds" over two days.
HAP1 cells were obtained from Horizon (clone C631, sex: male with lost Y chromosome, RRID: CVCL_Y019) and HAP1-Cas9 cells were generated analagous to described protocols (Hart et al., 2015). HAP1 cells were cultured in DMEM without sodium pyruvate, with sodium bicarbonate, 1.982g/L glucose and 0.161g/L L-glutamine (Wisent Bioproducts) with 10% FBS (GIBCO) and 1% penicillin/streptomycin (ThermoFisher).

extract_protocol:
Genomic DNA was extracted from screen cell pellets using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer's instructions.
Sequencing libraries were preparaed by amplifying gRNA inserts via a 2-step PCR using primers that include Illumina TruSeq adaptors with i5 and i7 indices.

treatment_protocol:
Cells grown on MEFs: 48 hours prior to infection with the lentiviral pLCKO-TKOv3 library, H1-iCas9 cells were treated with DOX (1.5ug/ml, Sigma). Approximately 6x10^7 cells were infection in suspension (MOI~0.44, 370-fold library coverage) before being plated onto MEFs. 24 hours post infection, hESC medium was repalced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. After selection, cells were harvested, split into three replicates containing 1.5x10^7 cells each and exposed to another 24 hours of DOX. Cells were counted and passaged every 4 days in presence of ROCKi.
Cells grown on laminin: 48 hours prior to infection with the lentiviral pLCKO-TKOv3 library, H1-iCas9 cells were treated with DOX (1.5ug/ml, Sigma) with a fraction of cells left untreated. 24 hours prior to infection, cells were dissociated using ReLeSR and plated at a density of 1.5x10^6 cells/10cm dish with 10um ROCKi with and without DOX (1.5ug/ml). Approximately 8x10^7 adherent DOX-treated cells and 4x10^7 cells without DOX were infected with pLCKO-TKOv3 library and ROCKi (MOI~0.17 and ~0.42 respectively). 24 hours post infection, mTeSR1 medium was replaced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. Following selection, cells without DOX were harvested and collected for genomic DNA extraction, and DOX-treated cells were split into three replicates containing 1.5x10^7 cells each.

tag: culture substrate

value: Tissue culture plastic

tag: crispr library

tag: timepoint


title: GTFR230_H3K27Ac

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

description: Two biological replicates; Rep A and Rep B. Single End Sequencing (R1) files available.

data_processing:
ChIP-Seq peaks were generated with the AQUAS pipeline.
Reads were aligned with BWA to the reference human genome hg38.
Peak calling was performed with MACS2, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available (HEYA8, ES2 and RMG-II) pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Peaks sets were lifted into hg19 using the LiftOver tool.
Genome_build: hg19
Supplementary_files_format_and_content: Narrowpeak files were created in hg38 and then lifted to hg19 and converted to bed files. These files contain the co-ordinates of peaks enriched for H3K27Ac.

source_name: GTFR230 Cell Line

extract_protocol:
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated  to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K27ac was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, according to the manufacturer's instructions. Library construction was carried out according to the manufacturer's instructions using Bio NextFLex adaptors diluted 1:50. Final PCR on a portion of the adaptor ligation was performed for 12 cycles. Products were evaluated on an Agilent Bioanalyzer, using high-sensitivity DNA chips. ChIP libraries were quantified using the Kapa Biosystems Illumina library quantification kit, before pooling for sequencing.

tag: tissue

value: Model of mucinous Ovarian Cancer

tag: cell line


title: GTFR230_Input


title: Max

source_name: Human Max

value: Max


title: Kuramochi_Input

source_name: Kuramochi Cell Line

value: Model of High Grade Serous Ovarian Cancer from metastatic (ascites) sample

value: Kuramochi


title: OAW42_H3K27Ac

source_name: OAW42 Cell Line


title: MCAS_Input

source_name: MCAS Cell Line

value: Model of Mucinous Ovarian Cancer

value: MCAS


title: Kuramochi_H3K27Ac


title: CaOV3_H3K27Ac

description: No fastq files are available for this experiment.

source_name: CaOV3 Cell Line

value: Model of High Grade Serous Ovarian Cancer


title: MCAS_H3K27Ac


title: JHOC5_Input

source_name: JHOC5 Cell Line

value: Model of Clear Cell Ovarian Cancer


title: 6M_CC_WT3

city: Gainesville

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Sequencing adapters were trimmed using Cutadapt and low quality reads were pre-filtered by FASTX-Toolkit before mapping.  The quality of reads after filtering was examined using fastQC.
All filtered reads were aligned to mouse reference genome (GRCm38/mm10) by Tophat (v2.0.10) using SAMtools (v0.1.18) and Bowtie (v2.1.0) with default parameters
Individual mapped reads were fed to Cufflinks (v1.2.1) to construct transcriptome models and any novel genes and transcripts that did not fit the supplied gene models were also assembled.
Cuffmerge was used to converge individual transcriptome to produce a master gene model.
Cufflinks was run to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) by using RefSeq genes as reference
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKMs

extract_protocol:
cDNA synthesis and amplification was performed using 100 cumulus cells per sample and Smart-Seq2 protocol.
Sequencing libraries were constructed using the amplified cDNA and Nextera® XT DNA Library Preparation Kit (Illumina, San Diego, CA) and indexed using Nextera® XT Index Kit (Illumina). Library quality was confirmed using DNA 1000 kit on Tapestation 2200 (Aglilent Technologies), and the libraries were then sequenced on Illumina’s Hiseq 2500 platform with 75bp pair-end reads.

treatment_protocol: Mature female mice were superovulated by intra-peritoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG; Sigma, St. Louis, MO) to stimulate follicle development. To collect cumulus cells from COCs, mice were euthanized 44 h later by CO2 inhalation, the ovaries removed, and COCs were isolated by puncturing the ovaries with a 26-1/2 G needle under the dissecting microscope (Olympus SZH-ILLK).

value: 6 months

tag: genotype/variation

value: wild type

value: Cumulus cells

tag: passage


title: 6M_CC_KO2

value: ClpP-/-


title: 6M_CC_KO1


title: 3M_CC_KO2

value: 3 months


title: 3M_CC_WT3


title: 6M_CC_WT1


title: 6M_CC_WT2


title: 3M_CC_KO1


title: 3M_CC_WT2


title: 3M_CC_WT1


title: JN-DSRCT-1_Input_rep3_ChIPseq

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome using bwa and then use the MACS2 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

source_name: JN-DSRCT-1 cell line

growth_protocol: JN-DSRCT-1 cells are grown in DMEM/F12 (high glucose) + 10% FBS

extract_protocol:
The chromatin was prepared using the Covaris TruChIP kit according to the manufacturer’s protocol. Briefly, cells were fixed in 1% methanol-free paraformaldehyde for 5 min, quenched, and lysed. Nuclei were collected and sonicated on a Covaris M220 focused ultrasonicator. The final fragment size was determined using the TapeStation2200 (Agilent) and ranged from 100 to 300 bp. Equal concentration of crosslinked chromatin was immunoprecipitated
Sequencing libraries were made from the purified DNA using the Kapa Hyper Library Preparation Kit (KAPA Biosystems)

treatment_protocol: ChIP experiment was performed on JN-DSRCT-1 cells growing as a monolayer in culture under standard conditions until they reached 90% confluence

value: EWS-WT1 positive DSRCT cell line

tag: chip antibody


title: JHOC5_H3K27Ac


title: JN-DSRCT-1_Input_rep2_ChIPseq


title: OAW42_Input


title: JN-DSRCT-1_RNA_PolIII_rep3_ChIPseq


title: JN-DSRCT-1_Input_rep1_ChIPseq


title: 6M_CC_KO3

tag: strain


title: JN-DSRCT-1_RNA_PolIII_rep2_ChIPseq


title: 3M_CC_KO3


title: JN-DSRCT-1_EWS-WT1_rep3_ChIPseq


title: JN-DSRCT-1_EWS-WT1_rep1_ChIPseq


title: VOA1056_Input

source_name: VOA1056 Cell Line

value: Model of Low Grade Serous Ovarian Cancer


title: RMG-II_H3K27Ac

description: No biological replicate available. Paired End Sequencing (R1/R2) files available.

source_name: RMG-II Cell Line

value: RMG-II


title: VOA1056_H3K27Ac

description: Two biological replicates; Rep A and Rep B. Paired End Sequencing (R1/R2) files available.


title: ES2_Input

source_name: ES2 Cell Line


title: EFO27_Input

source_name: EFO27 Cell Line


title: ES2_H3K27Ac


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 Wild-type-3

city: Irvine

last: Li

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
RNA-seq reads were mapping to human hg19 genome using STAR (version:2.4.1) with default parameters
The sorted BAM files were then converted to wig format using samtools (version: 0.1.19)
The wig files were further converted to bigwig format using wigtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format

source_name: DAOY (Xenograft tumor)

extract_protocol:
Total RNA was extracted from cultured cells or xenograft tumors using RNeasy kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina TruSeq mRNA.

tag: xenograft tumor

value: DAOY


title: HeyA8_H3K27Ac

source_name: HeyA8 Cell Line


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 M341R-1

value: SBC mutant


title: RMG-II_Input


title: EFO27_H3K27Ac


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 M341R-2


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 M341R-3


title: CT00D CD14+ high VL

city: Charlestown

first: Pritha

last: Sen

state: Massachusetts

address: 149 13th street

institute: Massachusetts General Hospital

description: raw data at dbGAP

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Gene-count matrices were calculated using scumi
Downstream analysis was performed using Pegasus
Genome_build: hg19

extract_protocol:
Desired monocyte populations for sorted by flow cytometry and RNA was harvested using Qiagen RNeasy micro kit and on column Dnase digestion was performed. RNA quantity and quality was analyzed on Agilent Bioanalyzer.
Lexogen QuantSeq Kit was used for the construction of bulk sequencing libraries. SureCell WTA 3' Library Prep Kit was used for the construction of single-cell sequencing libraries for in vitro infections. The inDrop platform was used for the construction of single-cell sequencing libraries from transplant patients. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells were stimulated with PMA at 100 ng/ml for 48 hours prior to infection with TB40/E-5. Human peripheral blood mononuclear cells (PBMC) were isolated from CMV IgG negative immunocompetent donors and cultured ex vivo in donor autologous serum and infected with TB40/E-5.

tag: gender

value: M

tag: immune status

value: heart transplant

tag: virus strain

value: clinically infected with CMV


title: CT00C CD14+ low VL

description: raw data at dbGAP

value: F


title: CT00D CD14+ low VL

description: raw data at dbGAP


title: CT00B CD14+ low VL

description: raw data at dbGAP


title: CT00C CD14+ high VL

description: raw data at dbGAP


title: CT00B CD14+ high VL

description: raw data at dbGAP


title: CT00A CD14+ low VL

description: raw data at dbGAP


title: CT00A CD14+ high VL

description: raw data at dbGAP


title: Sample_C1

city: Zhengzhou

first: Jiaqing

last: Zhang

address: No. 116 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

institute: Henan Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to pig reference genome using Tophat2 (version 2.1.0) with default parameters (max read mismatches 2, max gap length 2, max insertion/deletion 3, and min anchor length 8) (Trapnell et al. 2009; Kim et al. 2013)
Fragments per Kilobase of exon per Million were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010
Genome_build: Susscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: Ovary

extract_protocol: Intact ovaries, hypothalamuses and pituitaries derived from the sows in normal estrus (n=3) and the sows in which anestrus was induced by inactive ovaries (n=3) were immediately sampled separately, snap-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: landrace x large white sows

value: ovary

tag: developmental stage

value: anestrous primiparous sows


title: JN-DSRCT-1_RNA_PolIII_rep1_ChIPseq

tag: cell type


title: JN-DSRCT-1_EWS-WT1_rep2_ChIPseq


title: Sample_C

value: estrous primiparous sows


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 Wild-type-1

value: wild type


title: DAOY (3B6) MAGE-A11 Knockout / MAGE-A11 Wild-type-2


title: Sample_B1

source_name: Pituitary

value: pituitary


title: Sample_B


title: Sample_A1

source_name: Hypothalamus

value: hypothalamus


title: Sample_A


title: Mx3CT-11-3CT

city: Zurich

first: Frederic

middle: Francois

last: Guillaume

address: Winterthurerstrasse 190

department: Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

data_processing:
reads were mapped against the reference genome(ftp://ftp.ensemblgenomes.org/pub/release30/metazoa/gtf/tribolium_castaneum/Tribolium_castaneum.Tcas3.30.gtf.gz) with STAR v.2.5  (adaptors were trimmed and  the first 10 bases were hard trimmed, minimum average quality Q10, minimum tail quality 10, minimum read length 20).
Number of reads per gene were counted with FeatureCounts (gtfFeatureType: exon, featureLevel: gene, allowMultiOverlap=TRUE, minFeatureOverlap=10, minMapQuality=10)
Genome_build: Tcas3.30
Supplementary_files_format_and_content: tab-delimited text files: raw read counts data for each sample

organism: Tribolium castaneum

source_name: females, whole body

growth_protocol: Beetles were kept in 24h darkness on sterilised organic wheat flour mixed with 10% organic baker's yeast. We sequenced adult reproducing females from different replicate selection lines (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines) under different climate conditions (control, dry, hot, hot-dry). Selection lines had lived under these conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions.

extract_protocol:
RNA Mini Prep kit (Zimo Research, California, USA)
LEXOGEN mRNA-Seq Library Kit (LEXOGEN GmbH, Vienne, Austria)

treatment_protocol: Beetles were kept in climate chambers that could control temperature and air humidity. Conditions were: Control: 33°C, 70% relative humidity; Dry : 33°C and 30% r. h.; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h.

tag: selection regime

value: Control

tag: treatment


title: Mx2HD-5-4CT

value: Hot-Dry


title: Mx3CT-11-4HD


title: Mx3CT-11-2CT


title: Mx3CT-11-1HD


title: Mx3CT-11-1CT


title: Mx2HD-5-3HD


title: Mx2HD-5-3CT


title: Mx3CT-11-3HD


title: Mx2HD-5-1HD


title: Mx2HD-5-1CT


title: Mx1HD-3-4HD


title: Mx2HD-5-2CT


title: Mx1HD-3-4CT


title: Mx1HD-3-3HD


title: Mx1HD-3-2HD


title: Mx1HD-3-2CT


title: Mx1HD-3-1CT


title: Mx1HD-3-1HD


title: HeyA8_Input

value: Model of High Grade Serous Ovarian Cancer


title: Mx1CT-1-4HD


title: Mx1CT-1-3HD


title: Mx1CT-1-2HD


title: Mx2HD-5-4HD


title: Mx1CT-1-3CT


title: Mx1CT-1-4CT


title: Mx2HD-5-2HD


title: Mx1CT-1-2CT


title: Mx1CT-1-1HD


title: L6HD-12-1HD


title: L6HD-12-4HD


title: Mx1CT-1-1CT


title: L6HD-12-1CT


title: L6HD-12-2CT


title: L6HD-12-2HD


title: L6HD-12-3CT


title: Mx1HD-3-3CT


title: L6HD-12-3HD


title: L6HD-12-4CT


title: L6D-5-4CT

value: Dry


title: L6D-5-4H

value: Hot


title: L6D-5-3D


title: L6D-5-4D


title: L6D-5-2H


title: L6D-5-3H


title: L6D-5-2D


title: L6D-5-2CT


title: L6D-5-1H


title: L6D-5-1D


title: L6D-5-1CT


title: L6D-13-4H


title: L6CT-8-4D


title: L6CT-8-4CT


title: L6D-13-2H


title: L6CT-8-3HD


title: L6CT-8-4H


title: L6CT-8-4HD


title: L6CT-8-3H


title: L6D-5-3CT


title: L6CT-8-1H


title: L6CT-8-2CT


title: L6CT-8-2HD


title: L6CT-8-1D


title: L6CT-8-3D


title: L5HD-4-3CT


title: L6CT-8-1_HD


title: L5HD-4-2HD


title: L5HD-4-4CT


title: L6CT-8-2D


title: L6CT-8-1CT


title: L5HD-4-3HD


title: L5HD-4-2CT


title: L5H-13-4H


title: L5H-13-4CT


title: L5HD-4-1HD


title: L5HD-4-1CT


title: L5H-13-3CT


title: L5H-13-3H


title: L5H-13-2H


title: L5H-13-1H


title: L5D-3-4CT


title: L5H-13-2CT


title: L5H-13-1CT


title: L5D-3-3CT


title: L6CT-8-3CT


title: L5HD-4-4HD


title: L5D-3-1D


title: L5D-3-1CT


title: L5D-3-2CT


title: L5CT-2-4H


title: L5CT2-4HD


title: L5CT-2-4D


title: L5CT-2-2HD


title: L5CT-2-4CT


title: L5CT-2-3H


title: L5CT-2-3D


title: L5CT-2-3CT


title: L5CT-2-2H


title: L5CT-2-3HD


title: L5CT-2-2CT


title: L5CT-2-1HD


title: L5CT-2-1D


title: L5CT-2-1CT


title: L5-D-3-3D


title: L5D-3-4D


title: L5CT-2-1H


title: L5-CT-2-2D


title: L5D-3-2D


title: L4H-9-3H


title: L4H-9-2H


title: L4H-9-3CT


title: L4H-9-4CT


title: L4H-9-4H


title: L4H-9-1H


title: L4H-9-1CT


title: L4H-9-2CT


title: L4CT-16-4D


title: L4CT-16-3H


title: L4CT-16-3D


title: L4CT-16-2D


title: L4CT-16-2HD


title: L4CT-16-3CT


title: L4CT-16-2H


title: L4CT-16-2CT


title: L4CT-16-1HD


title: L4CT-16-1CT


title: L4CT-16-1D


title: L3HD-4-4H


title: L3HD-4-4HD


title: L3HD-4-4CT


title: L3HD-4-3CT


title: L3HD-4-3HD


title: L4CT-16-1H


title: L3HD-4-2H


title: L3HD-4-1CT


title: L3HD-4-1H


title: L3H-8-1H


title: L3HD-10-2H


title: L3H-8-2H


title: L4CT-16-4CT


title: L4CT-16-4HD


title: L3H-15-3H


title: L3H-15-4CT


title: L3H-15-3CT


title: L4CT-16-4H


title: L3H-15-2CT


title: L3H-15-1H


title: L3H-15-1CT


title: L3CT-5-4HD


title: L3CT-5-3H


title: L3CT-5-3D


title: L3HD-4-2HD


title: L3HD-4-1HD


title: L3CT-5-2D


title: L3CT-5-2H


title: L3CT-5-3CT


title: L3CT-5-2CT


title: L3CT-5-1HD


title: L3CT-5-1H


title: L3CT-5-1D


title: L3-CT-5-4H


title: L2HD-8-3HD


title: L3CT-5-1CT


title: L2HD-8-4HD


title: L2HD-8-3H


title: L3CT-5-4D


title: L2HD-8-2HD


title: L3CT-5-3HD


title: L2HD-8-2H


title: L2HD-8-1CT


title: L2HD-2-3H


title: L2H8-4H


title: L2H-9-2CT


title: L2H-8-4CT


title: L3CT-5-2HD


title: L2H-8-3H


title: L2H-8-2H


title: L2H-8-3CT


title: L2D3-1H


title: L2D-3-4H


title: L2H-8-2CT


title: L2H-8-1H


title: L2HD-8-3CT


title: L2D-3-2D


title: L2D-3-3H


title: L2D-3-3D


title: L2D-3-3CT


title: L2HD-8-1H


title: L2D-3-1D


title: L2D-3-4D


title: L2D-3-4CT


title: L2D-3-2CT


title: L1HD-3-4CT


title: L2D-3-1CT


title: L1HD-3-3HD


title: L1HD-3-3H


title: L1HD-3-2HD


title: Patient 32 (ER-/PgR+)

city: Gdańsk

first: Wojciech

last: Biernat

address: Smoluchowskiego 17

department: Department of Pathomorphology

country: Poland

institute: Medical Univeristy of Gdańsk

hyb_protocol: Extracted RNA (3 µl) was subjected to miRNA expression profiling with nCounter Human v3 miRNA Expression Assay (NanoString Technologies) according to the manufacturer’s procedures for hybridization, detection, and scanning.

data_processing: For each analyzed sample correction and normalization were performed using nSolver 4.0 software. The background level was estimated by thresholding over the mean plus 2 standard deviations of the negative control counts. Subsequently, the data were normalized according to the global mean of the counts of positive controls and all miRNA genes. The negative and positive control probes were included in the assay.

label: not provided

source_name: primary breast cancer

extract_protocol: Total RNA including miRNA was isolated from archival FFPE blocks (four 20 µm-thick sections per block) using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) following the manufacturers’ protocol. RNA concentration and purity were determined using NanoDrop 1000 spectrophotometer (Thermo Scientific).

value: primary breast cancer

tag: group

tag: age [years]

tag: grade

tag: er status

value: negative

tag: pgr status

value: positive

tag: her2 status

tag: ki67 status [%]

tag: tumor size [mm]

tag: t stage (8th edition)

tag: n stage (8th edition)

tag: m stage (8th edition)


title: Patient 31 (ER-/PgR+)

scan_protocol: Extracted RNA (3 µl) was subjected to miRNA expression profiling with nCounter Human v3 miRNA Expression Assay (NanoString Technologies) according to the manufacturer’s procedures for hybridization, detection, and scanning.

tag: tissue


title: L1HD-3-2H

tag: strain


title: Patient 28 (ER-/PgR+)

label_protocol: Extracted RNA (3 µl) was subjected to miRNA expression profiling with nCounter Human v3 miRNA Expression Assay (NanoString Technologies) according to the manufacturer’s procedures for hybridization, detection, and scanning.


title: Patient 26 (ER-/PgR+)


title: Patient 29 (ER-/PgR+)


title: Patient 27 (ER-/PgR+)


title: Patient 30 (ER-/PgR+)


title: L1HD-3-2CT


title: L1HD-3-1HD


title: Patient 25 (ER-/PgR+)


title: L1HD-3-1H


title: L1HD-3-1-CT


title: L1HD-3-4H


title: L1H-15-4H


title: Patient 24 (ER-/PgR+)


title: Patient 20 (ER-/PgR+)


title: Patient 23 (ER-/PgR+)


title: L2HD-8-4CT


title: Patient 22 (ER-/PgR+)


title: L1H-15-4CT


title: Patient 19 (ER-/PgR+)


title: L1H-15-1H


title: L1H-15-3CT


title: L1H-15-2H


title: L1H-15-1CT


title: L1H-15-2CT


title: L1D-7-4H


title: L1D-7-4D


title: Patient 21 (ER-/PgR+)


title: Patient 11 (ER+/PgR-)


title: Patient 13 (ER+/PgR-)


title: Patient 14 (ER+/PgR-)


title: Patient 16 (ER-/PgR+)


title: Patient 12 (ER+/PgR-)


title: Patient 15 (ER-/PgR+)


title: L1D-7-3H


title: L1D-7-4CT


title: L1D-7-3D


title: Patient 18 (ER-/PgR+)


title: L1H-15-3H


title: Patient 17 (ER-/PgR+)


title: L1D-7-3CT


title: Patient 8 (ER+/PgR-)


title: Patient 7 (ER+/PgR-)


title: Patient 9 (ER+/PgR-)


title: L1D-7-2D


title: L1D-7-2CT


title: L2HD-8-2CT


title: Patient 6 (ER+/PgR-)


title: mutant biol. rep 3

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

data_processing:
reads were aligned against TAIR10 applying the Tuxedo protocol: Trapnel et al. Nature Protocols, 7(3), 562–578. doi:10.1038/nprot.2012.016
tophat -i 10 -I 11000
cufflinks -p 8 --min-intron-length 10 --max-intron-length 11000
cuffmerge -g
cuffdiff
Genome_build: TAIR10
Supplementary_files_format_and_content: differential expression values (log2) with p and q values

organism: Arabidopsis thaliana

source_name: whole seedlings (aerial parts)

growth_protocol: Plants were grow under long day condition (16h light) at 24 degrees in a Sanyo MLR-350 chamber

extract_protocol:
total RNA was extracted using the Ambion mirVana kit according to manufacturer instructions
TruSeq RNA_SamplePrepKit v2 Illumina, SR50

tag: age

value: 17 days

value: seedling

tag: genotype

tag: genetic background


title: Patient 10 (ER+/PgR-)


title: mutant biol. rep 1


title: mutant biol. rep 2


title: L1D-7-1D

tag: selection regime

tag: treatment


title: Patient 5 (ER+/PgR-)

tag: group

tag: age [years]


title: wild type biol. rep 3


title: L1D-13-4H


title: Patient 3 (ER+/PgR-)

tag: grade

tag: er status


title: Patient 2 (ER+/PgR-)

tag: pgr status

tag: her2 status


title: Patient 4 (ER+/PgR-)

tag: ki67 status [%]

tag: tumor size [mm]


title: Patient 1 (ER+/PgR-)

tag: t stage (8th edition)

tag: n stage (8th edition)


title: L1D-7-1CT


title: L2HD-8-1HD


title: wild type biol. rep 2

tag: tissue


title: L1HD-3-3CT

tag: strain


title: L1D-7-2H


title: L1CT-4-4HD


title: wild type biol. rep 1

tag: age


title: L1CT-4-4H


title: IT_7741246983

city: Philadelphia

first: Danielle

middle: R

last: Reed

state: PA

address: 3500 Market St

department: Not applicable

institute: Monell Chemical Senses Center

data_processing: cell ranger 3.02

source_name: surgical biopsy  inferior turbinate

extract_protocol: Dataset consists of a total of four single-cell datasets generated using    the 10x Genomics Chromium platform. Prior to GEM generation, tissue sample    was taken fresh from OR rinses 3x in phosphate buffered saline, cut into    1-3mm sized pieces and gently digested in Liberase TL solution for 1-hr at    37C. The reaction was quenched with serum and digested cell suspension were    filtered through a 70micron filter centrifuged  gently at 4C and rinsed x2    with pbs followed by lysis of red blood cells with an rbc lysis solution.    This was followed by 2 rinses with phosphate buffered saline. Viability was    assessed by trypan blue of a small aliquot and at this point cells were    used for the Next-generation sequencing libraries that were prepared    following the 10X Single Cell v2 protocol without modification. Sample    quality was evaluated using Agilentâ€™s Bioanalyzer High Sensitivity reagent    kit following cDNA amplification and library construction. The completed    libraries were quantified using the Kapa Library Quantification Kit and the    Life Technologies Viia7 Real-time PCR instrument. Libraries were sequenced    in a paired-end, single-indexed format on the Illumina. Cells were    sequenced to target a depth of at least 27,000 reads per cell

value: surgical biopsy  inferior turbinate

tag: diagnosis

tag: race

value: white

tag: gender

value: Female


title: P_2009946466

source_name: surgical biopsy nasal polyps

value: surgical biopsy nasal polyps


title: L1CT-4-4CT

tag: selection regime

tag: treatment


title: L1CT-4-3HD


title: L1CT-4-3H


title: HAP1_WT-T18-B

description: gRNA amplicon

source_name: HAP1 cell line

tag: culture substrate

value: Tissue culture plastic

tag: crispr library

tag: timepoint


title: HAP1_WT-T18-C

description: gRNA amplicon


title: L3HD-4-2CT