title: 32248_iris  [Sample_31]

value: iris & ciliary body


title: iPSC-derived off-target tissue, biological rep2

status: Public on Feb 26 2022

type: RNA

city: Kobe

first: Kenji

last: Watari

address: 5th floor, 1-5-2 Minatojima Minamimachi, Chuo-ku

country: Japan

institute: Sumitomo Pharma Co., Ltd.

description: Sample-E

hyb_protocol: Biotinylated cRNA were hybridized for 16 hr at 45°C on U133 Plus2.0 Array in the hybridization oven 640 (Affymetrix 800138). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix 00-0079).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix 00-0074).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software ver1.4 (Affymetrix 690036).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: off-target tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Feeder-free human iPSCs were self-organized into 3D-retinas by previously described methods (Kuwahara et al., Nat Commun, 2015; Kuwahara et al., Sci Rep, 2019) with slight modifications. See a preprint on bioRxiv for more details (doi:10.1101/2022.02.18.480968).

extract_protocol: Tissues were lysed with Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol, and total RNA was extracted and purified using an RNeasy Micro Kit (Qiagen).

tag: tissue

value: hiPSC-derived off-target tissue


title: iPSC-derived retinal tissue, biological rep1

description: Sample-A

source_name: retinal tissue

value: hiPSC-derived retinal tissue


title: H4r-rep1-HS3-H3ChIP

type: SRA

city: Szeged

first: Andrea

last: Ábrahám

state: Csongrád

address: Közép fasor 52.

country: Hungary

institute: University of Szeged

library_source: genomic

data_processing:
trimming via Trim Galore (0.6.6.)
alignment to the Drosophila melanogaster (dm6) genome with Bowtie2 (2.4.2)
filter to blacklisted reads via BAM Filter Galaxy Version 0.5.9 software
determining reads on genes via BedCov Galaxy Version 2.0.2
converting to BigWig via MACS (2.2.7.1)
Genome_build: dm6
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Flies were held on standard Drosophila media until treatment

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA Library Prep Kit for Ilumina according the recommendations of the manufacturer, without size selection

treatment_protocol: heat-shocked flies were exposed to heat shock at 37°C for 20 minutes, heat-shocked and regenerated flies were exposed to heat shock at 37°C for 20 minutes and regenerated at room temperature for 3 hours prior to freeze in liquid nitrogen

value: Brain

tag: treatment

value: heat-shocked and regenerated

tag: genotype

value: w; 3xFlag-H4r


title: 32250_cornea  [Sample_36]

city: Wauwatosa

first: Iris

last: Kassem

state: Wisconsin

address: 8701 W Watertown Plank Rd

department: Ophthalmology

country: USA

institute: Medical College of Wisconsin

library_source: transcriptomic

data_processing:
Filtering and trimming with SOAPnuke software version 1.5.2 using parameters: -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G found at: https://github.com/BGIflexlab/SOAPnuke
Alignment using HISAT2 v2.0.4, using parameters: -p 8 --phred33 --sensitive -I 1 -X 1000 found at http://www.ccb.jhu.edu/software/hisat
Clean reads mapped to the reference genome using Bowtie v2.2.5 Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Gene expression levels calculated with RSEM v1.2.12
Genome_build: GCF_000003625.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Oryctolagus cuniculus

source_name: cornea

extract_protocol:
Tissues were homogenized using a Mini-Bead beater 16 (Biospec Products) at 10 °C. Samples were homogenized for approximately 90 seconds and then cooled for 90 seconds on ice for three rounds. Following homogenization, RNA was extracted using a RNeasy Extraction kit (Qiagen, Germantown, MD), according to the manufacturer’s protocol, with an additional wash step of 500 microliters of Buffer RPE prior to adding the RNAse-free water. Following this step, 50 microliters of RNAse-free water was added to the spin-column membrane to extract the total RNA. Total RNA samples were sent to BGI Group for quality control verification and library preparation.
Library constructed by BGI using DNBseq platform.

tag: breed

value: New Zealand white rabbit

value: cornea

tag: age

value: 6 months

tag: tissue treatment

value: unoperated


title: iPSC-derived retinal tissue, biological rep2

description: Sample-B


title: iPSC-derived retinal tissue, biological rep3

description: Sample-C


title: PROseq_Ints9depl_Replicate2

city: Boston

first: Emily

last: Kaye

state: MA

address: 45 Shattuck Street

institute: Harvard Medical School

description:
nascent RNA
biotin labeled nascent RNA isolated from Drosophila S2 permeabilized cells

data_processing:
Paired-end reads were trimmed to 41nt, for adaptor sequence and low quality 3' ends using cutadapt 1.14, discarding those containing reads shorter than 20nt (-m 20 -q 10).
Remaining pairs were paired-end aligned (using Bowtie 1.2.2) to the hg38 spike genome index to determine spike-normalization ratios based on uniquely mapped reads. Mappable pairs were omitted from subsequent analysis.
Remaining unmapped pairs were aligned to the dm3 genome assembly. Identical parameters were used in each alignment described: up to 2 mismatches, and uniquely mappable and unmappable pairs routed to separate output files (-v2, -un, --best).
Pairs mapping to dm3, representing biotin-labeled RNA 3' ends, were separated, and strand-specific counts of the 3' mapping positions determined at single nucleotide resolution, genome-wide, and expressed in bedGraph format with "plus" and "minus" strand labels swapped for each 3' bedGraph, to correct for the "forward/reverse" nature of Illumina paired-end sequencing.
Based on similar recovery of spike-in reads, depth normalization was performed and bedGraphs from replicates of each condition were combined by summing counts per nucleotide.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph containing combined count of end 1 3' mapping locations for all three replicates for a given treatment

source_name: Drosophila S2 cells

growth_protocol: S2 cells were grown under standard conditions at 27C.

extract_protocol:
Cells were washed in PBS, then permeabilized and flash frozen in 1M cell aliquots. Permeabilized S2 cells were spiked with permeabilized HEK cells, then PRO-seq run-on reactions were performed using biotin-NTPs. Nascent RNA was extracted using a Total RNA Purification Kit following manufacturer instructions (Norgen Biotek Corp.).
Extracted RNA was chemically fragmented with magnesium chloride and heat, followed by bead purication and trizol extraction of nascent RNA. Purified RNA was then subjected to 3' adaptor ligation, bead purification, 5' decapping, and 5' hydroxyl repair, followed by 5' adaptor ligation. Libraries were prepared by on-bead reverse transcription and 9-10 cycle amplification of final PRO-seq libraries.
PRO-seq

treatment_protocol: Cells were treated with dsRNA for 45 min in serum-free conditions, then grown for 3 days in media with a final concentration of 10% heat inactivated-fetal bovine serum.

tag: cell type

value: Derived from male late stage embryo cells

value: IntS9 targeting dsRNA (3 days)


title: PROseq_Ints9depl_Replicate3


title: H4r-rep2-HS-H3ChIP

value: heat-shocked


title: 32246_cornea  [Sample_30]

value: operated


title: 32249_cornea  [Sample_34]


title: PROseq_control_Replicate3

value: β-galactosidase targeting dsRNA (3 days)


title: 32249_iris  [Sample_33]

source_name: iris & ciliary body


title: H4r-rep1-HS-H3ChIP


title: BT474 cells-B3_PROG

city: TORONTO

first: ELEFTHERIOS

middle: P

last: DIAMANDIS

state: ONTARIO

address: 60 Murray St

country: Canada

institute: Mount Sinai Hospital

data_processing:
Read Pre-processing: The sequencing data is in FASTQ format generated using bcl2fastq2 v2.17. The quality of the data is assessed using FastQC v.0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adaptors are trimmed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) v. 0.4.0. Trim Galore is running Cutadapt (https://cutadapt.readthedocs.org/en/stable/) v. 1.8. Trim Galore is run with the following parameters:    -q 20 – the reads are trimmed from the 3' end base by base, trimming stops if the quality of the base is greater than 20;   --clip_R1 6, --clip_R2 6 – clip the first 6 nucleotides from the 5' ends of read 1 and read 2;   --illumina – 13 bases universal to the Illumina primers are recognized and the reads are trimmed from the point of encountering of the primer fragment on;    --stringency 5 – at least 5 nucleotides overlap with the Illumina primer sequence are needed for trimming;   --length 40 – any read that is shorter than 40 nucleotides as a result of trimming is discarded;   --paired – only pairs of reads are retained (for paired-end reads only, not for single reads).   The quality of the trimmed reads is re-assessed with FastQC. The trimmed reads are also screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/). To assess the read distribution, positional read duplication and confirm the strandedness of the alignments we use the RSeQC package (http://rseqc.sourceforge.net/), v. 2.3.7. The distribution of reads across exonic, intronic and intergenic sequences is assessed by the read_distribution.py program, infer_experiment.py is used for confirming strandedness, and read_duplication.py is used to obtain the positional read duplication (reads mapping to exactly the same genomic location). Sufficient proportion of reads should map to the exonic sequences (ideally > 70-80%). Large amounts of reads mapping to intronic sequences will suggest significant presence of pre-mRNA or other issues with RNA preparation. For stranded RNA-seq experiments all reads should map exclusively to one strand, same or opposite to the transcript, depending on the method of preparation of the stranded RNA-seq library. For non-stranded experiments the reads should be equally distributed to both strands.
Read Alignment: The raw trimmed reads are aligned to the reference genome specified above using Tophat v. 2.0.11 (http://ccb.jhu.edu/software/Tophat/index.shtml).   Tophat uses Bowtie2 to align reads to a genome. Bowtie2 is used in a mode of searching for multiple alignments for each read, and reporting the best one. In case of several equally good alignments, Bowtie2/Tophat reports by default up to 20 of them. These multiple alignments per read are present in the “.bam” alignment file and have their NH:i flag set to a number higher then 1, as per the SAM format specification (https://samtools.github.io/hts-specs/SAMv1.pdf), however they are not counted for the differential analysis (refer for details to section 3.3, Obtaining Gene Counts).  The “.bam” together with the “.bai” files can be used for viewing of the alignments in IGV (https://www.broadinstitute.org/igv/).
Obtaining Gene Counts: Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2(HTSeq, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). Assigning reads to genes by htseq-count is done in the mode “intersection_nonempty”, i.e. if a read overlaps with two overlapping genes and the overlap to gene A is greater than the overlap to gene B, the read is counted towards gene A, while if a read overlaps equally with gene A and gene B, then it is not counted towards either gene. Htseq_count does not count reads with multiple alignments to avoid introducing bias in the expression results. Only uniquely mapping reads are counted.
Principal Component Analysis (PCA): Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0 (http://bioconductor.org/packages/release/bioc/html/DESeq.html). PCA (Principal Component Analysis) is performed to assess relation among samples; an empirical permutation-based procedure is used to identify informative principal components. Relation among the samples is visualized as grouping of similar samples together, and separating different samples apart across informative principle components. In this analysis the informative components of the PCA are PC1 and PC2. The samples group very well by treatment, the controls group away from both sample treatment groups, as expected, and the inter-group variability is small. This distinct grouping provides for better comparison of the transcriptomes between the groups.
Differential Expression (DE) Analysis: Two-condition differential expression was done with the edgeR R package, v.3.8.6 (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html). In the filtered data set are retained only genes whose cpm (counts per million reads) is > 0.4 in at least 2 samples (this is intended to remove genes that are not expressed). The method used for normalizing the data was TMM, implemented by the calcNormFactors(y) function. All samples were normalized together, then divided into groups by treatment and analysed.
Genome_build: hg19, RefSeq gene definitions
Supplementary_files_format_and_content: *RPKM_All.txt: Text document files include RPKM values for each Control-vs-Hormone group, filtered and unfiltered results.
Supplementary_files_format_and_content: *_htsqct.txt: Text document files with raw gene counts for every gene and every sample.

source_name: BT474-Breast cancer cell line

growth_protocol: Cells were cultured in the appropriate growth media (phenol-free RPMI-1640 media suppl with 1mM glutamine, 1mM sodium pyruvate, 0.01 mg/mL human recombinant insulin), at 5% CO2 and 37 oC. Then, the cells were transferred in T-25 and cultured until treatment.

extract_protocol:
Total RNA was extracted from the cell lysates using the RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol. Briefly, 350 ng of total RNA was used as the input material. The material was enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94oC and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98oC for 10 seconds, followed by 12 cycles of: 98oC for 10 seconds, 60oC for 30 seconds and 72oC for 30 seconds, and finally an extension step for 5 minutes at 72oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

treatment_protocol: Once cells reached the 80% confluency, they were subjected to starvation for 24 hours using growth media supplemented with 10% charcoal-stripped Fetal Bovine Serum. They were stimulated with 10 nM dihydrotestosterone or progesterone and left for 24 hours.

tag: cell line

value: progesterone


title: BT474 cells-C3_PROG


title: H4r-rep2-HS3-H3ChIP


title: 32246_iris  [Sample_29]


title: BT474 cells-A3_PROG


title: H4r-rep2-NC-H3ChIP

value: non-treated


title: BT474 cells-C2_DHT

value: dihydrotestosterone


title: H4r-rep1-NC-H3ChIP


title: PROseq_Ints9depl_Replicate1

description:
nascent RNA
biotin labeled nascent RNA isolated from Drosophila S2 permeabilized cells
dm3_PROseq_Ints9_N3depth_F.bedGraph
dm3_PROseq_Ints9_N3depth_R.bedGraph


title: PROseq_control_Replicate1

description:
nascent RNA
biotin labeled nascent RNA isolated from Drosophila S2 permeabilized cells
dm3_PROseq_Lz_N3depth_F.bedGraph
dm3_PROseq_Lz_N3depth_R.bedGraph


title: 32245_iris  [Sample_26]

value: iris & ciliary body


title: 32230_cornea  [Sample_25]

value: 6.5 weeks


title: BT474 cells-B2_DHT


title: 32230_iris  [Sample_24]


title: BT474 cells-A2_DHT


title: BT474 cells-C1_EtOH

value: ethanol (control)


title: BT474 cells-B1_EtOH


title: H4r-rep1-HS-FLAGChIP

value: Brain


title: 32229_iris  [Sample_21]


title: BT474 cells-A1_EtOH


title: H4r-rep2-NC-FLAGChIP

value: w; 3xFlag-H4r


title: 32228_cornea  [Sample_20]

value: New Zealand white rabbit


title: PROseq_control_Replicate2


title: H4r-rep1-NC-FLAGChIP


title: 32245_cornea  [Sample_27]

value: cornea


title: ATAC_Naive_rep3

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops). Barcoded nuclei in a biological sample are divided into 2-3 tubes and their libararies are prepared and sequenced separately, which are then added together for each sample informatically after mapping.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
10X Genomics gene expression assay data were demultiplexed and mapped using cellranger
10X Genomics ATAC assay data were demultiplexed and mapped using cellranger-atac
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts tables from each sample were then combined by their respective experiment into the raw counts files available in GEO

organism: Mus musculus

source_name: Trigeminal ganglia

extract_protocol:
For snRNA-seq data, mouse trigeminal ganglia were dissociated into a single nuclei suspension as described in Renthal et al. 2020 and Yang et al. 2021. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020. For snATAC-seq samples, TG were collected using a non-gradient protocol described previously (Slyper et al., 2020), and GFP+ nuclei were sorted and collected using FACS.
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017. 10X Genomics gene expression assay and ATAC assay were prepared according to the user manuals.

tag: strain/genotype

value: Vglut2-Cre; Sun1-GFP

tag: Sex

value: pooled male and female

tag: assay

value: 10X Genomics ATAC assay

tag: headache model

value: Naive


title: 32228_iris  [Sample_19]


title: H4r-rep2-HS3-FLAGChIP

value: heat-shocked and regenerated


title: H4r-rep1-HS3-FLAGChIP


title: 32222_cornea  [Sample_18]

value: 5 weeks

value: unoperated


title: ATAC_Naive_rep2


title: Day 110 hStrO from hiPSC-7-2(scRNA-seq)

city: Shanghai

first: Lixiang

last: Ma

address: Dong'an road No.130

department: School of Basic Medical Sciences

country: China

institute: Fudan University

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw-count
Supplementary_files_format_and_content: matrix

source_name: human striatal organoids

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent cording the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).All the remaining procedures of single cell including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain Organoids

tag: tag

value: striatum

value: CAGs 59


title: H4r-rep2-HS-FLAGChIP

value: heat-shocked


title: 32229_cornea  [Sample_22]

value: 6.5 weeks

value: operated


title: amiR-SUL ab57_Rep3_sRNA

city: Shenzhen

first: Xuemei

last: Chen

state: Guangdong

address: Nanhai Road 3688

institute: Shenzhen University

description: amiR-SUL ab57_Rep3

data_processing:
The data analysis was performed the pRNASeqTools pipeline (https://github.com/grubbybio/pRNASeqTools).
The raw reads were aligned to the TAIR10 genome using ShortStack.
Normalization was performed by calculating the RPMR (reads per million of 45S rRNA reads) value.
For AGO1 IP sRNA-Seq, normalization was performed by calculating the reads per million mapped reads (RPM)
Differentially expressed genes (DEGs) were identified between amiR-SUL and amiR-SUL ab57 mutant samples with 1.5 fold-change cutoff as well as P<0.01 by DESeq2. All DEGs were plotted using the value of log2 (RPMR).
Differentially expressed genes (DEGs) were identified among Col_input,ab57_input, Col-AGO1 IP and ab57_AGO1 IP samples with 1.5 fold-change cutoff as well as P<0.01 by DESeq2. All DEGs were plotted using the value of log2 (RPM).
Genome_build: Arabidopsis thaliana (assembly TAIR10)
Supplementary_files_format_and_content: wig, bw

organism: Arabidopsis thaliana

source_name: amiR-SUL ab57_15d-old seedlings

growth_protocol: All seeds were grown on petri dishes containing 1/2 Murashige and Skoog Basal Medium (Sigma-Aldrich, M5519) plus 2% Sucrose and 0.8% Agar. All plants were grown under 16 h light (22°C)/8 h dark (18°C) period in growth chambers at a light intensity of 120–150 μmolm−2 s−1.

extract_protocol:
Total RNAs were isolated from 15-day-old seedlings with TRI reagent (Molecular Research Center, TR118).
Total RNA extracted from 15-day-old seedlings of both wild type and mutants. For library construction, 30μg total RNA were resolved on a 15% polyacrylamide gel with 8M urea. Small RNAs in the 15-40 nt size range were recovered as described (Liu et al., 2012). Small RNA libraries were prepared using the library preparation kit (NEB, E7100), and sequenced with an Illumina HiSeq2500 platform at BerryGenomics, China. For AGO1 IP, 1g of 15-day-old seedlings were grinded in liquid nitrogen and IP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% NP-40, 1x cocktail and 1x PMSF) was added with incubating for 20 min with gently shaking at 4°C. Before immunoprecipitation, the supernatant was incubated with 100μL of dynabeads (Invitrogen, 10002D) for 2h at 4°C. After centrifuge and filtered, the supernatant was used for IP. 50 ul was taken out as input, the rest were incubated with AGO1 antibody (Agrisera, AS09527) for 2 h at 4 ℃. The beads were washed with wash buffer (IP buffer with 0.5% NP-40), 1/10 volume was added 2x SDS-loading buffer for western blots and 9/10 volume was for RNA isolation. And the small RNA libraries were prepared using the library preparation kit (NEB, E7100), and sequenced with an illumina Nextseq platform at BerryGenomics, China.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: amiR-SUL ab57

value: 15-day-old seedlings


title: Day 80 hStrO from hiPSC-12-4 (Bulk RNA-seq) 3

description:
H12_4_hStrO_80_3
H12_4.7_2.count.matrix.xls

value: CAGs 55


title: ATAC_Naive_rep1

value: Vglut2-Cre; Sun1-GFP

value: Male


title: 32222_iris  [Sample_17]

value: New Zealand white rabbit

value: iris & ciliary body


title: Day 80 hStrO from hiPSC-12-4 (Bulk RNA-seq) 2

description:
H12_4_hStrO_80_2
H12_4.7_2.count.matrix.xls


title: amiR-SUL ab57_Rep2_sRNA

description: amiR-SUL ab57_Rep2


title: 32221_cornea  [Sample_15]

value: cornea


title: Naive_female_rep1

molecule: polyA RNA

value: Female

value: 10X Genomics gene expression assay

value: Naive


title: 32221_iris  [Sample_14]

value: 5 weeks

value: unoperated


title: lung cancer_H322m_strained_0hr

city: Taoyuan City

first: TSAI

middle: CHI

last: LIU

address: No. 300, Zhongda Rd., Zhongli District,

department: Department of Biomedical Sciences and Engineering

country: Taiwan

institute: National Central University

description: Gene expression data from lung cancer cell lines were subjected to chronic cyclic strain in a strain cell culture device for 0h.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. The hybridized arrays were washed and stained in the Affymetrix Fluidics Station for GeneChip450.

scan_protocol: GeneChips were scanned with the Scanner GCS3000 (Affymetrix).

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: H322m cells were subjected to cyclic strain for 0 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All lung cell lines were seeded to the portable strain chambers, and then placed into the Strain Cell Culture Device at 37 °C in an incubator. After cells were subjected to cyclic strain according to the different strain condition.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen). All the procedures were performed according to the manufacturers’ instructions.

treatment_protocol: Pellet the appropriate number of cells by centrifuging for 5 min at 300 x g in a centrifuge tube. Carefully remove all cell-culture medium by aspiration. Pellet were washed with PBS two times and then placed on ice.

value: lung

value: non-small cell lung cancer

tag: strain condition

value: 15% surface distension, 0.5Hz


title: Day 80 hStrO from hiPSC-12-4 (Bulk RNA-seq) 1

description:
H12_4_hStrO_80_1
H12_4.7_2.count.matrix.xls

value: Brain Organoids

value: striatum


title: amiR-SUL ab57_Rep1_sRNA

description: amiR-SUL ab57_Rep1

value: Columbia

value: amiR-SUL ab57

value: 15-day-old seedlings


title: Day 80 hStrO from hiPSC-7-2 (Bulk RNA-seq) 3

description:
H7_2_hStrO_80_3
H12_4.7_2.count.matrix.xls

value: CAGs 59


title: Naive_female_rep2


title: lung cancer_H322m_strained_24hr

description: Gene expression data from lung cancer cell lines were subjected to chronic cyclic strain in a strain cell culture device for 24h.

source_name: H322m cells were subjected to cyclic strain for 24 h


title: lung cancer_A549_strained_0hr

source_name: A549 cells were subjected to cyclic strain for 0 h

value: carcinoma


title: lung cancer_H322m_strained_4hr

description: Gene expression data from lung cancer cell lines were subjected to chronic cyclic strain in a strain cell culture device for 4h.

source_name: H322m cells were subjected to cyclic strain for 4 h


title: 32220_cornea  [Sample_13]

value: New Zealand white rabbit


title: lung cancer_A549_strained_24hr

source_name: A549 cells were subjected to cyclic strain for 24 h


title: LA Baf53b siRNA rep2

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Fastq files were generated using bcl2fastq (v2.19.1.403)
The sequenced reads were aligned using TopHat (v2.1.1; --no-novel-juncs, --library-type fr-firststrand) to mm10 (Gencode vM13).
Each gene was quantified by Cufflinks(v2.2.1; --library-type fr-firststrand)
FPKM values of all samples from gene.fpkm_tracking (Cufflinks outputs) are merged.
Genome_build: mm10

source_name: lateral amygdala

extract_protocol:
Lateral amygdala tissues from 4 mice were dissected, flash frozen on dry ice, and RNA was harvested using QIAGEN RNeasy lipid tissue mini kit (Cat#74804). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were constructed using the Illumina Truseq Stranded mRNA LP kit. Briefly, mRNA was purified by oligo-dT beads and fragmented through enzymatic reaction. After fragmentation, through reverse transcription, cDNA was generated. The cDNA libraries were constructed and followed by paired-end sequencing by Illumina Nextseq 550 platform.

tag: strain

value: 129xC57BL/6 hybrid

value: lateral amygdala

value: 2-3 months old

value: male


title: amiR-SUL_Rep3_sRNA

source_name: amiR-SUL_15d-old seedlings

value: amiR-SUL

tag: tissue


title: lung cancer_A549_strained_4hr

source_name: A549 cells were subjected to cyclic strain for 4 h


title: LA Baf53b siRNA rep1


title: normal_BEAS-2B_strained_0h

description: Gene expression data from normal lung cell lines were subjected to chronic cyclic strain in a strain cell culture device for 0h.

source_name: BEAS-2B cells were subjected to cyclic strain for 0 h

value: normal epithelial cells


title: 32220_iris  [Sample_12]

value: iris & ciliary body

value: 5 weeks

value: unoperated


title: Day 80 hStrO from hiPSC-7-2 (Bulk RNA-seq) 2

description:
H7_2_hStrO_80_2
H12_4.7_2.count.matrix.xls

value: Brain Organoids


title: LA scrambled siRNA rep2


title: Day 80 hStrO from hiPSC-7-2 (Bulk RNA-seq) 1

description:
H7_2_hStrO_80_1
H12_4.7_2.count.matrix.xls

value: striatum


title: LA scrambled siRNA rep1


title: 32217_cornea  [Sample_11]

value: cornea

value: operated


title: 32217_iris  [Sample_10]


title: corresponding paracancer tissues of patient 4

city: Jinhua

first: Pu

last: Wu

address: No. 365 Renmin East Road, Jinhua 321000

institute: Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua

description: PTC patient

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.  After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into five parts by the horizontal line  1) Prefix - All tRF & tiRNA ID start with the prefixe 'tRF' or 'tiRNA' that stands for 'tRNA related fragments' or 'tRNA halves'.  2) Position - The second part includes the start and end positions of the tRF & tiRNA relative to the source tRNA. The two positions are separated by a colon. The standard Sprinzl tRNA position numbering is used. If the position is located at the leader or trailer sequence of the precursor tRNA gene, the numbering will be preceded with a letter 'L' or 'T' respectively. For example, L3 stands for position - 3 and T5 stands for position +5 of the source tRNA gene.  3) Source tRNA - This is the name of the tRNA from which the tRF & tiRNA are derived. tRNA names from Genomic tRNA Database or the results predicted by tRNAscan-SE are used. If the tRF& tiRNA are derived from a mature tRNA transcript, only the isotype, anticodon, and transcript ID will be included as in the figure above. If the tRF is derived from a pre-tRNA gene that has unique leader or trailer sequence, the gene copy number will also be included, for example, Val-AAC-1-2.  4) Matching tRNA transcripts - A tRF & tiRNA may be derived from multiple tRNAs due to identical sequence in some parts of different tRNA transcripts. If this occurs, an optional component with prefix 'M'and the number of matching tRNAs will be added to the tRF & tiRNA ID.  5) Mismatch - Comma-separated list of mismatch descriptors. If there are no mismatches in the alignment between the tRF & tiRNA and the source tRNA, this field is empty. A single descriptor has the format offset:reference-base>read-base. The offset is expressed as a 0-based offset from the high-quality (5') end of the read. (note: this field can only occur in tRF-1, tRF-3a/b and tiRNA-3)
The differentially expressed tRFs & tiRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Heat Map and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: text file with abundance

source_name: thyroid gland

extract_protocol:
Total RNAs that were extracted from tissues were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.
The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.

value: thyroid gland

tag: group

value: Control group


title: amiR-SUL_Rep1_sRNA

value: Columbia

value: 15-day-old seedlings


title: LA Control rep2

value: 129xC57BL/6 hybrid


title: Day 60 hStrO from hiPSC-12-4(Bulk RNA-seq) 3

description:
12_4_hStrO_60_3
hStrO_12_4.7_2.count.matrix.xls

value: CAGs 55


title: Day 60 hStrO from hiPSC-12-4(Bulk RNA-seq) 2

description:
12_4_hStrO_60_2
hStrO_12_4.7_2.count.matrix.xls


title: corresponding paracancer tissues of patient 3

description: PTC patient


title: Day 60 hStrO from hiPSC-12-4(Bulk RNA-seq) 1

description:
12_4_hStrO_60_1
hStrO_12_4.7_2.count.matrix.xls


title: corresponding paracancer tissues of patient 2

description: PTC patient


title: 32216_cornea  [Sample_8]

source_name: cornea

value: New Zealand white rabbit


title: 32216_iris  [Sample_7]


title: amiR-SUL_Rep2_sRNA


title: Day 60 hStrO from hiPSC-7-2 (Bulk RNA-seq) 3

description:
7_2_hStrO_60_3
hStrO_12_4.7_2.count.matrix.xls

value: CAGs 59


title: PIM3

city: Cambridge

first: Julie

last: Takagi

state: CA

address: 70 Massachusetts Ave, 56-230

institute: MIT

data_processing:
For mucin RNA sequencing experiments, reads were mapped to the C. albicans SC5314 haplotype A genome, version A22-s05-m05-r03, retrieved from the Candida Genome Database (www.candidagenome.org) using Rsubread v1.28.180.   Differential expression analysis was performed using limma v3.34.983 with voom-transformed read counts. Genes were considered differentially expressed when P<0.05 after the false-discovery rate was controlled85.
Read summarization was performed on the gene level using featureCounts81 using annotations from a modified version of C. albicans SC5314 haplotype A, which only contained protein coding genes.
Multimapping read pairs, read pairs mapping across more than one gene, and read pairs in which ends mapped to different chromosomes were removed from downstream analyses.
Genes that had <10 counts per million in at least two samples were discarded. Remaining gene counts were normalized using trimmed mean of M-values.
Differential expression analysis was performed using limma v3.34.983 with voom-transformed read counts. Genes were considered differentially expressed when P<0.05 after the false-discovery rate was controlled.
Genome_build: Candida albicans SC5314

organism: Candida albicans

source_name: Planktonic fungal cultures

growth_protocol: Batch cultivation of Candida albicans was carried out shaking at 37 °C in RPMI media. Overnight cultures were grown in YEPD and washed three times in PBS. 10uL of the overnight culture was inoculated in  1mL of RPMI medium with or without (0.5%) MUC5AC, (0.5%) MUC5B, (0.5%) MUC2,  and grown for 8 h at 37 °C in shaking conditions.

extract_protocol:
RNA was extracted using the Epicentre MasterPure Yeast RNA Purification Kit and treated with Sigma-Aldrich AMPD1 amplification-grade DNase I.
TruSeq Stranded mRNA LT Sample Prep for the sample prep. Libraries were tested on the bioanalyzer and  sequenced using MiSeq, 150bp, paired end reads.

tag: agent


title: PTC tissues of patient 4

description: PTC patient

value: Disease group


title: 32215_cornea [Sample_5]

tag: breed


title: PGM3


title: Day 60 hStrO from hiPSC-7-2 (Bulk RNA-seq) 2

description:
7_2_hStrO_60_2
hStrO_12_4.7_2.count.matrix.xls


title: Day 60 hStrO from hiPSC-7-2 (Bulk RNA-seq) 1

description:
7_2_hStrO_60_1
hStrO_12_4.7_2.count.matrix.xls


title: PTC tissues of patient 3

description: PTC patient


title: corresponding paracancer tissues of patient 1

description: PTC patient


title: PGM2


title: PGM1


title: FGF Xentrop replicate  3

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Reads were aligned against reference genome using STAR software
Genome_build: Xenopus_tropicalis_v9.1 for Xenopus tropicalis and Ptychodera flava ver. V3.0 for Ptychodera flava
Supplementary_files_format_and_content: Tables of abundances were computing using the kallisto software, which contain Transcripts per Million normalized counts

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: embryos were treated with the antagonists for FGF pathway from late blastula (stage 9) to late gastrula stage (stage 12).

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen)

tag: developmental stage


title: RNA-seq in zebrafish, Wnt treatment, replicate 3

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Wnt_rep3

data_processing:
Reads were aligned against reference genome using STAR software, and assigned to genes using HTSeq.
Genome_build: Amphioxus Bl71 (Marlètaz et al., 2018. Nature 564:64-70. doi: 10.1038/s41586-018-0734-6), Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Read counts per transcript

organism: Danio rerio

source_name: RNA-seq in zebrafish, Wnt treatment

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol: Embryos were fixed in RNAlater (Thermo Fisher Scientific) and RNA extracted using RNeasy Mini Kit (Qiagen)

value: 80% epiboly

tag: treatment

value: Wnt treatment

value: whole embryo


title: 32215_iris [Sample_4]

source_name: iris & ciliary body

value: iris & ciliary body

tag: age

value: 5 weeks

tag: tissue treatment

value: unoperated


title: RNA-seq in zebrafish, Wnt treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Wnt_rep2


title: LA Control rep1

value: lateral amygdala

value: 2-3 months old

value: male


title: FGF Xentrop replicate  1


title: PTC tissues of patient 2

description: PTC patient

value: thyroid gland


title: 32213_iris  [Sample_1]

value: operated


title: HSM2


title: Unsort control-rep2 [A03]

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

data_processing:
The raw data was analyzed by MAGeCK (Li et al., 2014)
Supplementary_files_format_and_content: sgRNA rank and gene rank text files

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in Dulbecco’s modified Eagle’s medium(DMEM) (ATCC) supplemented with 10% fetal bovine serum(ATCC) and 1% Penicillin-Streptomycin(Gibco) and maintained in a 5% CO2 incubator at 37 °C.

extract_protocol:
Sorted cells were lysed in STE buffer (10mM Tris pH8.0, 100mM NaCl, 1mM EDTA, 0.4%SDS, 0.2mg/mL Proteinase K). 5µL RNaseA (2mg/mL) was added after Proteinase K reaction. Lysate were then separated by phenol-chloroform-isoamyl alcohol (PCI) and the aqueous layer was collected for ethanol precipitation. Precipitated DNA was resuspended in 30uL H2O. Unsorted cells were lysed in Tissue & Cell Lysis Solution (Lucigen) and the protein was removed by centrifuge after adding MPC Protein Precipitation Solution. The supernatant was collected, precipitated by isopropanol, and resuspended by 1.2mL H2O/3x10^7 cells.
Guides were amplified from genomic DNA by ExTaq following the protocol from previously published work(Sanson et al., 2018). PCR product was purified by AMPure XP.

treatment_protocol: Cells were incubated with 3µM snap-cell TMR-STAR(NEB) in complete medium for 30min at 37°C to label pre-existing ribosomes. After labeling, cells were washed 3 times with complete medium and incubated with complete medium for 30min to remove unreacted snap substrate. Cells were then grown in complete medium for 24h. At the time of blocking, cells were incubated with 20µM snap-cell Block (NEB) in complete medium for 30min at 37°C to block unlabeled snap-tag. After blocking, cells were washed 2 times with complete medium and were grown in complete medium until Oregon green labeling. At the time of new ribosome labeling, cells were incubated with 5µM snap-cell Oregon Green (NEB) in complete medium for 30min at 37°C to label newly synthesized ribosomes. After labeling, cells were washed 3 times with complete medium and incubated with complete medium for 30min to remove unreacted snap substrate. The chase starts at the time of the final medium change.

tag: cell type

tag: cell population

value: Unsorted cells, control for CRISPR screen


title: PTC tissues of patient 1

description: PTC patient


title: HSM3


title: Unsort control-rep1 [A03]


title: PIM1


title: RNA-seq in zebrafish, Wnt treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Wnt_rep1


title: RNA-seq in zebrafish, RA treatment, replicate 3

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_RA_rep3

source_name: RNA-seq in zebrafish, RA treatment

value: RA treatment


title: HSM1


title: High Old/new-rep2 [A01]

value: Sorted cells with high red signal(old ribosome) and low green signal(new ribosome)


title: Nodal Xentrop replicate 3

growth_protocol: embryos were treated with the antagonists for  Nodal pathway from late blastula (stage 9) to late gastrula stage (stage 12).


title: Nodal Xentrop replicate 2


title: Nodal Xentrop replicate 1


title: RPMI2

description: media

value: media


title: DMSO Xentrop replicate 3

growth_protocol: embryos were treated with DMSO from late blastula (stage 9) to late gastrula stage (stage 12).

value: DMSO


title: FGF Xentrop replicate  2


title: RNA-seq in zebrafish, RA treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_RA_rep1


title: RPMI3

description: media


title: RNA-seq in zebrafish, RA treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_RA_rep2


title: RNA-seq in zebrafish, Nodal treatment, replicate 3

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Nodal_rep3

source_name: RNA-seq in zebrafish, Nodal treatment

value: Nodal treatment


title: SW480 cells at pH 6.6, replicate 2

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

description:
NextSeq500 in SW480 cells at pH 6.6, replicate 2
JM_22_2_rra_corr.gene_summary.txt
JM_22_2_rra_corr.sgrna_summary.txt
drugz-output_22_2.txt
2BC-rep2

data_processing:
Data were analyzed using MaGeck pipeline. Version downloaded: liulab-mageck-0.5.9.2.tar.gz
FASTQ files were downloaded from CRISPRCloud2, merged and processed by MAGeCK-VISPR
Pairwise gene hits were identified by MaGeCK RRA
Quality-control and assignment of beta score levels were performed by FlutemMLE
DrugZ was used to identify chemogenic interactions and rank hits by z-score
JM_22_2_rra_corr.sgrna_summary.txt:
Control is 22 (bicarbonate), i.e., physiological pH
Treatment is 2 (bicarbonate), i.e., acid pH
JM_22_5_rra_corr.sgrna_summary.txt:
Control is 22 (bicarbonate), i.e., physiological pH
Treatment is 5 (bicarbonate), i.e., mildly acid pH

source_name: SW480 colorectal cancer cells

growth_protocol: SW480 cells were infected with TKO v3 virus library with a target MOI of 0.3 After puromycin selection, 3 million cells per 15 cm-dish were seeded and were incubated with 32 mL medium (NaHCO3-free DMEM D7777) containing either 22 mM, 5.5 mM or 2.75 mM sodium bicarbonate (equilibrated in 5% CO2 to pHe 7.4, 6.9 and 6.63) supplemented with various concentrations of NaCl to maintain constant osmolarity. The cells were exposed to different pH levels for 11 days. The screen was carried out in duplicate, independent experimental setups.

extract_protocol:
Genomic DNA (gDNA) was purified from two infection replicates from each of the three pHe conditions (pHe 7.4, pHe 6.9 and pHe 6.63). PCR of gDNA to attach Illumina sequencing adapters and sample barcodes was performed using the TKO v3 protocol
DNA libraries were constructed according to the TKO v3 protocol. Samples were sequenced on a NextSeq 500 using a 75 cycles NextSeq 500/550 High Output Kit v2.5 (Illumina 20024906).

treatment_protocol: Following infection with TKO v.3 library, cells were incubated in 2.75 mM NaHCO3-containing medium for 11 days

tag: cell line

value: colorectal cancer cells

tag: infection

value: infection with TKO v.3 library


title: RPMI1

description: media


title: SW480 cells at pH 6.9, replicate 2

description:
NextSeq in SW480 cells at pH 6.9, replicate 2
JM_22_5_rra_corr.gene_summary.txt
JM_22_5_rra_corr.sgrna_summary.txt
drugz-output_22_5.txt
5BC-rep2

treatment_protocol: Following infection with TKO v.3 library, cells were incubated in 5.5 mM NaHCO3-containing medium for 11 days


title: RNA-seq in zebrafish, Nodal treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Nodal_rep2

value: 80% epiboly

value: whole embryo


title: SW480 cells at pH 7.4, replicate 2

description:
NextSeq500 in SW480 cells at pH 7.4, replicate 2
JM_22_2_rra_corr.gene_summary.txt
JM_22_2_rra_corr.sgrna_summary.txt
drugz-output_22_2.txt
22BC-rep2

treatment_protocol: Following infection with TKO v.3 library, cells were incubated in 22 mM NaHCO3-containing medium for 11 days


title: Nodal PtyFlav replicate 3

organism: Ptychodera flava

growth_protocol: embryos were treated with SB505124 (Nodal antagonist) at the late blastula stage (18 hpf) and collected at the lategastrula stage (43 hpf) for RNA-seq


title: RNA-seq in zebrafish, Nodal treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Nodal_rep1


title: RNA-seq in amphioxus, Wnt treatment, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Wnt_rep3

organism: Branchiostoma lanceolatum

source_name: RNA-seq in amphioxus, Wnt treatment

value: Wnt treatment


title: RNA-seq in zebrafish, FGF treatment, replicate 3

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_FGF_rep3

source_name: RNA-seq in zebrafish, FGF treatment

value: FGF treatment


title: RNA-seq in zebrafish, FGF treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_FGF_rep2


title: FGF PtyFlav replicate 3

growth_protocol: embryos were treated with  SU5402 (FGF antagonist) at the late blastula stage (18 hpf) and collected at the lategastrula stage (43 hpf) for RNA-seq


title: SW480 cells at pH 6.6, replicate 1

description:
NextSeq500 in SW480 cells at pH 6.6, replicate 1
JM_22_2_rra_corr.gene_summary.txt
JM_22_2_rra_corr.sgrna_summary.txt
drugz-output_22_2.txt
2BC-rep1


title: Nodal PtyFlav replicate 1


title: SW480 cells at pH 6.9, replicate 1

description:
NextSeq in SW480 cells at pH 6.9, replicate 1
JM_22_5_rra_corr.gene_summary.txt
JM_22_5_rra_corr.sgrna_summary.txt
drugz-output_22_5.txt
5BC-rep1


title: RNA-seq in amphioxus, Wnt treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Wnt_rep2


title: High Old/new-rep1 [A01]


title: SW480 cells at pH 7.4, replicate 1

description:
NextSeq500 in SW480 cells at pH 7.4, replicate 1
JM_22_2_rra_corr.gene_summary.txt
JM_22_2_rra_corr.sgrna_summary.txt
drugz-output_22_2.txt
22BC-rep1


title: RNA-seq in zebrafish, FGF treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_FGF_rep1


title: DMSO Xentrop replicate 1


title: Nodal PtyFlav replicate 2


title: FGF PtyFlav replicate 2


title: RNA-seq in amphioxus, RA treatment, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_RA_rep3

source_name: RNA-seq in amphioxus, RA treatment


title: RNA-seq in amphioxus, Wnt treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Wnt_rep1


title: Day 110 hStrO from hiPSC-8-12(scRNA-seq) Str8_12

description:
Day 110 hStrO from hiPSC-8-12(scRNA-seq)
scRNA

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw-count

source_name: hiPS cell line

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent cording the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).All the remaining procedures of single cell including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3).
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq and ScRNA-Seq

value: Brain Organoids

tag: structure

value: striatum


title: RNA-seq in zebrafish, control sample, replicate 3

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Control_rep3

source_name: RNA-seq in zebrafish, control sample

value: control sample


title: DMSO Xentrop replicate 2


title: FGF PtyFlav replicate 1


title: Day 110 hStrO from hESC-H9(scRNA-seq) StrH9

description:
Day 110 hStrO from hESC-H9(scRNA-seq)
scRNA

source_name: hES cell line


title: RNA-seq in amphioxus, RA treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_RA_rep2


title: DMSO PtyFlav replicate 3

growth_protocol: embryos were treated with DMSO at the late blastula stage (18 hpf) and collected at the lategastrula stage (43 hpf) for RNA-seq


title: RNA-seq in amphioxus, RA treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_RA_rep1


title: RNA-seq in zebrafish, control sample, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Control_rep2


title: Day 80 hStrO from hiPSC-8-12 (Bulk RNA-seq) H8_12_hStrO_80_3


title: RNA-seq in zebrafish, control sample, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_RNAseq_Control_rep1


title: DMSO PtyFlav replicate 2


title: RNA-seq in amphioxus, Nodal treatment, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Nodal_rep3

source_name: RNA-seq in amphioxus, Nodal treatment


title: RNA-seq in amphioxus, Nodal treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Nodal_rep2


title: Day 80 hStrO from hESC-H9 (Bulk RNA-seq) H9_hStrO_80_2


title: Day 80 hStrO from hiPSC-8-12 (Bulk RNA-seq) H8_12_hStrO_80_1


title: RNA-seq in amphioxus, FGF treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_FGF_rep2

source_name: RNA-seq in amphioxus, FGF treatment


title: RNA-seq in amphioxus, Nodal treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Nodal_rep1


title: WT_3

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Metarhizium robertsii ARSEF 23

source_name: Metarhizium robertsii ARSEF 23

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARSEF 23

value: hyphal

tag: genotype

value: wild type


title: Day 80 hStrO from hESC-H9 (Bulk RNA-seq) H9_hStrO_80_3


title: Day 60 hStrO from hiPSC-8-12 (Bulk RNA-seq) hStrO_8_12_60_3


title: Day 80 hStrO from hESC-H9 (Bulk RNA-seq) H9_hStrO_80_1


title: RNA-seq in amphioxus, FGF treatment, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_FGF_rep3


title: RNA-seq in amphioxus, FGF treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_FGF_rep1


title: WT_2


title: ATAC-seq in zebrafish, Wnt treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Wnt_rep2
Danrer_ATAC_Wnt_IDR_peaks.bed

data_processing:
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Amphioxus Bl71 (Marlètaz et al., 2018. Nature 564:64-70. doi: 10.1038/s41586-018-0734-6), Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework

source_name: ATAC-seq in zebrafish, Wnt treatment

extract_protocol:
Wild type embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109


title: ATAC-seq in zebrafish, Nodal treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Nodal_rep2
Danrer_ATAC_Nodal_IDR_peaks.bed

source_name: ATAC-seq in zebrafish, Nodal treatment


title: ATAC-seq in zebrafish, RA treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_ATAC_RA_rep2
Danrer_ATAC_RA_IDR_peaks.bed

source_name: ATAC-seq in zebrafish, RA treatment

value: RA treatment


title: ATAC-seq in zebrafish, Wnt treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Wnt_rep1
Danrer_ATAC_Wnt_IDR_peaks.bed


title: ATAC-seq in zebrafish, Nodal treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Nodal_rep1
Danrer_ATAC_Nodal_IDR_peaks.bed


title: DMSO PtyFlav replicate 1

source_name: whole embryo


title: C1_2

value: cfp1 mutant


title: ATAC-seq in zebrafish, FGF treatment, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_ATAC_FGF_rep2
Danrer_ATAC_FGF_IDR_peaks.bed

source_name: ATAC-seq in zebrafish, FGF treatment


title: WT_1


title: C1_3


title: Day 60 hStrO from hiPSC-8-12 (Bulk RNA-seq) hStrO_8_12_60_1


title: RNA-seq in amphioxus, control sample, replicate 6

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep6

source_name: RNA-seq in amphioxus, control sample


title: RNA-seq in amphioxus, control sample, replicate 5

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep5


title: Day 60 hStrO from hiPSC-8-12 (Bulk RNA-seq) hStrO_8_12_60_2


title: C1_1


title: ATAC-seq in zebrafish, RA treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_ATAC_RA_rep1
Danrer_ATAC_RA_IDR_peaks.bed


title: ATAC-seq in zebrafish, FGF treatment, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_ATAC_FGF_rep1
Danrer_ATAC_FGF_IDR_peaks.bed


title: Day 80 hStrO from hiPSC-8-12 (Bulk RNA-seq) H8_12_hStrO_80_2


title: Day 60 hStrO from hESC-H9 (Bulk RNA-seq) hStrO_H9_60_3


title: RNA-seq in amphioxus, control sample, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep3


title: RNA-seq in amphioxus, control sample, replicate 4

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep4


title: ATAC-seq in zebrafish, control sample, replicate 2

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Control_rep2
Danrer_ATAC_Control_IDR_peaks.bed

source_name: ATAC-seq in zebrafish, control sample


title: ATAC-seq in zebrafish, control sample, replicate 1

description:
Zebrafish (Danio rerio)
Danrer_ATAC_Control_rep1
Danrer_ATAC_Control_IDR_peaks.bed


title: ATAC-seq in amphioxus, Wnt treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Wnt_rep2
Amphi_ATAC_Wnt_IDR_peaks.bed

source_name: ATAC-seq in amphioxus, Wnt treatment

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage

extract_protocol:
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109


title: RNA-seq in amphioxus, control sample, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep1


title: Day 60 hStrO from hESC-H9 (Bulk RNA-seq) hStrO_H9_60_1


title: ATAC-seq in amphioxus, Wnt treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Wnt_rep1
Amphi_ATAC_Wnt_IDR_peaks.bed


title: Kp supernatant + doxorubicin + shp53 rep3

city: Solna

first: Sylvain

last: Peuget

state: Stockholm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institute

data_processing:
Sequenced reads were processed using nf-core/rnaseq pipeline (v1.4 ) and then mapped to GRCh38.97 whole genome using HISAT2 (v2.1.0)
Read quantification was computed using featureCounts (v1.6.4).
Differential analysis was performed with the R package DESeq2
Genome_build: GRCh38.97
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Immortalized fibroblasts

growth_protocol: BJ hTert cells were grown at 37°C in DMEM, 10% FBS supplemented with penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the mirVana miRNA isolation kit according to supplier instructions (Ambion). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. The NGS library pool was analysed on a Shimadzu MultiNA microchip electrophoresis system.
Poly(A)+ RNA was isolated from the total RNA samples. First-strand cDNA synthesis was primed with a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. In this way, a strand specific PCR amplification of the cDNA was achieved using a proof reading enzyme. For Illumina sequencing, the cDNA samples were pooled in approximately equimolar amounts. The library pool was fractionated in the size range of 300-450 bp using a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA pool was paired-end sequenced on an Illumina NextSeq 500 system using 2x150 bp read length.

treatment_protocol: Cells were treated for 8 hours. K. pneumoniae supernatant was used at 1/10 v/v from a bacterial culture of O.D. 2.0 grown in DMEM, 10% FBS

value: BJ hTert shp53

value: K. pneumoniae supernatant and doxorubicin 0.2 μM

value: p53 shRNA


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep1 [mRNA-seq]

city: Baltimore

first: Deqiang

last: Li

state: Maryland

address: 800W Baltimore street

department: Surgery

institute: University of Maryland

data_processing:
For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.6.3). The padj<0.05 was set as the threshold for significantly differential expression by default
Genome_build: mm10

source_name: Epicardial cell line

growth_protocol: MEC cells were incubated by cultured dish (100 mm) in Dulbecco's Modified Eagle Medium, high glucose - Thermo Fisher) medium supplemented with Fetal Bovine Serum.

extract_protocol:
RNA from MEC cells was harvested using Trizol reagent
llumina standard protocols

value: Mouse Epicardial cell (MCEC)

tag: lentivirus transduction

value: Empty vector lentivirus transduction


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep4 [mRNA-seq]

value: Hdac3 sgRNA lentivirus transduction


title: ATAC-seq in amphioxus, RA treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_RA_rep1
Amphi_ATAC_RA_IDR_peaks.bed

source_name: ATAC-seq in amphioxus, RA treatment

value: whole embryo


title: RNA-seq in amphioxus, control sample, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_RNAseq_Control_rep2


title: Mouse Epicardial Cells - Empty vector (EV) - rep4 [mRNA-seq]


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep2 [mRNA-seq]


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep3 [mRNA-seq]


title: Mouse Epicardial Cells - Empty vector (EV) - rep3 [mRNA-seq]


title: Kp supernatant rep3

value: BJ hTert

value: K. pneumoniae supernatant


title: Kp supernatant + doxorubicin rep3


title: Control rep3

value: Untreated (vehicle)


title: Doxorubicin rep3

value: Doxorubicin 0.2 μM


title: Kp supernatant + doxorubicin + shp53 rep2


title: Mouse Epicardial Cells - Empty vector (EV) - rep2 [mRNA-seq]


title: ATAC-seq in amphioxus, Nodal treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Nodal_rep1
Amphi_ATAC_Nodal_IDR_peaks.bed

source_name: ATAC-seq in amphioxus, Nodal treatment

value: Nodal treatment


title: ATAC-seq in amphioxus, RA treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_RA_rep2
Amphi_ATAC_RA_IDR_peaks.bed


title: Kp supernatant + doxorubicin rep2


title: Mouse Epicardial Cells - Empty vector (EV) - rep1 [mRNA-seq]


title: Day 60 hStrO from hESC-H9 (Bulk RNA-seq) hStrO_H9_60_2

value: Brain Organoids

value: striatum


title: ATAC-seq in amphioxus, FGF treatment, replicate 4

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_FGF_rep4
Amphi_ATAC_FGF_IDR_peaks.bed

source_name: ATAC-seq in amphioxus, FGF treatment

value: FGF treatment


title: ATAC-seq in amphioxus, FGF treatment, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_FGF_rep3
Amphi_ATAC_FGF_IDR_peaks.bed


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep3 [miRNA-seq]

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 50bp single-end reads were generated
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3). The P-value of 0.05 was set as the threshold for significantly differential expression by default
Genome_build: mm10

extract_protocol:
RNA from MEC cells was harvested using Trizol reagent
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.


title: Doxorubicin rep2

value: wild type


title: Kp supernatant rep2


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep2 [miRNA-seq]


title: ab57_Rep3 [RNA-seq]

data_processing:
Clean reads were trimmed to remove adapter sequences and mapped to Arabidopsis genome ARAPORT11 using STAR with default setting.
Transcript levels were calculated in FPKM+1
Differentially expressed genes (DEGs) were identified between Col and ab57 mutant samples with 2 fold-change cutoff as well as P<0.05 for filter. All the Genes and DEGs were plotted used the value of log2 (FPKM+1).
Genome_build: Arabidopsis thaliana (assembly ARAPORT11)

source_name: ab57_15d-old seedlings

extract_protocol:
Total RNAs were isolated from 15-day-old seedlings with TRI reagent (Molecular Research Center, TR118).
Total RNA extracted from 15-day-old seedlings of both wild type and mutants were sent to Novogene, China, for mRNA-seq library construction and the libraries were sequenced on an Illumina Hiseq X10 platform to generate single-end reads of 150bp in length.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 15-day-old seedlings


title: Control rep2


title: ATAC-seq in amphioxus, FGF treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_FGF_rep2
Amphi_ATAC_FGF_IDR_peaks.bed

tag: tissue


title: ab57_Rep2 [RNA-seq]


title: Mouse Epicardial Cells - Empty vector (EV) - rep3 [miRNA-seq]


title: ab57_Rep1 [RNA-seq]


title: Mouse Epicardial Cells - Hdac3 Crispr/cas9 Knockout (KO) - rep1 [miRNA-seq]


title: Kp supernatant + doxorubicin rep1

value: K. pneumoniae supernatant and doxorubicin 0.2 μM


title: ATAC-seq in amphioxus, control sample, replicate 4

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Control_rep4
Amphi_ATAC_Control_IDR_peaks.bed

source_name: ATAC-seq in amphioxus, control sample

value: control sample


title: Kp supernatant + doxorubicin + shp53 rep1

value: BJ hTert shp53

value: p53 shRNA


title: Mouse Epicardial Cells - Empty vector (EV) - rep2 [miRNA-seq]

value: Mouse Epicardial cell (MCEC)

value: Empty vector lentivirus transduction


title: Col_Rep3 [RNA-seq]

source_name: Col_15d-old seedlings


title: Doxorubicin rep1

value: BJ hTert


title: ATAC-seq in amphioxus, control sample, replicate 3

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Control_rep3
Amphi_ATAC_Control_IDR_peaks.bed

value: whole embryo


title: ATAC-seq in amphioxus, control sample, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Control_rep2
Amphi_ATAC_Control_IDR_peaks.bed


title: Col_Rep2 [RNA-seq]


title: Kp supernatant rep1

value: K. pneumoniae supernatant


title: Col_Rep1 [RNA-seq]


title: ATAC-seq in amphioxus, control sample, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Control_rep1
Amphi_ATAC_Control_IDR_peaks.bed


title: ATAC-seq in amphioxus, Nodal treatment, replicate 2

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_Nodal_rep2
Amphi_ATAC_Nodal_IDR_peaks.bed


title: Control rep1

value: Untreated (vehicle)


title: ATAC-seq in amphioxus, FGF treatment, replicate 1

description:
Amphioxus (Branchiostoma lanceolatum)
Amphi_ATAC_FGF_rep1
Amphi_ATAC_FGF_IDR_peaks.bed


title: young inflorescences, S1-2

status: Public on Feb 25 2022

city: shanghai

first: zheng

last: Yuan

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 20%;
 Cell Gene Number < 5000;
 Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: IRGSP1.0
Supplementary_files_format_and_content: cellname.list file and counts.tsv.gz file contain counts for each barcode and gene

organism: Oryza sativa Japonica Group

source_name: young inflorescences

growth_protocol: All rice (O. sativa L. ssp. japonica) varieties were planted in the paddy fields of Shanghai Jiao Tong University (30 °N, 121 °E) during the normal growing season (June–September).

extract_protocol:
For protoplast isolation, samples were firstly cut into small pieces with a fresh sharp razor blade, then digested at room temperature in RNase-free enzyme solution [1.5 % (w/v) cellulase R-10, 1 % (w/v) macerozyme R-10 (Yakult), 0.4 M mannitol, 20 mM MES pH 5.7, 20 mM KCl, 10 mM CaCl2, 0.1 % BSA (Sigma-Aldrich)]. Protoplasts were filtered using a 45 μm cell strainer (Biologix), and centrifuged at 200 g for 3 min. After the supernatant was removed, the pellet was washed three times with 8 % (w/v) mannitol, and cell viability was determined by AO/PI (acridine orange/propidium iodide) staining (Countstar® Rigel, ALIT Life Science). Digestion progress was assayed every hour for 6 h, with the optimum time for cell viability and protoplast digestion determined to be 2 h.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.
scRNA-seq

value: young inflorescences

tag: Stage

value: stage 1 (S1)


title: young inflorescences, S1-1


title: Mouse Epicardial Cells - Empty vector (EV) - rep1 [miRNA-seq]


title: oe-HOTTIOP exosomes

first: Huaili

last: Jiang

state: 上海

address: 枫林路180号

institute: 复旦大学

description: miRNA expression in the exosomes derived from oe-NC FaDu cells

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: FaDu cell exosomes

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: FaDu

value: Transfection with HOTTIP overexpression plasmid lentivirus

tag: rna poulation

value: exosome


title: young inflorescences, S2-2

value: stage 2 (S2)


title: leaves, L

source_name: leaves

value: leaves (covering the inflorescence)


title: Microglia pCD11b-shEfnB3 2 Sick

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.7.2) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene

source_name: Microglia

growth_protocol: CNS was harvested and digested with papain and collagenase D, myelin removed by precol gradient and Astrocytes and Microglia were isolated by flow cytometry

extract_protocol:
Arcturus® PicoPure®
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

treatment_protocol: Mice at day 7 after EAE induction where intrathecally injected with the lentiviral vector expressing a control vector (CTRL), a vector to  knockdown  EphB3 specifically in Astrocytes (pGFAP-shEphB3) or a vector to knock down EfnB3 in Microglia (pCD11b-shEfnB3)

tag: strain

tag: disease state

value: undergoing EAE

tag: Sex

value: Female

value: 10 weeks

value: FACS Sorted Microglia from CNS


title: Microglia pCD11b-shEfnB3 1 Sick

tag: age

tag: treatment


title: Microglia pCD11b-shEfnB3 3 Sick

tag: cell type


title: Microglia CTRL4 Sick

value: CTRL


title: Microglia CTRL5 Sick


title: Microglia pGFAP-shEphB3 1 Sick


title: Microglia CTRL3 Sick


title: Microglia pGFAP-shEphB3 3 Sick


title: Microglia pGFAP-shEphB3 4 Sick


title: oe-NC exosomes

description: miRNA expression in the exosomes derived from oe-HOTTIP FaDu cells

value: Transfection with NC plasmid lentivirus


title: Astrocytes pCD11b-shEfnB3 3CFSick

source_name: Astrocytes

value: FACS Sorted Astrocytes from CNS


title: Microglia CTRL1 Sick


title: Astrocytes pCD11b-shEfnB3 2CFSick


title: MDA-MB-134VI_1

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

description: RNA-seq of polyA mRNA from cell lystates

data_processing:
Transcript quantification for each sample was then performed using Kallisto (v0.45.0)  with the GRCh38 build of the human transcriptome and the -b 50 bootstrap option. The R package Sleuth (v0.30.0)  was then used to model gene expression changes between cell lines and the Wald’s test was used to test for differential expression. Gene sets (GO Terms) enriched in the differentially expressed genes (adjusted p < 0.05, |model beta coefficient| > 0.5) were assessed using DAVID (https://david.ncifcrf.gov).
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM Matrix: A matrix containing gene-level transcript quantifications for each sample

extract_protocol:
RNA was isolated from VIVA1 or MDA-MB-134VI cells using the RNeasy Kit (Qiagen, Toronto ON) and RNA concentration in ng/μl determined by measuring absorbance using a ND-1000 Nanodrop Spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  RNAseq was performed at the Biomedical Research Core at the University of British Columbia (Vancouver BC).
RNA quality was confirmed using the Agilent 2100 Bioanalyzer, and then used to generate cDNA libraries following the standard manufacturer’s protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs, Whitby, ON).
Sequencing was performed on the Illumina NextSeq 500 (Illumina, San Diego, CA) with Paired End 42bp × 42bp reads.

value: Invasive Lobular Carcinoma


title: VIVA1_1


title: young inflorescences, S2-1


title: VIVA1_2


title: Microglia pGFAP-shEphB3 2 Sick

city: Boston


title: Astrocytes pGFAP-shEphB3 4GPSick


title: Astrocytes pCD11b-shEfnB3 1CFSick


title: Astrocytes pGFAP-shEphB3 2GPSick


title: JW_02: SCR_02

first: Srinivasa

middle: R

last: Rao

address: Botnar Research Centre, Institute of Musculoskeletal Sciences, Windmill Road, Headington

department: Nuffield Dept. of Surgical Sciences

data_processing:
Base calling was performed using bcl2fastq v2.20 to produce fastq files through demultiplexing of single-indexed raw data
Paired-end reads from fastq files were aligned to the human genome (hg38) using STAR v2.5.3a.
Differential expression analysis was performed comparing two groups scrambled (SCR) and G6PD knockdown (shG6PD) using DESeq2 v1.20 in R statistical software v3.6
Genome_build: hg38
Supplementary_files_format_and_content: CSV format with the gene symbol as the row name and sample names as column names.

source_name: Prostate cancer cell line

growth_protocol: PC3 cells were routinely maintained in RPMI 1640 medium (Sigma, Cat. R0883) supplemented with 10% fetal bovine serum (FBS) (Cat. FCS-SA, Labtech), 1% L-glutamine (Cat. G7513, Sigma), 1% penicillin/streptomycin (Cat. P0781, Sigma), 1% vitamins (Cat. 11120-037, Gibco), 1% sodium pyruvate (S8636, Sigma), 1% non-essential amino acids (Cat. M7145, Sigma) (complete RPMI medium). By maintaining cells in the same culture medium, we avoid any metabolic response to differences in culture conditions. Cells were routinely validated by genotyping and periodically tested to ensure the absence of mycoplasma contamination. All cell lines were maintained at 37˚C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from cultured cells using a RNeasy kit (Cat. 74106, Qiagen) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop 100 spectrophotometer (Thermofisher). Quality of the RNA was assessed by measuring the ratios of absorbance (A260/A280 and A260/A230); ratios greater than 1.8 were considered suitable for further analysis. cDNA synthesis
RNA was DNase I treated, cleaned and concentrated according to the manufacturer’s instructions using Zymo RNA Clean and Concentrator -5 (R1013, Zymo). mRNA was enriched from total RNA according to the manufacturer’s instructions using a NEBnext poly(A) mRNA magnetic isolation module. Firstly mRNA was isolated and fragmented from total RNA using oligo dT beads and a magnetic rack. Beads were mixed with 1μg RNA and then washed twice. Samples were then heated to 65˚C for 5mins before being washed. Tris buffer was added and samples were heated once again to 80˚C and held at 25˚C to perform the first elution of the mRNA from the beads. Beads were subsequently washed and mRNA was eluted and fragmented with the addition of first strand synthesis reaction buffer and random primer mix. Samples were heated to 94˚C for 15 min and held at 4˚C Sequencing libraries were prepared according to the manufacturer’s recommendations using the NEBNext Ultra II RNA Library Prep kit (E7770S, NEB). Briefly, first and second strand cDNA synthesis was performed using mRNA isolated as above. Double strand cDNA was purified using NEBNext sample purification beads, and DNA was eluted in 0.1X TE buffer. End prep reaction and adaptor ligation was performed and purification was done using sample purification beads. RNA and DNA quantification was performed using HS RNA and HS DNA assay kits (Q32852, Q32851, Invitrogen) Qubit fluorometer (Life Tech) according to the manufacturer’s instructions. RNA and DNA quality was determined using High Sensitivity RNA Screentape and D1000 High Sensitivity DNA Screentape respectively on Agilent 4200 tapestation system according to the manufacturer’s instructions. Single-indexed and multiplexed samples were run on an Illumina Next Seq 500 sequencer using a NextSeq 500 v2 kit (150 cycles) (FC-404-2005) for paired-end sequencing (75 bases x 2). Results from RNA-Seq were aligned to the human genome assembly version 38 (hg38 or GRCh38). At least 14 million aligned reads were obtained per sample

treatment_protocol: Short hairpin RNA (shRNA) and Open Reading Frame (ORF) Transfection G6PD MISSION shRNA (TRCN0000281204, TRCN0000281206, TRCN0000281207, G6PD MISSION TRC3 ORF (TRCN000046117), and scrambled control (Cat. SHC002) bacterial glycerol stocks and MISSION BFP TRC3 ORF (ORFBFPV) lentivirus were purchased from Sigma. Colonies were grown on agar with ampicillin (0.1 mg/ml). After 24 hr at 37°C a single colony was picked and grown in LB broth with ampicillin (0.1 mg/ml) overnight on a shaker at 200 RPM. The plasmid was then purified using Qiagen Endofree plasmid purification kit according to the manufacturer’s instructions. Plasmid DNA was eluted in water and purity and concentration were checked using a Nanodrop 100 spectrophotometer. Lentiviral packaging was performed in HEK 293T cells using a 2nd generation packaging system. Briefly, HEK 293T cells were seeded in 100 mm tissue culture dishes (Corning) and incubated at 37°C at 5% CO2 in a humidified incubator until they were ~90% confluent. 10 µg of transfer vector was added to 5 µg psPAX2, 5 µg pMD2.G and 500 µl OptiMEM (Cat. 31985062, Life Technologies). Separately 30 µl Lipofectamine 2000 (Cat. 11668019, Life Technologies,) was added to 500 µl OptiMEM. These were then mixed and incubated at room temperature for 20 min with regular inversion. The transfection solution (1 ml) was then added to the HEK 293T cells in 10 ml of antibiotic-free DMEM media. Plates were incubated at 37°C for 72 hr and culture supernatant containing the lentivirus was collected. Transfection was confirmed at this point by expression of fluorescent protein in the HEK 293T cells transfected with a control fluorescent construct. The supernatant was centrifuged at 4000 RPM for 10 min at 4°C and then filtered through a 0.45 um polyethersulfone (PES) filter. The lentivirus was made into a 10 times concentrated stock using the Lenti-X Concentrator Solution (Cat. 631232, Clontech). The solution was incubated at 4°C overnight before being centrifuged at 1500 g for 45 min at 4°C. The supernatant was then removed and the pellet re-suspended, flash frozen in liquid nitrogen and stored at -80°C. Prostate cancer cells were seeded at 5 x 105 in 6 well plates and treated with 200 µl of virus and 8 µg/ml Polybrene (Cat. H9268, Sigma) to enhance transduction efficiency, and incubated for 72 hr at 37°C.

value: PC3-EGFP prostate cancer cells

tag: shRNA

value: scrambled


title: Astrocytes pGFAP-shEphB3 3GPSick


title: JW_04: ShG6PD_01

tag: cell line

value: G6PD shRNA


title: Astrocytes pGFAP-shEphB3 1GPSick


title: Astrocytes CTRL5 Sick


title: Microglia.EAE.mCherry.positive.1

data_processing:
Reads were aligned against the GRCm38 mouse genome using Kallisto (0.46.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: A compressed file which included the counts data in different format

source_name: Gfap-RABVgp4/TVA mice undergoing EAE that had been transduced with Rab-deltaG-mCherry EnvA pseudotyped a week in advance

growth_protocol: CNS was harvested and digested with papain and collagenase D, myelin removed by precol gradient and Microglia were isolated by flow cytometry

tag: type

value: mCherry+


title: MDA-MB-134VI_2


title: Astrocytes CTRL4 Sick


title: Astrocytes CTRL2 Sick


title: Microglia.EAE.mCherry.positive.2


title: JW_05: ShG6PD_02


title: Microglia CTRL2 Sick


title: Astrocytes CTRL3 Sick


title: Microglia.EAE.mCherry.negative.1

value: mCherry-


title: Microglia.pGFRAPshEphB3.5

description: Microglia pGFAPshEphB3

source_name: mice undergoing progressive model of EAE

treatment_protocol: Mice were transduced twice at day 37 and 44 after EAE induction with either shCtrl vector or pGFAPshEphB3 vector. A38 group was treated twice a day with A38 or control Vehicle starting at day 30 after EAE induction (beginning of progressive phase).

value: NOD/ShiLtJ


title: JW_06: ShG6PD_03


title: Microglia.pGFRAPshEphB3.4

description: Microglia pGFAPshEphB3


title: JW_03: SCR_03


title: input_H4K8ac_mitosis_2

city: Montpellier

first: Maelle

last: Bellec

address: 1919 route de mende

country: France

institute: CNRS

description: ChIP_H4K8ac_mitosis_700000_merge_rep1_rep2.wig

data_processing:
Reads from ChIP-seq and Input experiments were trimmed for quality using a threshold of 20 and filtered for adapters using Cutadapt (v1.16). Reads shorter than 30 bp after trimming were removed. Reads were mapped to Drosophila melanogaster genome (dm6 release) using Bowtie2. Aligned sequences were processed with the R package PASHA to generate the used wiggle files. Pasha elongates in silico the aligned reads using the DNA fragment size estimated from paired-reads. Then, the resulting elongated reads were used to calculate the coverage score at each nucleotide in the genome. Wiggle files representing average enrichment score every 50 bp were generated. In order to normalize the enrichment scores to reads per million, we rescaled the wiggle files using PASHA package. Besides, in order to reduce the over-enrichment of some genomic regions due to biased sonication and DNA sequencing, we subtracted from ChIP sample wiggle files the signal present in Input sample wiggle files. The Rescaled and Input subtracted wiggle files from biological replicate were then used to generate the final wiggle file representing the mean signal.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: wig files

source_name: Wild type yw embryos

growth_protocol: 1-2h30 AEL embryos.

extract_protocol:
1000 embryos per sample.
NEBNext UltraII DNA Library Prep Kit.

treatment_protocol: H3S10ph immuno-staining.

tag: developmental stage

value: 1-2h30 AEL embryos

value: whole body

value: yw

value: Wild type

tag: cell cycle stage

value: mitosis

tag: experiment

value: ChIP-seq

tag: chip antibody


title: Microglia.pGFRAPshEphB3.3

description: Microglia pGFAPshEphB3

value: Female

value: 10 weeks

value: FACS Sorted Microglia from CNS


title: input_H4K8ac_mitosis_1

tag: genotype


title: JW_01: SCR_01

value: scambled


title: Microglia.EAE.mCherry.negative.2


title: input_H4K8ac_interphase_1

description: ChIP_H4K8ac_interphase_700000_merge_rep1_rep2.wig

tag: tissue

value: interphase


title: Microglia.pGFRAPshEphB3.2

description: Microglia pGFAPshEphB3


title: Microglia.pGFRAPshEphB3.1

description: Microglia pGFAPshEphB3


title: ChIP_H4K8ac_interphase_1

description:
Immunostained with H3S10ph for sorting.
ChIP_H4K8ac_interphase_700000_merge_rep1_rep2.wig

value: anti-H4K8ac (abcam 15823)


title: ChIP_H4K8ac_interphase_2


title: ChIP_H4K8ac_mitosis_2

description:
Immunostained with H3S10ph for sorting.
ChIP_H4K8ac_mitosis_700000_merge_rep1_rep2.wig


title: ChIP_H4K8ac_mitosis_1


title: input_H4K8ac_interphase_2


title: Microglia.shCTRL.5

description: Microglia Control

value: shCTRL


title: input_GAF_mitosis_2

description: ChIP_GAF_mitosis_700000_merge_rep1_rep2.wig


title: input_GAF_interphase_3

description: CHIP_GAF_interphase_700000_merge_rep1_rep2_rep3.wig


title: Microglia.shCTRLplusA38.6

description: Microglia A38

value: shCTRL + A38


title: input_GAF_interphase_2


title: Microglia.shCTRLplusA38.1

description: Microglia A38


title: Microglia.shCTRLplusA38.4

description: Microglia A38


title: Microglia.shCTRLplusA38.2

description: Microglia A38


title: Astrocytes CTRL1 Sick

value: undergoing EAE

value: CTRL

value: FACS Sorted Astrocytes from CNS


title: Microglia.shCTRL.3

description: Microglia Control

value: NOD/ShiLtJ


title: ChIP_GAF_mitosis_2

description:
Immunostained with H3S10ph for sorting.
ChIP_GAF_mitosis_700000_merge_rep1_rep2.wig

value: 1-2h30 AEL embryos

value: whole body

value: anti-GAF (G. Cavalli Lab)


title: input_GAF_mitosis_1

value: yw

value: Wild type

value: mitosis


title: Microglia.shCTRL.1

description: Microglia Control

value: Female

value: 10 weeks


title: CHIP_GAF_interphase_3

description:
Immunostained with H3S10ph for sorting.
CHIP_GAF_interphase_700000_merge_rep1_rep2_rep3.wig

value: ChIP-seq


title: Microglia.shCTRL.2

description: Microglia Control

value: FACS Sorted Microglia from CNS


title: Microglia.shCTRLplusA38.5

description: Microglia A38


title: ChIP_GAF_interphase_1

value: interphase


title: Microglia.shCTRLplusA38.3

description: Microglia A38


title: Astrocytes.pGFRAPshEphB3.5

description: Asctrocyte pGFAPshEphB3


title: ChIP_GAF_interphase_2


title: Astrocytes.pGFRAPshEphB3.3

description: Asctrocyte pGFAPshEphB3


title: Astrocytes.pGFRAPshEphB3.4

description: Asctrocyte pGFAPshEphB3


title: Microglia.shCTRL.4

description: Microglia Control

value: shCTRL


title: MCF-7 YAP Treatment

first: Xu

address: 6000 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
Demultiplexing by CASAVA
Bowtie2 for Genomic Mapping
Remove duplicates by PICARD
peak-calling by MACS2
HOMER for Annotate Peaks
Genome_build: hg19

source_name: MCF-7 cells

growth_protocol: high glucose DMEM + 10% FBS

extract_protocol:
Qiagen PCR kit
KAPA Kit

treatment_protocol: 3um XMU-MP-1 6 hours

value: MCF-7 cells

tag: antibody

value: YAP


title: Astrocytes.shCTRLplusA38.4

description: Astrocyte A38

value: shCTRL + A38


title: Astrocytes.shCTRLplusA38.5

description: Astrocyte A38

value: FACS Sorted Astrocytes from CNS


title: MCF-7 TEAD Control

value: DMSO

value: TEAD


title: Astrocytes.shCTRLplusA38.3

description: Astrocyte A38

value: NOD/ShiLtJ


title: Astrocytes.shCTRLplusA38.2

description: Astrocyte A38


title: MCF-7 ER Treatment

value: ER


title: MCF-7 TEAD Treatment


title: MCF-7 YAP Control


title: Astrocytes.shCTRLplusA38.6

description: Astrocyte A38


title: input_GAF_interphase_1

value: 1-2h30 AEL embryos

value: whole body

value: yw


title: ChIP_GAF_mitosis_1

value: Wild type

value: mitosis

value: anti-GAF (G. Cavalli Lab)


title: Astrocytes.shCTRLplusA38.1

description: Astrocyte A38

value: Female

value: 10 weeks


title: MCF-7 ER Control


title: 200-49-2-2

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2
Transcript abundance values were obtained from circRNA gene count matrices were generated by CIRI2
CircRNA gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential circRNA gene expression by DEseq2 was performed on normalized gene counts, using batch effects and the Sertoli cells .
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample
Supplementary_files_format_and_content: raw counts

source_name: retina pigment epithelium cells

growth_protocol: ARPE-19 cells were purchased from American Type Culture Collection, and cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA), penicillin (100 U/mL), and streptomycin (100 U/mL) at 37°C, 5% CO2.

extract_protocol:
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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ARPE-19 cells were maintained in complete medium added with H2O2 (200 µM) for 48 h before collection.

value: human ARPE-19 cells

value: treated with H2O2 for 48h


title: MCF-7 Input

value: MCF-7 cells

value: input


title: Astrocytes.pGFRAPshEphB3.1

description: Asctrocyte pGFAPshEphB3

value: FACS Sorted Astrocytes from CNS


title: Astrocytes.pGFRAPshEphB3.2

description: Asctrocyte pGFAPshEphB3


title: 0-2

value: untreated


title: Astrocyte.shCTRL.4

description: Astrocyte Control

value: shCTRL


title: K9M_3

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

description: Isolation of nuclei

data_processing:
Reads were aligned to the zebrafish genome with Bowtie2 v.2.3.4.1
Duplicates and mitochondrial reads were removed with Samtools v1.8
Peaks were called with Genrich (https://github.com/jsh58/Genrich) in ATAC-seq mode.
Genome_build: GRCz10
Supplementary_files_format_and_content: Atac-seq peaks are identified

growth_protocol: A375 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Nuclei were isolated from sorted cells as detailed in Corces, et al., Nature Methods 2017 Oct; 14(10): 959-962 and a transposase reaction was performed.
ATAC-seq library preparation was performed as described in Buenrostro JD, et al Molecultar Biology 2015: 109:21.29.1-21.29.9
Illumina 50bp paired end reads

treatment_protocol: A375 cells were transfected with constructs expressing mScarlet-H3.3 (wildtype) or mScarlet(H3.3(K9M)). mScarlet positive cells were isolated by FACS

value: Melanoma

tag: transfection


title: 200-48h-1


title: K9M_2

description: Isolation of nuclei


title: Astrocyte.shCTRL.1

description: Astrocyte Control

tag: strain

value: NOD/ShiLtJ


title: Astrocyte.shCTRL.2

description: Astrocyte Control


title: K9M_1

description: Isolation of nuclei


title: H33_3

description: Isolation of nuclei


title: H33_2

description: Isolation of nuclei


title: H33_1

description: Isolation of nuclei


title: PHH HBV 500 HDV 50 3

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Reads were generated using GASAVA v. 1.8.2 and clipped for low qualited bases using proprietary software developed by Q2 Solutions.
Clipped fastq files were aligned to reference genome using STAR2.7
gene level quantification using featureCounts v1.4.6-p1 with Gencode annotation v32.
Genome_build: hg38
Supplementary_files_format_and_content: Tab separated gene count matrix

source_name: Primary human hepatocyte

extract_protocol:
Qiagen Allprep kit
Illumina TruSeq Stranded mRNA

value: liver

tag: timepoint

value: day 6

tag: cohort

value: HBV+HDV


title: PHH IFN J1 3

value: day 1

value: IFN