title: LowHR Breast Cancer Specimen 12


title: WCM1358 MATRIGEL rep3

status: Public on Oct 01 2021

type: SRA

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

country: USA

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
All reads were independently aligned with STAR_2.4.0f141 for sequence alignment against the human genome sequence build hg19, downloaded via the UCSC genome browser [http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/], and SAMTOOLS v0.1.1942 for sorting and indexing reads. Cufflinks (2.0.2)43 was used to estimate the expression values (FPKMS), and GENCODE v1944 GTF file for annotation. The gene counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: WCM1358 prostate cancer organoid

extract_protocol:
RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280))
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-sequencing and data processing of synthetic organoids was performed according to the protocol described earlier by our group. Briefly, RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280)). Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2. RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen). Sequencing was then performed on HiSeq 2000, or HiSeq 2500.

tag: donor

tag: tissue

value: Castration resistant prostate cancer (CRPC)

tag: treatment

value: MATRIGEL


title: WCM1358 MATRIGEL rep2


title: Wildtype Rep 2

city: Baltimore

first: Erin

middle: M

last: Green

state: MD

address: 1000 Hilltop Cir, Bs 325

department: Biological Sciences

institute: UMBC

data_processing:
Data quality visualized using FastQC
Adaptor removal and read trimming performed with Trimmomatic in paired-end mode (Headcrop:10 used to trim first 10 bases)
Read mapping performed with BWA-MEM through Galaxy
Transcript assembly performed with Stringtie through Galaxy
Log fold-change values calculated using DeSeq2
Genome_build: sacCer3
Supplementary_files_format_and_content: excel file with log fold change values calculated from DeSeq2 (mut/wt)

organism: Saccharomyces cerevisiae

source_name: whole cell lysate

growth_protocol: YPD medium, 30 degrees C, mid log phase growth

extract_protocol:
total RNA isolation from yeast with rRNA depletion using Illumina ribo zero kit
standard Illumina library preparation using stranded TruSeq library preparation kit

tag: strain

tag: genotype

value: wildtype


title: Wildtype Rep 1


title: LowHR Breast Cancer Specimen 9

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.463  based on the statistical language R version 3.5.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Breast biopsy

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

tag: gender

value: Female

tag: subtype

value: LowHR

value: Negative


title: WCM1358 MATRIGEL rep1


title: LowHR Breast Cancer Specimen 13


title: micu-1;mcu-1_3 [8265]

city: Bonn

first: Daniele

last: Bano

address: Sigmund-Freud-Strasse 27

institute: DZNE

data_processing:
Libraries were sequenced SR 75 cycles on a NextSeq500 system (Illumina) using High Output v2 chemistry
Base call files were converted to fastq format and demultiplexed using bcl2fastq v2.20.
The 75 bp single-end reads were aligned to the C.elegans reference transcriptome WBcel235 by kallisto v0.44.0 using default parameters
Data analysis was performed using Shiny-Seq.
Genome_build: WBcel235
Supplementary_files_format_and_content: abundance measurements for each sample and a matrix table integrating all replicates across three different strains

organism: Caenorhabditis elegans

source_name: micu-1(bon20); mcu-1(ju1154)_whole body

growth_protocol: worms were bleached onto OP50-seeded NGM plates and grown until the 1st day of adulthood

extract_protocol:
worms were collected, pelleted and dissolved in 1mL Trizol. Total RNA was extracted using the miRNeasy Micro kit (Qiagen) according to manufacturer’s protocol.
cDNA libraries were prepared from 5 ng total RNA using the SMART-seq2 protocol and tagmented with the Nextera XT kit (Illumina). Library purification and size selection was carried out with AMPure XP beads (Beckman-Coulter) and final library size distribution was measured via High Sensitivity D5000 assay on a TapeStation 4200 System (Agilent). Library concentration was determined using the HS dsDNA assay on a Qubit 3.

tag: age

value: 1st day of adulthood

value: whole body


title: WCM1358 GFOGER rep2

value: GFOGER


title: micu-1;mcu-1_1 [8263]


title: WCM1358 GFOGER rep3


title: micu-1_3 [8261]

source_name: micu-1(bon20)_whole body


title: LowHR Breast Cancer Specimen 8


title: A549_KRAS_32

city: Boston

first: Oana

last: Ursu

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
demultiplex: cellranger mkfastq. Cellranger 2.1.1
alignment and counts: cellranger count. Cellranger 2.1.1. This results in the deposited files (genes.tsv, barcodes.tsv and matrix.mtx), quantifying the number of UMIs/gene/cell.
Genome_build: human transcriptome version GRCh38-1.2.0
Supplementary_files_format_and_content: variant2cell.csv: The metadata files for the TP53 and KRAS experiments contain additonal information about the cells in our experiments as follows: one column for each variant, specifying the number of UMIs supporting the presence of each variant in each cell, the name of the cell, and the batch (10X channel) of each cell. Each cell name also contains the batch in which it was sequenced. These names correspond to the names in the h5ad files.    processed_datasets: To filter out low-quality cells and keep the most informative genes, we removed cells with <200 genes/cell, and then removed genes present in less than 3 of the remaining cells. We then further filtered out cells with fewer than 7,000 UMIs/cell and those with a percent mitochondrial UMIs/cell >20%. Finally, we down-sampled cells with >50,000 UMIs to 50,000 UMIs, to avoid cells with unusually high sequencing depth. After filtering and the above down-sampling, to account for any differences in sequencing depth between the 64 10x channel batches, we further down-sampled the UMIs per cell such that all batches would have a median of 20,000 UMIs/cell. For this, we computed the median number of UMIs/cell in each channel, and then down-sampled the UMIs of each cell by a factor defined as the 20,000 desired UMIs/cell divided by the median number of UMIs/cell in the batch of the cell. Specifically, given a cell and this down-sampling factor, we went through each gene and obtained the adjusted number of UMIs by sampling from a binomial distribution with p=down-sampling factor and N=number of UMIs observed for this gene in the cell. This down-sampling procedure adjusted the distributions of UMIs/cell in each batch to have more similar medians. Batches with a median UMI/cell less than 20,000 did not go through this procedure. Note that in practice, similar results are obtained even without this down-sampling. We normalized the expression UMIs per cell to sum to 10,000 in each cell, and then transformed the normalized values to log(normalized expression+1) to obtain a raw expression matrix. We selected variable genes by identifying the genes for which the variance (scaled to a z-score relative to other genes in similar expression bins) exceeded 0.5. We also filtered the variable genes to have raw expression levels between 0.0125 and 4 (Zheng et al. 2017).mWe regressed out batch (as a discrete {0,1} variable), the number of UMIs/cell, the percent of mitochondrial reads, and the normalized expression of the variant barcode, and converted the resulting residuals to z-scores for each gene across cells. The analyses in this work use these z-scores, unless otherwise noted. We performed PCA for dimensionality reduction, keeping the first 50 principal components. We represented the cells in a low dimension using UMAP, using the default values of 15 nearest neighbors per cell and the default minimum distance between embedded points of 0.5. We used the resulting nearest neighbor graph to cluster cells using Louvain clustering (Blondel et al. 2008; Levine et al. 2015). We then subsampled the cells, to obtain 1000 for each variant.  The following are included in these files:   - processed.obs.csv (metadata for each cell): batch, percent mitochondrial reads (percent_mito), total UMIs/cell after downsampling (n_counts_downsampled), total UMIs/cell before downsampling (n_counts_original), the total UMIs from variant barcodes (vbc.counts), Louvain cluster assignment (louvain), cell cycle scores (G1.S, G2.M, M, M.G1, S), cell cycle phase assignment (phase.multi), variant(s) present in the cell (variant), variants(s) present in the cell where cells with multiple variants are labelled as "multiple" (variant.compact), functional class of the variant in the cell (variant_functional_class), gene program scores (P0, P1, ...), PC scores (PC0, PC1, ...), UMAP embedding coordinates (UMAP1, UMAP2)  - processed.genes.csv (metadata for each gene): number of cell in which the genes was detected (n_cells), highly variable (whether a gene is highly variable), mean expr (means), dispersion, normalized dispersion, gene program, contribution of gene to PCs (PC0, PC1, ...)  - processed.expr.csv (expression matrix): z-scores, as described above
Supplementary_files_format_and_content: processed_datasets: To filter out low-quality cells and keep the most informative genes, we removed cells with <200 genes/cell, and then removed genes present in less than 3 of the remaining cells. We then further filtered out cells with fewer than 7,000 UMIs/cell and those with a percent mitochondrial UMIs/cell >20%. Finally, we down-sampled cells with >50,000 UMIs to 50,000 UMIs, to avoid cells with unusually high sequencing depth. After filtering and the above down-sampling, to account for any differences in sequencing depth between the 64 10x channel batches, we further down-sampled the UMIs per cell such that all batches would have a median of 20,000 UMIs/cell. For this, we computed the median number of UMIs/cell in each channel, and then down-sampled the UMIs of each cell by a factor defined as the 20,000 desired UMIs/cell divided by the median number of UMIs/cell in the batch of the cell. Specifically, given a cell and this down-sampling factor, we went through each gene and obtained the adjusted number of UMIs by sampling from a binomial distribution with p=down-sampling factor and N=number of UMIs observed for this gene in the cell. This down-sampling procedure adjusted the distributions of UMIs/cell in each batch to have more similar medians. Batches with a median UMI/cell less than 20,000 did not go through this procedure. Note that in practice, similar results are obtained even without this down-sampling. We normalized the expression UMIs per cell to sum to 10,000 in each cell, and then transformed the normalized values to log(normalized expression+1) to obtain a raw expression matrix. We selected variable genes by identifying the genes for which the variance (scaled to a z-score relative to other genes in similar expression bins) exceeded 0.5. We also filtered the variable genes to have raw expression levels between 0.0125 and 4 (Zheng et al. 2017).mWe regressed out batch (as a discrete {0,1} variable), the number of UMIs/cell, the percent of mitochondrial reads, and the normalized expression of the variant barcode, and converted the resulting residuals to z-scores for each gene across cells. The analyses in this work use these z-scores, unless otherwise noted. We performed PCA for dimensionality reduction, keeping the first 50 principal components. We represented the cells in a low dimension using UMAP, using the default values of 15 nearest neighbors per cell and the default minimum distance between embedded points of 0.5. We used the resulting nearest neighbor graph to cluster cells using Louvain clustering (Blondel et al. 2008; Levine et al. 2015). We then subsampled the cells, to obtain 1000 for each variant.
Supplementary_files_format_and_content: The following are included in these files:
Supplementary_files_format_and_content: - processed.obs.csv (metadata for each cell): batch, percent mitochondrial reads (percent_mito), total UMIs/cell after downsampling (n_counts_downsampled), total UMIs/cell before downsampling (n_counts_original), the total UMIs from variant barcodes (vbc.counts), Louvain cluster assignment (louvain), cell cycle scores (G1.S, G2.M, M, M.G1, S), cell cycle phase assignment (phase.multi), variant(s) present in the cell (variant), variants(s) present in the cell where cells with multiple variants are labelled as "multiple" (variant.compact), functional class of the variant in the cell (variant_functional_class), gene program scores (P0, P1, ...), PC scores (PC0, PC1, ...), UMAP embedding coordinates (UMAP1, UMAP2)
Supplementary_files_format_and_content: - processed.genes.csv (metadata for each gene): number of cell in which the genes was detected (n_cells), highly variable (whether a gene is highly variable), mean expr (means), dispersion, normalized dispersion, gene program, contribution of gene to PCs (PC0, PC1, ...)
Supplementary_files_format_and_content: - processed.expr.csv (expression matrix): z-scores, as described above

molecule: polyA RNA

source_name: A549 lung cancer cell line

extract_protocol:
We loaded 7,000 cells per channel across 32 channels for each cDNA library to obtain a total of 224,000 cells per library (448,000 total).
Paired-end libraries were sequenced over 32 lanes for each of TP53 and KRAS on an Illumina Hiseq 2500 per sequencing parameters recommended by 10X Genomics: cell barcode read length 26 bp, index read length 8 bp and transcript read length 98 bp. No dial-out PCR was done, in contrast to typical Perturb-seq (Dixit et al. 2016; Jaitin et al. 2016; Adamson et al. 2016) (Variant assignment is described in the section “Assigning variants to cells”.)

treatment_protocol: 1 million A549 cells (ATCC CCL-185) were transduced with either KRAS or TP53 lentiviral pools at an MOI of 0.1 to attain a single integration event per cell, and selected with 2  μg/mL puromycin for 2 days to obtain a final library representation of ~1,000 cells per variant for both KRAS and TP53. Cells were allowed to recover for 2 days after selection and then loaded onto a 10X Chromium chip using the 10X Chromium Single Cell 3’ v2 kit (10X Genomics #120237).

tag: cell type

value: lung cancer

tag: cell line

tag: gene

value: KRAS

tag: lane

tag: index


title: micu-1_2 [8260]


title: LowHR Breast Cancer Specimen 5


title: LowHR Breast Cancer Specimen 11

value: Positive


title: micu-1;mcu-1_2 [8264]


title: WCM1358 GFOGER rep1


title: A549_KRAS_31


title: micu-1_1 [8259]


title: wt_3 [8257]

source_name: wild-type_whole body

value: wild-type


title: wt_2 [8256]


title: wt_1 [8255]


title: A549_KRAS_30


title: A549_KRAS_29


title: A549_KRAS_26


title: A549_KRAS_27


title: BAN329_5

data_processing:
Libraries were quantified using the Qubit hs dsDNA assay and library fragment size distribution was determined using the D1000 assay on a Tapestation 4200 system (Agilent).
Samples were pooled and clustered at 1.4pM on a NextSeq500 system (Illumina) to generate ~10M single end reads per sample using High Output v2.5 chemistry.
Sequencing data was demultiplexed using bcl2fastq2 v2.20 and pseudo aligned to Caenorhabditis elegans.
WBcel235.98 transcriptome using kallisto v.0.44.0.
Data analysis was performed using Shiny-Seq.
Genome_build: WBcel235.98
Supplementary_files_format_and_content: abundance measurements for each sample and a matrix table integrating all replicates across three different strains

source_name: intestine

growth_protocol: worms were bleached onto OP50-seeded NGM plates and grown for 5 days

extract_protocol:
worms were placed in M9 and 20 intestines per sample were dissected out and flash frozen in 1mL Qiazol. Total RNA was extracted using the miRNeasy Micro kit (Qiagen) according to manufacturer’s protocol.
Smart-seq2  was used for the generation of non-strand-specific, full transcript sequencing libraries using standard reagents and procedures as previously described (Picelli et al, 2014)

value: 5 days old

tag: sample id


title: LowHR Breast Cancer Specimen 10


title: A549_KRAS_25


title: BAN329_4


title: A549_KRAS_24


title: LowHR Breast Cancer Specimen 2


title: BAN329_2


title: A549_KRAS_28


title: BAN329_1


title: LowHR Breast Cancer Specimen 7


title: LowHR Breast Cancer Specimen 14


title: BAN329_3


title: gas-1_5


title: gas-1_3


title: LowHR Breast Cancer Specimen 6


title: A549_KRAS_23


title: A549_KRAS_21


title: A549_KRAS_20


title: A549_KRAS_18


title: A549_KRAS_22


title: A549_KRAS_19


title: gas-1_2


title: gas-1_4


title: gas-1_1


title: wt_5


title: wt_3


title: wt_4


title: A549_KRAS_13


title: A549_KRAS_15


title: wt_2


title: A549_KRAS_16


title: Input

library_source: genomic

data_processing:
Peaks were called using either the MACS or SICER algorithms
MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp
Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: bigwig files, which contain both the signal map and peak metrics, and can be opened with genome browsers.

source_name: whole body

growth_protocol: worms bleached onto OP50-seeded NGM plates and allowed to reach the L4 stage

extract_protocol:
Worms were collected in M9, snap frozen and stored at -80°C. Chromatin extracted as previously described (Askjaer, P., et. al. Modern techniques for the analysis of chrmatin and nuclear organization in C. elegans (April 2, 2014), WormBook, et. The C. elegans Research Community, Woembook, doi/10.1895/wormbook.1.169.1, http://wormbook.org
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.

value: pooled input


title: wt_1


title: LowHR Breast Cancer Specimen 1


title: A549_KRAS_10


title: A549_KRAS_11


title: A549_KRAS_12


title: A549_KRAS_17


title: A549_KRAS_9


title: 1mM (+)-Abscisic acid, 4

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description: F. graminearum infected and exogenous application of 1.0mM ABA

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0 and Fusarium graminearum (http://fungi.ensembl.org/, Release 35)
Supplementary_files_format_and_content: In excel file format, including Raw read counts data; Normalized read counts data; Alignment summary; DEGs; Summary

organism: Triticum aestivum

growth_protocol: T. aestivum ‘Fielder’ was grown in SunshineR Mix 8 (Sungrow Horniculture, Agawam, MA) and maintained in climate controlled chambers with a 16 h photoperiod, at 25 °C followed by 8 h of dark at 16 °C every day. Plants were watered as needed and fertilized biweekly with 20-20-20 (N-P-K). At the two-leaf stage plants were treated Intercept™ (Bayer Crop Science, Calgary, AB) as a powdery mildew and aphid preventative.

extract_protocol:
Total RNA was extracted, purified, quantified and sequenced as described previously (Buhrow et al., 2016). In total, 35 samples were collected; total RNA, containing both the plant and  pathogen RNA present in the samples, was extracted using the TriReagent (Molecular Research Center Inc.) followed by a treatment with DNase I (RNase-Free DNase set, Qiagen) onto columns (RNeasy Mini kit, Quiagen) according to instructions provided by the manufacturer.  RNA was processed for deep paired-end RNA sequencing using Illumina HiSeq 2500 by the  National Research Council Canada sequencing service
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: Five ‘Fielder’ spikelets (biological replicates) were each challenged with F. graminearum in the presence and absence of 1.0 mM ABA, GA or AS6. Similarly, five ‘Fielder’ spikelets (biological replicates) each treated with 1.0 mM of either ABA, GA or distilled water (mock treated control) in the absence of pathogen.  Samples were taken 24 hours after treatment

value: wheat

value: spikelet

value: F. graminearum


title: A549_KRAS_7


title: 1mM (+)-Abscisic acid, 5


title: A549_KRAS_8


title: A549_KRAS_6


title: A549_KRAS_14


title: BAN125


title: BAN129


title: BAN126


title: LowHR Breast Cancer Specimen 4


title: 1mM (+)-Abscisic acid, 3


title: A549_KRAS_4


title: 1mM (+)-Abscisic acid, 1


title: A549_KRAS_5


title: A549_KRAS_3


title: Gibberellic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 5

description: F. graminearum infected and exogenous application of 1.0mM GA


title: A549_KRAS_2


title: LowHR Breast Cancer Specimen 3


title: Gibberellic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 4


title: A549_KRAS_1


title: Wiltype Rep 3


title: Gibberellic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 3


title: Gibberellic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 2


title: A549_TP53_31


title: A549_TP53_30


title: A549_TP53_32


title: Gibberellic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 1


title: Fg4

description: F. graminearum infected 24h dpi

source_name: FHB-infected 24hrs dpi


title: A549_TP53_28


title: A549_TP53_29


title: Fg2

description: F. graminearum infected 24h dpi


title: Fg5

description: F. graminearum infected 24h dpi


title: A549_TP53_27


title: A549_TP53_26


title: 1mM (+)-Abscisic acid, 2


title: Fg1

description: F. graminearum infected 24h dpi


title: A549_TP53_25


title: A549_TP53_24


title: WT5

description: Water mock treated

value: water


title: A549_TP53_23


title: WT4

description: Water mock treated


title: A549_TP53_21


title: ileal mucosa FMT pig 657

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads was performed using TrimGalore (Babraham Binoinformatics).
Alignment against the porcine reference genome Sscrofa11.1 was performed with the RNA-Seq aligner Tophat2.
Gene counts were obtained with HTSeq-count, using gene annotations from the Ensembl genome assembly (release 91).
Statistical analysis of differential gene expression between groups was performed by DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: htseq-count output, including 2 columns (Ensembl gene ID and raw counts of sequencing reads).

organism: Sus scrofa

source_name: ileal mucosa

extract_protocol:
Total RNA was isolated with RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed using NEBNext Ultra RNA library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) and sequenced on the Illumina HiSeq 4000 platform with paired-end 150-bp reads production.

tag: litter

tag: Sex

value: M

value: ileal mucosa

value: FMT


title: WT3

description: Water mock treated


title: A549_TP53_20


title: A549_TP53_22


title: ileal mucosa CON pig 656

value: CON


title: Fg3

description: F. graminearum infected 24h dpi


title: A549_TP53_19


title: ileal mucosa FMT pig 655

value: F


title: WT1

description: Water mock treated


title: WT2

description: Water mock treated


title: A549_TP53_16


title: ileal mucosa FFTo pig 654

value: FFTo


title: ileal mucosa CON pig 653


title: A549_TP53_17


title: ABA-signaling inhibitor-primed; Fusarium graminearum-challenged 24hrs dpi, 5

description: F. graminearum infected and exogenous application of 1.0mM AS6, an ABA-signaling inhibitor.


title: A549_TP53_14


title: ileal mucosa FMT pig 652


title: A549_TP53_15


title: WCM1358 REDV rep1

value: Castration resistant prostate cancer (CRPC)

value: REDV


title: ABA-signaling inhibitor-primed; Fusarium graminearum-challenged 24hrs dpi, 4


title: ileal mucosa FFTr pig 651

value: FFTr


title: A549_TP53_10

value: lung cancer


title: A549_TP53_11


title: A549_TP53_12


title: ABA-signaling inhibitor-primed; Fusarium graminearum-challenged 24hrs dpi, 3


title: A549_TP53_9


title: ileal mucosa FFTo pig 650


title: A549_TP53_8


title: A549_TP53_18


title: ileal mucosa CON pig 649


title: A549_TP53_7


title: A549_TP53_6


title: ABA-signaling inhibitor-primed; Fusarium graminearum-challenged 24hrs dpi, 1


title: A549_TP53_13


title: 1mM(+)-Gibberellic acid, 5

description: Exogenous application of 1.0mM gibberellic acid


title: A549_TP53_2


title: 1mM(+)-Gibberellic acid, 4


title: A549_TP53_5


title: ileal mucosa FFTr pig 647


title: A549_TP53_3


title: A549_TP53_1


title: ileal mucosa FMT pig 644


title: DE160/DE160-D35-rep2

city: Shanghai

first: Bin

last: Li

address: Dong'an Road

department: Department of Physiology and Pathophysiology

country: China

institute: Fudan University

data_processing:
RNA sequencing reads were quality filtered and processed using the pseudoalignment-based Kallisto algorithm with GRCh37 comprehensive transcript set as reference transcriptome.
none provided by the submitter
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for every gene and every sample.

source_name: HESC-derived cardiomyocytes

extract_protocol:
Total mRNAs were isolated from normal and mutant H7-derived cardiomyocytes on day 14 and day 35 post differentiation using TRIZOL (Invitrogen) according to the directions. Poly(A) RNA was purified from total RNA using the MicroPoly(A)TM kit (Life Technologies).
1 ug of total RNA was enriched for the Poly-A mRNA and reversed to cDNA, which was end-repaired, 3' ends adenylated, and barcoded with multiplex adapters.

tag: disese state

value: day35 (D35) post cardiac differentiation

value: cTnT-DE160 mutation


title: WT/DE160-D35-rep3


title: A549_TP53_4


title: ileal mucosa FMT pig 648


title: 1mM(+)-Gibberellic acid, 3


title: ileal mucosa CON pig 645


title: DE160/DE160-D35-rep3


title: ileal mucosa FFTr pig 643


title: DE160/DE160-D14-rep3

value: day14 (D14) post cardiac differentiation


title: 1mM(+)-Gibberellic acid, 2

value: wheat


title: 1mM(+)-Gibberellic acid, 1

value: spikelet


title: ABA-signaling inhibitor-primed; Fusarium graminearum-challenged 24hrs dpi, 2

value: F. graminearum


title: DE160/DE160-D14-rep2


title: ileal mucosa CON pig 642


title: Abscisic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 5

description: Exogenous application of of 1.0mM abscisic acid


title: ileal mucosa FMT pig 641


title: WT-D35-rep3

value: wild type


title: DE160/DE160-D35-rep1


title: DE160/DE160-D14-rep1


title: ileal mucosa CON pig 640

value: M


title: WT/DK210-D35-rep3

value: cTnT-DK210 mutation


title: Abscisic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 4


title: WT/DE160-D14-rep3


title: DK210/DK210-D14-rep3


title: Abscisic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 3


title: DK210/DK210-D35-rep3


title: ileal mucosa FFTo pig 639

value: ileal mucosa


title: WT/DE160-D35-rep2


title: WT-D14-rep3


title: Abscisic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 2


title: ileal mucosa FFTr pig 637


title: WT-D35-rep2


title: Abscisic acid-primed; Fusarium graminearum-challenged 24hrs dpi, 1


title: WT/DK210-D35-rep2


title: ileal mucosa FFTo pig 635


title: OIR miR-143 mimic 2

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

data_processing:
The quality of the raw reads were were assessed by the FASTQC (Andrews 2010) and assured that all read have phred score > 28.
The transcriptome reads were mapped to the Rattus norvegicus (rn6) refenerce genome retrieved from the iGenomes (obtained on 19th June 2017, https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Differential gene and transcript expression analysis were done by using TopHat and Cufflinks (Trapnell et al. 2012).
Expression level and function analysis were done by using Cuffdiff (Zhang et al. 2014) statistical method and CummeRbund R statistical package (Trapnell et al. 2012).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Retina

extract_protocol:
The enucleated rat eyes were harvested and stored in the RNAlater (Qiagen), and retinas were dissected immediately under the dissection microscope. Total RNA and miRNA were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate was prepared as per the manufacturers’ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2500 RNA-seq platform as 50 bp single-end chemistry.
miRNA libraries were prepared for sequencing using a standard Illumina protocols

value: Sprague Dawley

value: Retina

value: Wild type

tag: disease state

value: oxygen-induced retinopathy

tag: transfection

value: miR-143 mimic


title: WT/DE160-D14-rep2


title: OIR miR-143 mimic 3

tag: tissue


title: DK210/DK210-D14-rep2


title: ileal mucosa FMT pig 634

tag: treatment

value: FMT


title: OIR scrambled RNA 2

tag: strain

tag: genotype

value: scrambled


title: DK210/DK210-D35-rep1

value: day35 (D35) post cardiac differentiation


title: WT/DK210-D14-rep3


title: WT/DE160-D35-rep1

value: cTnT-DE160 mutation


title: OIR scrambled RNA 1


title: WT/DK210-D35-rep1


title: ileal mucosa FMT pig 638


title: DK210/DK210-D35-rep2


title: ileal mucosa FFTr pig 633

value: FFTr


title: ileal mucosa FFTo pig 631

value: FFTo


title: WT-D14-rep2

value: day14 (D14) post cardiac differentiation


title: Sham miR-143 mimic 2

value: control


title: DK210/DK210-D14-rep1


title: WT-D35-rep1

value: wild type


title: ileal mucosa FMT pig 630

value: M


title: WT/DE160-D14-rep1


title: ileal mucosa CON pig 628

value: F

value: CON


title: WT/DK210-D14-rep1

value: cTnT-DK210 mutation


title: Sham miR-143 mimic 1

value: Sprague Dawley

value: Retina


title: WT-D14-rep1


title: ileal mucosa FFTo pig 627

value: ileal mucosa


title: Sham scrambled RNA 3

value: Wild type


title: C_3

description:
control_3
processed data file: Kallisto_processed_data_all_miRNAs.csv

data_processing:
The quality of the raw reads were assessed by the FASTQC (Andrews 2010) and assured that all read have phred score > 28.
The quality reads were mapped to the reference genome and transcript abundance were quantified by using Kallisto (Bray, N.L., et al. 2016).
To identify the differential expressed genes between Control, OIR-miR126, OIR-miR143 and OIR-miR150 statistical method Sleuth (Pimentel, H., et al. 2017) were employed to calculate the expression from the quantified transcript abundance.
R statistical computing environment were used for functional analysis and generating plots.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Kallisto_processed_data_all_miRNAs.csv: Comma-separated text file including TPM values for each Sample.

source_name: HMEC-1 transfected with non-targeting scrambled RNAs

growth_protocol: Human dermal microvascular endothelial cell (HMEC-1) were cultured in endothelial cell basal medium-2 (EBM-2) supplied with EGM™-2 BulletKit™ (Lonza).

extract_protocol:
Total RNAs were isolated from the HMEC-1 by using a Qiagen RNeasy mini kit.
miRNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Synthetic human miRNA mimics (miR126, -143, and -150) and non-targeting scrambled RNAs (50 nM) were transfected using Lipofectamine RNAiMAX in HMEC-1. Cells were then collected for the RNA-Seq 48 hours after transfection.

value: Human dermal microvascular endothelial cell line

tag: miRNA mimic


title: WT/DK210-D14-rep2


title: ileal mucosa FMT pig 626

value: FMT


title: Sham scrambled RNA 2

tag: age

value: scrambled


title: C_2

description:
control_2
processed data file: Kallisto_processed_data_all_miRNAs.csv

tag: cell type


title: 150_4

description: processed data file: Kallisto_processed_data_all_miRNAs.csv

source_name: HMEC-1 transfected with miR150 mimic

tag: cell line


title: ileal mucosa FFTr pig 625


title: Sham miR-143 mimic 3

value: miR-143 mimic


title: ileal mucosa CON pig 624


title: Sham scrambled RNA 1


title: 143_3

source_name: HMEC-1 transfected with miR143 mimic


title: 143_2


title: 150_2


title: 143_4


title: C_4

description:
control_4
processed data file: Kallisto_processed_data_all_miRNAs.csv


title: 150_3


title: ileal mucosa FFTo pig 623


title: 126_4

source_name: HMEC-1 transfected with miR126 mimic


title: 126_2


title: ileal mucosa FMT pig 622


title: ileal mucosa FFTo pig 619


title: ileal mucosa CON pig 618


title: ileal mucosa FFTr pig 621

value: FFTr


title: 0hr_donor4

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Hi-C reads were trimmed at the de novo re-ligation sites (NheI sites generated from re-ligating Hind III digestion) and then mapped to hg38 reference genome by Bowtie2.
Unique mapped reads were subject to filtering to remove self-ligation, dangling ends and random breaking.
Filtered reads were then normalized by HOMER.
Biological replicates were combined and chromatin interactions at 25kb resolution were calculated by HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files. Output of chromatin interactions calculated by HOMER.

source_name: human naïve CD4 T cells

growth_protocol: Naïve CD4 T cells were cultured in RPMI 1640 (Gibico) supplemented with 100 U/ml Penicillin, 100 ug/ml Streptomycin and 10% FBS at 37° C with 5% CO2.

extract_protocol:
Naïve CD4 T cells were fixed by culture medium containing 1% formaldehyde for 5 minutes at room temperature and quenched by Tris (pH8.0). Nuclei were then isolated and subjected to SDS permeabilization followed by TritonX-100 to quench SDS. After that, nuclei pellets were subjected to HindIII digestion and re-ligation, at which step the biotin-dCTP was induced into the de novo ligation sites. Newly re-ligated genomic DNA were purified and sheared into 200bp fragments and fragments containing biotin-labeled de novo ligation sites were purified by M280 streptavidin beads (Invitrogen) and subjected to library preparation.
DNA fragment was subjected to end-repair and biotin-remove by a master mix containing T4 DNA ligase buffer, dNTP mix, T4 PNK, T4 DNA Polymerase I and DNA polymerase I Large (Klenow) Fragment. Then dATP was attached to fragment end by Klenow exo minus enzyme. Resulted DNA fragment was ligated with Illumina indexed adaptors and amplified using Illumina PCR primer 1 and 2.

treatment_protocol: Cells were activated with CD3/CD28 beads and collected 0, 8 or 24 hours after activation for downstream experiments.

tag: individual

value: naive CD4 T cells

value: activated by CD3/CD28 beads

tag: time


title: 8hr_donor4


title: 24hr_donor4

description: T24_HiC_siginteractions_res25kby100k.txt


title: 24hr_donor3


title: 8hr_donor3


title: ileal mucosa FFTr pig 617


title: 126_3


title: 0hr_donor3


title: 8hr_donor2


title: 24hr_donor2


title: ileal mucosa FMT pig 616


title: 0hr_donor2


title: ileal mucosa FFTr pig 614


title: 8hr_donor1


title: ileal mucosa FFTo pig 615

value: FFTo


title: RNA-Seq_24h_Ets21C_3

city: Salt Lake City

first: Bruce

middle: Alexander

last: Edgar

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
RNA-Seq_RawCounts.txt
RNASeq_DifferentiallyExpressedGenes.xlsx

data_processing:
Raw RNA-Seq and DamID-Seq reads were checked for quality using Fastqc and subsequently aligned to the Drosophila melanogaster BDGP genome (v6.94) using STAR (v2.6.1d) and Bowtie2 (v2.2.5), respectively.
RNA-Seq aligned reads with a quality score ≥ 30 were counted using HTSeq-count (v0.11.1) with mode “Union”. DamID-Seq aligned reads with a quality score ≥ 30 were extended 5’ to 3’ to a length of 350bp and mapped to the Drosophila melanogaster genome subdivided into 75bp contiguous fragments.
Genes showing a cpm value below 1 across samples were considered as poorly expressed and filtered out. Similarly, only genomic fragments showing mapped DamID-Seq reads counts above a threshold value were selected for subsequent analysis. The threshold value was calculated as the average read number of the fragments. This value was chosen since only relatively few bins in the genome are supposed to be bound by a transcription factor so the mean read count should be greatly biased by bins with low counts.
Filtered genes and genome fragments were then analyzed using DESeq2 (v1.18.1). Since our Pnt RNA-Seq and all DamID-Seq replicates were generated independently, we used a paired design, while Spitz and Ets21C samples were not paired. Resulting p-values were corrected by the Benjamini-Hochberg method. Subsequently, genes with an absolute fold change of 1.5 or more and an adjusted p-value lower than 0.05 were considered as significantly differentially expressed. Similarly, genome fragments with a positive fold change and an adjusted p-value lower than 0.01 were considered as significantly differentially bound.
Genome_build: BDGP 6.94
Supplementary_files_format_and_content: Matrix table with DamID-Seq raw genome fragment counts for every gene and every sample
Supplementary_files_format_and_content: Matrix of significantly enriched DamID-Seq binding peak coordinates for every sample
Supplementary_files_format_and_content: Matrix table with RNA-Seq raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix of significantly differentially expressed genes for every sample
Supplementary_files_format_and_content: Interpolation of DamID and RNA-Seq data, showing genes directly regulated by Ets21C, PntP1, or PntP2

organism: Drosophila melanogaster

source_name: FACS sorted Intestinal stem cells from adult Drosophila midgut

growth_protocol: Crosses were set up and maintained at 18°C.

extract_protocol:
RNA extraction: YFP positive and Propidium Iodide negative cells from digested midguts were sorted by FACS. RNA was harvested using Arcturus picoPure RNA Isolation Kit (ThermoFisher,  12204-01) in an RNAse-free environment.
Library preparation was carried out by Illumina TruSeq Stranded mRNA Kit (Illumina) according to its protocol.

treatment_protocol: Young female flies were selected three days post-eclosion and shifted to 29℃ for 24 hours. Flies were dissected in 1X PBS and midguts were immediately frozen using liquid nitrogen.

value: esgts; Su(H)-Gal80 > YFP, Ets21C

value: FACS sorted intestinal stem cells

tag: sample type

value: RNA-Seq

tag: molecule subtype

value: Amplified mRNA

value: female


title: RNA-Seq_24h_Ets21C_2


title: ileal mucosa FMT pig 613

tag: litter

value: F


title: RNA-Seq_24h_Ets21C_1

tag: Sex


title: RNA-Seq_24h_Spitz_3

value: esgts; Su(H)-Gal80 > YFP, Spi


title: RNA-Seq_24h_Spitz_2


title: ileal mucosa FFTo pig 612

value: ileal mucosa


title: ileal mucosa CON pig 611

value: CON


title: RNA-Seq_24h_Spitz_1


title: 24hr_donor1


title: ileal mucosa FFTr pig 610

value: M


title: RNA-Seq_24h_Ctrl_For_Spitz_Ets21C_2

value: esgts; Su(H)-Gal80 > YFP


title: RNA-Seq_24h_Ctrl_For_Spitz_Ets21C_3


title: RNA-Seq_24h_Ctrl_For_Spitz_Ets21C_1


title: RNA-Seq_8h_Ets21C_2


title: Caco2_transw_ctrl

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

label: biotin

source_name: Caco-2 cells, grown on collagen-coated Transwell insert, control condition, pool of 3 samples

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of pooled, total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Caco-2 cells (human epithelial colorectal adenocarcinoma cell, ATCC) were grown in Dulbecco's Modified Eagle Medium (DMEM, Lonza), supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin and 100 µg/ml streptomycin. Caco-2 cells were seeded on collagen-coated Transwell inserts (diameter 6.5 mm), or in regular 6 well plates (diameter 34.8 mm). Medium was refreshed every two days. Cells grown on the Transwell inserts reached confluency after 4 days of culture and differentiated to develop functional tight junctions as measured by trans-epithelial resistance (TER). Cells were used for experiments once TER remained stable, attained 14-21 days after seeding. Cells grown in the 6 well plates were used 14 days after seeding.

extract_protocol: Total RNA was isolated by using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s protocol. For microarray hybridization the isolated RNA was further column purified (SV total RNA isolation system Promega, Leiden, The Netherlands). RNA concentration was measured on a nanodrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on an Agilent 2100 bioanalyzer bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips, according to the suppliers protocol. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For each condition a pooled sample was hybridized that was composed of RNA from 3 samples.

treatment_protocol: The sodium salt of the bile acid cholic acid (cholate) was dissolved in 10 mM HEPES-buffered Hank's Buffered Salt Solution (HBSS) without calcium to prevent bile acid precipitation. Before the start of the incubation cells were washed twice with DMEM and TER was measured. The bile acid solution was added to the apical compartment and the plate at a concentration of 2 mM. The lower basolateral compartment of the Transwell contained colorless DMEM without FCS. The cells were incubated for 3h. Cells were washed twice with DMEM and TER was measured. Cells were then washed with PBS and lyzed in Trizol for RNA isolation.

tag: growth condition

value: collagen-coated transwell insert

value: vehicle (control)

tag: incubation time

value: 3 hr

tag: days of caco-2 cell differentiation

tag: number of rna sampes pooled


title: 0hr_donor1

value: naive CD4 T cells

tag: treatment


title: Caco2_plate_ctrl

source_name: Caco-2 cells, grown on regular cell culture plate, control condition, pool of 3 samples

value: human epithelial colorectal adenocarcinoma

value: regular 6 well plate


title: XVE_WIND1_treated_w_estrogen_24hr_rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with 10 micro M estradiol for 24 hours

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Quick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on MS-based agar media in growth chamber at 22 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Seedling was treated with 10 micro M estradiol or DMSO (mock).

tag: tissue

value: Seedling

value: 10 micro M estradiol

tag: treatment duration

value: 24 hours


title: Caco2_transw_cho

source_name: Caco-2 cells, grown on collagen-coated Transwell insert, treated with cholic acid for 3 hrs, pool of 3 samples

value: sodium cholic acid (2mM)


title: XVE_WIND1_treated_w_estrogen_24hr_rep1

tag: genotype


title: XVE_WIND1_treated_w_estrogen_24hr_rep3


title: RNA-Seq_8h_Spitz_3

value: FACS sorted intestinal stem cells

value: RNA-Seq

value: Amplified mRNA

value: female


title: RNA-Seq_8h_Ets21C_1

value: esgts; Su(H)-Gal80 > YFP, Ets21C


title: Caco2_plate_cho

source_name: Caco-2 cells, grown on regular cell culture plate, treated with cholic acid for 3 hrs, pool of 3 samples


title: RNA-Seq_8h_Spitz_2

value: esgts; Su(H)-Gal80 > YFP, Spi


title: RNA-Seq_8h_Spitz_1


title: XVE_WIND1_treated_w_estrogen_12hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with 10 micro M estradiol for 12 hours

value: 12 hours


title: ileal mucosa FFTo pig 608

value: F

value: ileal mucosa

value: FFTo


title: RNA-Seq_8h_Ctrl_For_Spitz_Ets21C_3

value: esgts; Su(H)-Gal80 > YFP


title: XVE_WIND1_treated_w_estrogen_24hr_rep2


title: ileal mucosa FMT pig 609

value: M

value: FMT


title: ileal mucosa CON pig 607

value: CON


title: RNA-Seq_8h_Ctrl_For_Spitz_Ets21C_2


title: ileal mucosa FFTr pig 606

value: FFTr


title: XVE_WIND1_treated_w_estrogen_12hr_rep3

value: Seedling

value: 10 micro M estradiol


title: XVE_WIND1_treated_w_estrogen_6hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with 10 micro M estradiol for 6 hours

value: 6 hours


title: RNA-Seq_8h_Ctrl_For_Spitz_Ets21C_1

value: FACS sorted intestinal stem cells

value: RNA-Seq


title: RNA-Seq_PntP2_3

extract_protocol:
RNA extraction: YFP positive and Propidium Iodide negative cells from digested midguts were sorted by FACS. RNA was harvested using Arcturus picoPure RNA Isolation Kit (ThermoFisher,  12204-01) in an RNAse-free environment.
Library preparation was carried out by Illumina TruSeq RNA Sample Prep Kit (Illumina, FC-122-1001) according to its protocol.

value: esgts; Su(H)-Gal80 > YFP, PntP2

value: Amplified mRNA

value: female


title: RNA-Seq_PntP2_1


title: XVE_WIND1_treated_w_estrogen_12hr_rep1

value: 12 hours


title: ileal mucosa FMT pig 605


title: RNA-Seq_PntP1_3

value: esgts; Su(H)-Gal80 > YFP, PntP1


title: ileal mucosa FFTo pig 604

value: ileal mucosa


title: RNA-Seq_PntP1_1


title: ileal mucosa CON pig 603


title: RNA-Seq_Ctrl_For_Pnt_3


title: RNA-Seq_Ctrl_For_Pnt_2


title: XVE_WIND1_treated_w_estrogen_12hr_rep2


title: RNA-Seq_Ctrl_For_Pnt_1


title: PntP2-Dam_05

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

data_processing:
Library strategy: DamID-seq
Raw RNA-Seq and DamID-Seq reads were checked for quality using Fastqc and subsequently aligned to the Drosophila melanogaster BDGP genome (v6.94) using STAR (v2.6.1d) and Bowtie2 (v2.2.5), respectively.
RNA-Seq aligned reads with a quality score ≥ 30 were counted using HTSeq-count (v0.11.1) with mode “Union”. DamID-Seq aligned reads with a quality score ≥ 30 were extended 5’ to 3’ to a length of 350bp and mapped to the Drosophila melanogaster genome subdivided into 75bp contiguous fragments.
Genes showing a cpm value below 1 across samples were considered as poorly expressed and filtered out. Similarly, only genomic fragments showing mapped DamID-Seq reads counts above a threshold value were selected for subsequent analysis. The threshold value was calculated as the average read number of the fragments. This value was chosen since only relatively few bins in the genome are supposed to be bound by a transcription factor so the mean read count should be greatly biased by bins with low counts.
Filtered genes and genome fragments were then analyzed using DESeq2 (v1.18.1). Since our Pnt RNA-Seq and all DamID-Seq replicates were generated independently, we used a paired design, while Spitz and Ets21C samples were not paired. Resulting p-values were corrected by the Benjamini-Hochberg method. Subsequently, genes with an absolute fold change of 1.5 or more and an adjusted p-value lower than 0.05 were considered as significantly differentially expressed. Similarly, genome fragments with a positive fold change and an adjusted p-value lower than 0.01 were considered as significantly differentially bound.
Genome_build: BDGP 6.94
Supplementary_files_format_and_content: Matrix table with DamID-Seq raw genome fragment counts for every gene and every sample
Supplementary_files_format_and_content: Matrix of significantly enriched DamID-Seq binding peak coordinates for every sample
Supplementary_files_format_and_content: Matrix table with RNA-Seq raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix of significantly differentially expressed genes for every sample
Supplementary_files_format_and_content: Interpolation of DamID and RNA-Seq data, showing genes directly regulated by Ets21C, PntP1, or PntP2

source_name: Intestinal stem cells from adult Drosophila midgut

extract_protocol:
DNA extraction: Midguts were homogenized in TENS buffer and gDNA was extracted using phenol-chloroform. gDNA was digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 350bp using a Covaris-S2 then digested with Sau3AI to remove the adaptors before processing with TruSeq DNA PCR-Free Sample Preparation kit (Ilumina, FC-121-3001), following its protocol.

value: esgts; Su(H)-Gal80 > PntP2-Dam

value: Intestinal stem cells

value: DamID-Seq

value: molecule:methylated gDNA


title: PntP2-Dam_04

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: PntP2-Dam_03

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: RNA-Seq_PntP1_2


title: PntP2-Dam_01

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: PntP1-Dam_05

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: esgts; Su(H)-Gal80 > PntP1-Dam


title: PntP2-Dam_02

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Striatum/thalamus_subject8 [NanoString]

city: Omaha

first: Eric

middle: S

last: Peeples

state: NE

address: 8200 Dodge Street

department: Pediatrics

institute: University of Nebraska Medical Center

description: Obtained 30 min after injury

hyb_protocol: Nanostring CodeSet Hybridization protocol

scan_protocol: nCounter MAX/FLEX device

data_processing: Data were uploaded to nSolver for analyses

organism: Mus musculus

source_name: Right striatum/thalamus

label_protocol: nCounter Mouse Neuroinflammation probes

extract_protocol: Each hemisphere was further dissected into three regions –  cortex, striatum/thalamus, and cerebellum – and then immediately frozen on dry ice and stored at -80°C until analysis. Regional brain tissue was then homogenized using a dounce homogenizer with Qiazol Lysis Reagent (Qiagen, Hilden, Germany) and the RNA extracted using the RNeasy Lipid Tissue Mini kit (Qiagen) per the manufacturer instructions.

treatment_protocol: At postnatal day 9, pups of both sexes were randomized to HIBI or control. The HIBI groups were induced with 5% isoflurane and then were anesthetized with 2.5% isoflurane. Analgesia was provided by injection of 2 mg/kg bupivacaine at the incision site. A small vertical incision was made in the midline of the ventral neck and the neck was dissected in order to identify, isolate, and cauterize the right common carotid artery [11]. Surgeries took no longer than five minutes. The control group underwent the same anesthesia, analgesia, and dissection, but the neck was closed without vessel ligation. Pups were maintained at normothermia throughout surgery and recovery. Once the pups were fully recovered, they were returned to the dam and littermates for a two-hour recovery period. After recovery, groups were again separated, and the HIBI group underwent 30 minutes at 8% oxygen in a hypoxia chamber at normothermia while the sham control group spent the same 30 minutes separated from the dam but in a warm normoxic environment. At 30 minutes after hypoxia or normoxia, pups were euthanized.

tag: strain

tag: postnatal age

value: 9 days

tag: injury

value: Sham surgery without hypoxia


title: PntP1-Dam_04

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

tag: cell type


title: XVE_WIND1_treated_w_estrogen_6hr_rep3

value: Seedling

value: 10 micro M estradiol


title: Cortex_subject8 [NanoString]

description: Obtained 30 min after injury

source_name: Right cortex


title: PntP1-Dam_03

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: ileal mucosa FMT pig 601

source_name: ileal mucosa

value: M

value: FMT


title: PntP1-Dam_02

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: XVE_WIND1_treated_w_estrogen_6hr_rep1

value: 6 hours


title: XVE_WIND1_treated_w_estrogen_6hr_rep2


title: ileal mucosa FFTr pig 602

value: FFTr


title: XVE_WIND1_treated_w_estrogen_3hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with 10 micro M estradiol for 3 hours

value: 3 hours


title: XVE_WIND1_treated_w_estrogen_3hr_rep2


title: XVE_WIND1_treated_w_estrogen_3hr_rep1


title: XVE_WIND1_treated_w_estrogen_1hr_rep3

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with 10 micro M estradiol for 1 hour

value: 1 hour


title: Cerebellum_subject8 [NanoString]

description: Obtained 30 min after injury

source_name: Right cerebellum


title: PntP1-Dam_01

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: female


title: Striatum/thalamus_subject7 [NanoString]

description: Obtained 30 min after injury

value: Right carotid ligation followed by 8% oxygen for 30 min


title: Dam_Ctrl_For_Pnt_5

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: esgts; Su(H)-Gal80 > Dam


title: Dam_Ctrl_For_Pnt_4

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: Intestinal stem cells


title: Dam_Ctrl_For_Pnt_3

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: DamID-Seq


title: Cortex_subject7 [NanoString]

description: Obtained 30 min after injury


title: XVE_WIND1_treated_w_mock_24hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with DMSO for 24 hours

value: DMSO (mock)

value: 24 hours


title: Cerebellum_subject7 [NanoString]

description: Obtained 30 min after injury

value: 9 days


title: XVE_WIND1_treated_w_estrogen_1hr_rep4


title: Dam_Ctrl_For_Pnt_2

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: molecule:methylated gDNA


title: XVE_WIND1_treated_w_estrogen_1hr_rep2

value: Seedling


title: XVE_WIND1_treated_w_estrogen_1hr_rep1

value: 10 micro M estradiol


title: Dam_Ctrl_For_Pnt_1

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Ets21C-Dam_3

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: esgts; Su(H)-Gal80 > Ets21C-Dam


title: Ets21C-Dam_2

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Dam_Ctrl_For_Ets21C_4

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Ets21C-Dam_1

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: XVE_WIND1_treated_w_mock_24hr_rep3


title: Dam_Ctrl_For_Ets21C_2

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Cortex_subject6 [NanoString]

description: Obtained 30 min after injury

value: Sham surgery without hypoxia


title: Dam_Ctrl_For_Ets21C_1

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx


title: Striatum/thalamus_subject5 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM46_Sterile_translocation_rep4

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
Pool of 20 testes  separated from seminal vesicle
F4_Adult_BM46_4

data_processing:
We used RTA v1.13 (Illumina, San Diego, CA) for base calling and bcl2fastq v1.8 (Illumina, San Diego, CA) to de-multiplex and convert BCL to FASTQ format. We removed the adaptors using Cutadapt settings -q 10 with minimum length 25bp. We created a reference using FlyBase r6.32 and aligned reads with Hisat2 v2.1.0 (Kim et al. 2015. PMID: 25751142) using default settings. We created a set of gene level counts using featureCounts v1.6.1 (Liao et al., 2014. PMID: 24227677) with default options except (-s 2) to create strand specific read counts using the FlyBase r6.32 GTF.
Genome_build: a reference using FlyBase r6.32
Supplementary_files_format_and_content: FeatureCounts_Translocations_Processed_data.txt

source_name: Testes

growth_protocol: We followed the "Growth protocol" as published in GSE115478. Briefly, we grew all the confirmed translocation flies on Fly food A (LabExpress Ann Arbor, MI) at 25°C in constant light and 60% relative humidity and tested for male sterility. In order to choose the L3 at a specific time point, we collected eggs from six mated females every 8-16 hr., allowed them to develop until the L3 stage and dissected the testes just after they are immobilized and prior to larval anterior spiracle extension. We also monitored gut clearance by providing second and third instar larvae with yeast/water paste containing 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO), and selected individuals with mostly cleared foreguts with the food only in mid and hindgut.

extract_protocol:
We dissected L3 larvae and adults in 1XPBS at 22°C (Gibco Life Technologies, Carlsbad, CA). We collected L3 testes without fatbody by enzymatically removing fatbody following the Extraction Protocol from GSE115478. Briefly, by treating the testes with 0.075 mg/ml Papain (Sigma-Aldrich, St. Louis, MO) and 0.075 mg/ml Collagenase enzyme (Sigma-Aldrich, St. Louis, MO) cocktail in PBS in 1.5ml Eppendorf tube for 3 min with gentle vortexing by flicking the tube with a forefinger, we separated the fatbody from testes. Once we decanted the floating fatbody cells, washed the testes 2X with 1XPBS. We separated the adult testis from seminal vesicle. We collected each sample in 350 μl RLT buffer (Qiagen, Cat. No. 79216. Valencia, CA), vortexed two times for 30 sec with a 30 sec interval and quickly frozen in a dry ice ethanol bath and stored at -80°C until RNA extraction. We extracted total RNA using RNeasy 96 kit (Qiagen, Cat. No. 1019545. Valencia, CA) and followed the manufacturer’s protocol. RNA was quantified using Quant-iT RiboGreen quantification kit (Life Technologies, Cat. No. R11490. Carlsbad, CA). RNA was stored in -80°C until the library preparation
We used 350 ng of total RNA and performed RNA-seq library preparation according to Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920). Briefly, PolyA+ selection was done using Dynabeads Oligo(dT)25 (Life technologies, Grand Island, NY), fragmented the selected mRNA, performed RT with the second strand synthesis by incorporating dUTPs. We used External RNA control consortium spike-ins pools 78A and 78B (SRM2374, Zook et al., 2012. PMID: 22859977) transcribed from standard reference. We used barcoded adaptors for indexing the libraries (Qiagen, 98 TruSeq v2 kit barcoded adaptors, Valencia, CA). We sequenced stranded eight multiplexed libraries using a single-ended 50 bp strategy on one lane using a HiSeq Illumina 2500 (Illumina, San Diego, CA).

tag: genot{gamma}pe

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM46 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f

value: male

tag: developmental stage

value: One-to-five day old adult


title: Ets21C-Dam_4

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

tag: sample type

tag: molecule subtype


title: Cortex_subject5 [NanoString]

description: Obtained 30 min after injury


title: Cerebellum_subject5 [NanoString]

description: Obtained 30 min after injury


title: Striatum/thalamus_subject6 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM46_Sterile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
F3_Adult_BM46_3

tag: Sex


title: Adult_Testes_BM46_Sterile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
F2_Adult_BM46_2


title: XVE_WIND1_treated_w_estrogen_3hr_rep3

value: 3 hours


title: Striatum/thalamus_subject4 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM46_Sterile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
F1_Adult_BM46_1


title: Dam_Ctrl_For_Ets21C_3

description:
DamID_RawCounts.txt
DamID_Peaks.xlsx

value: female


title: Cerebellum_subject6 [NanoString]

description: Obtained 30 min after injury


title: XVE_WIND1_treated_w_mock_24hr_rep2


title: Adult_Testes_BM24_Sterile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
E12_Adult_BM24_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM24 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: Adult_Testes_BM24_Sterile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
E10_Adult_BM24_2


title: Adult_Testes_BM24_Sterile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
E9_Adult_BM24_1


title: Adult_Testes_BM21_Fertile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
E8_Adult_BM21_4

value: C(1)M4, {gamma}/T(1;2)BM21 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: XVE_WIND1_treated_w_mock_12hr_rep3

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with DMSO for 12 hours

value: 12 hours


title: Cerebellum_subject4 [NanoString]

description: Obtained 30 min after injury

value: Right carotid ligation followed by 8% oxygen for 30 min


title: Adult_Testes_BM21_Fertile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
E7_Adult_BM21_3


title: XVE_WIND1_treated_w_mock_12hr_rep1

value: DMSO (mock)


title: XVE_WIND1_treated_w_mock_12hr_rep2


title: Adult_Testes_BM21_Fertile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
E6_Adult_BM21_2


title: Adult_Testes_BM21_Fertile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
E5_Adult_BM21_1


title: Adult_Testes_BM6_Sterile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
E4_Adult_BM6_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM6 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: XVE_WIND1_treated_w_mock_24hr_rep1

value: 24 hours


title: XVE_WIND1_treated_w_mock_12hr_rep4


title: Adult_Testes_BM24_Sterile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
E11_Adult_BM24_3


title: Cortex_subject3 [NanoString]

description: Obtained 30 min after injury

value: 9 days


title: XVE_WIND1_treated_w_mock_6hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with DMSO for 6 hours

value: Seedling

value: 6 hours


title: Striatum/thalamus_subject3 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM6_Sterile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
E2_Adult_BM6_2


title: Cerebellum_subject3 [NanoString]

description: Obtained 30 min after injury


title: XVE_WIND1_treated_w_mock_6hr_rep2


title: Cortex_subject4 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM6_Sterile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
E1_Adult_BM6_1


title: XVE_WIND1_treated_w_mock_6hr_rep3


title: Adult_Testes_BM5_Sterile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
D12_Adult_BM5_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM5 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: XVE_WIND1_treated_w_mock_6hr_rep1


title: Striatum/thalamus_subject2 [NanoString]

description: Obtained 30 min after injury

value: Sham surgery without hypoxia


title: Adult_Testes_BM5_Sterile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
D11_Adult_BM5_3


title: XVE_WIND1_treated_w_mock_3hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with DMSO for 3 hours


title: XVE_WIND1_treated_w_mock_3hr_rep3


title: XVE_WIND1_treated_w_mock_3hr_rep2


title: Adult_Testes_BM5_Sterile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
D10_Adult_BM5_2


title: Adult_Testes_BM6_Sterile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
E3_Adult_BM6_3


title: Adult_Testes_BM4_Fertile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
D8_Adult_BM4_4

value: C(1)M4, {gamma}/T(1;2)BM4 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: Cortex_subject2 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM5_Sterile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
D9_Adult_BM5_1

value: male


title: Adult_Testes_BM4_Fertile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
D7_Adult_BM4_3

value: One-to-five day old adult


title: Cerebellum_subject2 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM4_Fertile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
D6_Adult_BM4_2


title: Striatum/thalamus_subject1 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_BM4_Fertile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
D5_Adult_BM4_1


title: Adult_Testes_BM1_Sterile_translocation_rep2

description:
Pool of 20 testes  separated from seminal vesicle
D2_Adult_BM1_2

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM1 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: Adult_Testes_BM1_Sterile_translocation_rep3

description:
Pool of 20 testes  separated from seminal vesicle
D3_Adult_BM1_3


title: Adult_Testes_BM1_Sterile_translocation_rep4

description:
Pool of 20 testes  separated from seminal vesicle
D4_Adult_BM1_4


title: Cortex_subject1 [NanoString]

description: Obtained 30 min after injury


title: Adult_Testes_Control_Irradiated_Parental_Stock_rep4

description:
Pool of 20 testes  separated from seminal vesicle
C12_Adult_BMS_4

value: C(1)M4, {gamma}/ Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: Adult_Testes_BM1_Sterile_translocation_rep1

description:
Pool of 20 testes  separated from seminal vesicle
D1_Adult_BM1_1


title: Cerebellum_subject1 [NanoString]

description: Obtained 30 min after injury


title: XVE_WIND1_treated_w_mock_1hr_rep4

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings treated with DMSO for 1 hour

value: 1 hour


title: put-3

first: Liangling

last: Shen

address: 389 Xincun Road

institute: Tongji Hospital, Tongji University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gossypium hirsutum

source_name: ovule

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.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: ovule

value: wild type

value: putrescine


title: Adult_Testes_Control_Irradiated_Parental_Stock_rep3

description:
Pool of 20 testes  separated from seminal vesicle
C11_Adult_BMS_3


title: XVE_WIND1_treated_w_mock_3hr_rep1

value: DMSO (mock)

value: 3 hours


title: Adult_Testes_Control_Irradiated_Parental_Stock_rep2

description:
Pool of 20 testes  separated from seminal vesicle
C10_Adult_BMS_2


title: XVE_WIND1_treated_w_mock_1hr_rep1


title: XVE_WIND1_treated_w_mock_1hr_rep2


title: Adult_Testes_Control_Irradiated_Parental_Stock_rep1

description:
Pool of 20 testes  separated from seminal vesicle
C9_Adult_BMS_1


title: L3_Testes_BM46_Sterile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C8_L3_BM46_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM46 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: XVE_WIND1_0hr_rep3

source_name: Arabidopsis harboring G10-90pro::XVE(LexA:VP16:hER)::E9ter O_lexA::WIND1::3Ater 10-day seedlings

value: Seedling


title: L3_Testes_BM46_Sterile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C7_L3_BM46_3


title: L3_Testes_BM46_Sterile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C6_L3_BM46_2


title: L3_Testes_BM46_Sterile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C5_L3_BM46_1


title: ck-3

value: water


title: L3_Testes_BM24_Sterile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C4_L3_BM24_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM24 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: L3_Testes_BM24_Sterile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C3_L3_BM24_3


title: put-2


title: L3_Testes_BM24_Sterile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C2_L3_BM24_2


title: AW

city: Beltsville

first: Yahui

last: Gao

state: Maryland

address: 10300 Baltimore Ave Bldg 306

institute: ARS, USDA

description: one sample from cattle rumen

data_processing:
We first processed 10X Genomics raw data by the Cell Ranger Single-Cell Software Suite (release 3.1.0), including using Cell Ranger mkfastq to demultiplex raw base-call files into FASTQ files followed by the use of Cell Ranger count to perform alignment, filtering, barcode counting, and UMI counting. The raw reads were aligned to the ARS-USD1.2 cattle reference genome by Cell Ranger pipeline using default parameters. The output summary of the two samples is shown in Supplemental Table 1. All downstream single-cell analyses were performed using the Seurat 3.0 R package v3.6.3 unless explicitly mentioned.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Bos taurus

source_name: Rumen

extract_protocol:
Rumen epithelial tissue was collected from the anterior portion of the ventral sac of the rumen beneath the reticulum and below the rumen fluid layer at slaughter. The epithelial layer of the rumen tissue was separated manually from the muscular layer. After rinsing with tap water to remove residual feed particles, samples were further rinsed in ice-cold physiological saline and subsamples of epithelial tissues (approximately 600 mg) were fixed in RNAlater (Life Technologies, Grand Island, NY, USA) RNA stabilization solution according to the manufacturer’s instructions and stored at -80°C until use.
Rumen tissue samples from the one pre-weaned and one weaned calf were collected and processed by a commercial service provider, Singulomics (New York, NY, USA), for scRNA-seq analysis. Library preparation was performed according to instructions by using the 10X Genomics Chromium single-cell controller. The libraries were then pooled and sequenced on a HiSeq4000 (Illumina, San Diego, CA, USA).

value: post-weaning


title: put-1


title: L3_Testes_BM21_Fertile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B11_L3_BM21_3

value: C(1)M4, {gamma}/T(1;2)BM21 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: L3_Testes_BM21_Fertile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B12_L3_BM21_4

value: male


title: L3_Testes_BM6_Sterile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B8_L3_BM6_4

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM6 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: XVE_WIND1_treated_w_mock_1hr_rep3


title: L3_Testes_BM21_Fertile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B10_L3_BM21_2


title: XVE_WIND1_0hr_rep4


title: XVE_WIND1_0hr_rep2


title: AGS_shELF3-AS1

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. Q20, Q30, and GC-content of the raw datas were calculated.
miRBase20.0 was used as reference, software mirDeep_star_v38 was used to obtain the potential miRNA and the miRNA counts.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

source_name: gastric cancer cell

growth_protocol: The human gastric cancer cell line AGS were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). After purification of microRNAs, the miRNA sequencing was performed according to the manufacturer’s instructions.

treatment_protocol: Two different GC cell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: AGS

tag: transfection

value: ELF3-AS1 knockdown


title: XVE_WIND1_0hr_rep1


title: control_treated_w_estrogen_24hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 24 hours

value: Wild type Col-0

value: 10 micro M estradiol

value: 24 hours


title: ck-2

value: ovule

value: wild type


title: control_treated_w_estrogen_24hr_rep1


title: control_treated_w_estrogen_24hr_rep2


title: L3_Testes_BM6_Sterile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B6_L3_BM6_2


title: BW

description: one sample from cattle rumen

value: pre-weaning


title: AGS_shNC_2

value: negative control


title: ck-1


title: L3_Testes_BM24_Sterile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
C1_L3_BM24_1

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: control_treated_w_estrogen_12hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 12 hours

value: Seedling

value: 12 hours


title: L3_Testes_BM6_Sterile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B7_L3_BM6_3


title: AGS_shNC_1


title: L3_Testes_BM6_Sterile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B5_L3_BM6_1


title: L3_Testes_BM5_Sterile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B3_L3_BM5_3

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM5 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: AGS_ELF3-AS1_siRNA#3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

growth_protocol: The human gastric cancer cell line AGS and SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and the ELF3-AS1-targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR.

treatment_protocol: Two different GC cell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the ELF3-AS1-targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

tag: cell line


title: L3_Testes_BM5_Sterile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B2_L3_BM5_2


title: L3_Testes_BM5_Sterile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B1_L3_BM5_1


title: AGS_NC_rep2

value: negative control siRNA


title: AGS_ELF3-AS1_siRNA#2


title: L3_Testes_BM4_Fertile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A12_L3_BM4_4

value: C(1)M4, {gamma}/T(1;2)BM4 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: L3_Testes_BM4_Fertile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A11_L3_BM4_3

value: male


title: L3_Testes_BM4_Fertile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A10_L3_BM4_2


title: L3_Testes_BM5_Sterile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B4_L3_BM5_4


title: control_treated_w_estrogen_24hr_rep3


title: AGS_NC_rep1


title: L3_Testes_BM4_Fertile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A9_L3_BM4_1


title: SGC7901_ELF3-AS1_siRNA#3


title: control_treated_w_estrogen_12hr_rep2


title: control_treated_w_estrogen_12hr_rep3


title: SGC7901_ELF3-AS1_siRNA#2


title: L3_Testes_BM1_Sterile_translocation_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A6_L3_BM1_2

value: FM7i, P{ActGFP}JMR3 / T(1;2)BM1 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: L3_Testes_BM1_Sterile_translocation_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A8_L3_BM1_4


title: L3_Testes_BM1_Sterile_translocation_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A7_L3_BM1_3


title: L3_Testes_BM1_Sterile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A5_L3_BM1_1


title: L3_Testes_Control_Irradiated_Parental_Stock_rep4

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A4_L3_BMS_4

value: C(1)M4, {gamma}/ Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: SGC7901_NC_rep2


title: L3_Testes_Control_Irradiated_Parental_Stock_rep3

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A3_L3_BMS_3


title: L3_Testes_Control_Irradiated_Parental_Stock_rep2

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A2_L3_BMS_2


title: L3_Testes_Control_Irradiated_Parental_Stock_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
A1_L3_BMS_1


title: control_treated_w_estrogen_6hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 6 hours

value: 6 hours


title: L3_Testes_BM21_Fertile_translocation_rep1

description:
Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
B9_L3_BM21_1

value: C(1)M4, {gamma}/T(1;2)BM21 + Dp(1;1)scV1, {gamma}2 {gamma}+ sc+ scV1 su(wa) wa cv v f


title: SGC7901_NC_rep1


title: control_treated_w_estrogen_12hr_rep1

value: Wild type Col-0

value: 10 micro M estradiol


title: TBSIIAO

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

data_processing:
A minimum of 20 million 2x150bp sequencing reads were collected from each sample. The data were pre-processed to remove the adapters using Trimmomatic v0.36
pre-processed reads were mapped to the Nematostella vectensis genome (indexed bowtie2) by using STAR.
The number of reads mapping to each Nematostella gene models was extracted using HTSeq-count v0.6
Differential expression analyses were performed using limma (Galaxy Version 2.11.40.6) and DESeq2 (Galaxy Version 2.11.40.6)
Genome_build: Nematostella vectensis (ASM20922v1)
Supplementary_files_format_and_content: tab-delimited text file includes read counts generated using HTSeq-count v0.6 tool (The NVE gene models are available at https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696)

organism: Nematostella vectensis

source_name: larval aboral tissue

extract_protocol:
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual.
RNA-seq libraries were constructed using SENSE mRNA-Seq Library Prep Kit (Lexogen GmbH). Each library was indexed in order to multiplex samples on the Illumina.

value: larval aboral tissue

value: Late planula

tag: age

value: ~ 75-85 hours post fertilization


title: TP53_p.P278A_F21_OE015_x5_S4

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: processed data file: transcript_quants_log2TPM_KRAS-TP53.csv

data_processing:
Illumina HiSeq 4000 reads were aligned by STAR v2.5.3a to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: transcript_quants_log2TPM_EMPTY-EGFP.csv is a comma-separated values file of the log2 of TPM values of the negative control samples. Each row is a gene transcript and each column is a sample.
Supplementary_files_format_and_content: transcript_quants_log2TPM_KRAS-TP53.csv is a comma-separated values file of the log2 of TPM values. Each row is a gene transcript and each column is a sample.

source_name: cell line

growth_protocol: Cells were cultured for one day before and 96 hours after treatment.

extract_protocol:
Cells were lysed and RNA extracted with TRIzol (Invitrogen)
Nextera XT Index Kit v2, 75bp paired-end pre-pooled libraries

treatment_protocol: Cells were transduced with the ORF construct (if applicable) one day after plating. Infection efficiency is assessed at 24 hours post-infection with antibody selection.

value: lung adenocarcinoma

tag: genetic perturbation

tag: genotype/variation

value: Sample ectopically expressing variant TP53 p.P278A


title: TP53_p.P278T_A14_OE015_x5_S4

value: Sample ectopically expressing variant TP53 p.P278T


title: TP53_p.P278A_F21_OE015_x6_S4


title: TP53_p.P278T_A14_OE015_x6_S4


title: TP53_p.P278H_G09_OE015_x6_S4

value: Sample ectopically expressing variant TP53 p.P278H


title: TBSIAO

tag: tissue


title: control_treated_w_estrogen_3hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 3 hours

value: Seedling

tag: treatment

tag: treatment duration

value: 3 hours


title: TP53_p.P278H_G09_OE015_x5_S4


title: control_treated_w_estrogen_6hr_rep2

tag: genotype


title: TBSIIIB

source_name: larval body tissue

value: larval body tissue


title: control_treated_w_estrogen_3hr_rep1


title: TP53_p.P278A_F21_0E015_x3_C9


title: control_treated_w_estrogen_6hr_rep1


title: TBSIIIAO


title: TP53_p.P278H_G09_0E015_x2_D3


title: TP53_p.P278T_A14_0E015_x3_C7


title: TBSIIB


title: TP53_p.P278A_F21_0E015_x2_C3


title: TP53_p.P278H_G09_0E015_x3_D9


title: control_treated_w_estrogen_3hr_rep3


title: KRAS_p.G12C_J17_C4_S5

value: KRAS p.G12C

value: Sample ectopically expressing variant KRAS p.G12C


title: TBSIB


title: KRAS_p.G12C_J17_C10_S5


title: KRAS_p.G12V_E15_OE015_x6_S4

value: KRAS p.G12V

value: Sample ectopically expressing variant KRAS p.G12V


title: TP53_p.P278T_A14_0E015_x2_C1


title: control_treated_w_estrogen_1hr_rep4

source_name: Arabidopsis Col-0 10-day seedlings treated with 10 micro M estradiol for 1 hour

value: 1 hour


title: PSIIAO

value: planula

value: ~ 50-60 hours post fertilization


title: control_treated_w_estrogen_3hr_rep2

value: Wild type Col-0

value: 10 micro M estradiol


title: KRAS_p.G12V_E15_OE015_x5_S4


title: PSIAO

value: larval aboral tissue


title: KRAS_p.G12C_J17_OE014_x7_S3

value: lung adenocarcinoma


title: KRAS_p.G12C_J17_OE014_x8_S3


title: KRAS_p.G12V_E15_0E015_x3_B8


title: PSIIB


title: KRAS_p.G12V_E15_0E015_x2_B2


title: PSIB


title: control_treated_w_estrogen_1hr_rep1


title: KRAS_p.G12V_F22_H4


title: KRAS_WT_B22_H1

value: KRAS WT

value: Sample ectopically expressing wild-type KRAS


title: KRAS_WT_B21_G1


title: KRAS_p.G12V_E21_E4


title: control_treated_w_estrogen_1hr_rep2


title: KRAS_p.G12V_E22_F4


title: KRAS_p.G12V_F21_G4


title: EGFP_B06_OE015_x6_S4

description: processed data file: transcript_quants_log2TPM_EMPTY-EGFP.csv

value: EGFP

value: Negative control sample with ectopic expression of EGFP


title: EGFP_B06_OE015_x5_S4


title: control_treated_w_mock_24hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 24 hours

value: Seedling

value: DMSO (mock)

value: 24 hours


title: EGFP_B06_0E015_x3_E7


title: KRAS_WT_A21_E1


title: control_treated_w_mock_24hr_rep2


title: control_treated_w_mock_24hr_rep1


title: EGFP_B06_0E015_x2_E1


title: control_treated_w_mock_12hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 12 hours

value: 12 hours


title: control_treated_w_mock_12hr_rep4


title: control_treated_w_mock_12hr_rep2


title: EMPTY_D20_E8_S5

value: Negative control sample with no ectopic gene expression


title: EMPTY_D20_E2_S5


title: EMPTY_D19_D8_S5


title: control_treated_w_mock_6hr_rep3

source_name: Arabidopsis Col-0 10-day seedlings treated with DMSO for 6 hours

value: 6 hours


title: control_treated_w_mock_6hr_rep2


title: combi-2#3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression of HuCCT-1 cells transfected with siRNAs YAP2/TAZ3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Clariom D from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: HuCCT-1 cells

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

growth_protocol: Cells were cultured in RPMI (Sigma Aldrich, Steinheim, Germany) or DMEM (Gibco/Thermo Fisher Scientific, Waltham USA) containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO2 atmosphere. Cells were routinely tested for mycoplasma contamination and authentication was performed by short tandem repeat (STR) analysis (DSMZ, Braunschweig, Germany).

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: Gene-specific small interfering RNAs (siRNAs) were obtained from Eurofins MWG Operon (Ebersberg, Germany). For siRNA inhibition assays, cells were directly transfected after trypsination. Scrambled siRNA-treated cells served as control. Gene-specific siRNAs (final concentration of 40 nM for combinations of two siRNAs for YAP and TAZ) and the transfection reagent Lipofectamine RNAiMAX (Gibco/Thermo Fisher Scientific) were diluted, mixed in Opti-MEM (Gibco/Thermo Fisher Scientific) and incubated at room temperature, before being distributed onto the cells. Twenty-four hours after transfection, fresh medium was added.

value: siRNAs YAP2/TAZ3


title: combi-1#2

description: Gene expression of HuCCT-1 cells transfected with siRNAs YAP1/TAZ2

value: siRNAs YAP1/TAZ2


title: control_treated_w_mock_12hr_rep1


title: combi-2#1


title: EMPTY_D19_D2_S5


title: combi-1#3