title: LS200C22-A ko

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

institute: Albert Einstein College of Medicine

data_processing:
Alignment with STAR (v2.7.9a)
Counts with RSEM (v1.3.3)
DESeq2 (v1.38.3) for differential gene expression analysis
Differential expression analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: txt file of DESeq2 analysis

source_name: Glutamatergic Neurons

growth_protocol: Glutamatergic neuronal differentiation was induced using a protocol developed by Zhang et al., in which differentiation is driven by overexpression of the transcription factor Neurogenin2 (NGN2).72 A tet-inducible expression system was introduced, and lentivirus particles prepared from the plasmid vectors; pLV_TRET_hNgn2_UBC_Puro (RRID:Addgene_61474) and FUdeltaGW-rtTA (RRID:Addgene_19780), followed by treatment with doxycycline and selection with puromycin.

extract_protocol:
Trizol/chloroform followed by precipitation using isopropanol
Qiagen miRNeasy Mini kit (#217002)

treatment_protocol: day 45

value: Glutamatergic Neurons

tag: genotype

value: KO


title: gastroc normoxia replicate 07

status: Public on Oct 23 2023

type: RNA

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. All arrays were included for data processing and normalization. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

molecule: total RNA

organism: Mus musculus

source_name: gastroc, normoxia

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7).

growth_protocol: Male C57BL/6JOlaHsd mice arrived at 10 weeks of age and were individually housed and maintained under environmentally controlled conditions (21 ± 1ºC, 12 h/12 h light–dark cycle, 50 ± 10% humidity) and had ad-libitum access to feed and water. During the first three weeks of the study, mice could adapt to the new environment and received a purified low-fat diet that contained 10% energy from fat (Hoevenaars et al., Genes & Nutr 2012). Thereafter, mice received a purified high-fat diet that contained 40% energy from fat for the remaining 6 weeks of the study.

extract_protocol: Total RNA was isolated from the gastrocnemius muscle using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: After the 6 weeks of high-fat feeding, mice were fasted and were either exposed to hypoxia (12% oxygen) or remained under normoxia (20.9% oxygen) for a duration of 6 hours, according to Duivenvoorde et al., (J Gerontol A Biol Sci Med Sci. 2014). Mice were decapitated directly after the exposure and the gastrocnemius muscle was removed and snap-frozen in liquid nitrogen.

tag: strain

tag: gender

value: male

tag: tissue

value: gastrocnemius

tag: stress

value: normoxia

source_name: gastroc, reference pool of all samples

tag: sample type

value: reference pool of all samples


title: LS200C22-B ko

type: SRA

department: Genetics

country: USA

library_source: transcriptomic

organism: Homo sapiens

tag: cell line


title: gastroc hypoxia replicate 07

source_name: gastroc, hypoxia

value: hypoxia


title: gastroc normoxia replicate 04


title: gastroc normoxia replicate 05


title: gastroc hypoxia replicate 06


title: gastroc normoxia replicate 09


title: gastroc normoxia replicate 08


title: gastroc normoxia replicate 10


title: LS200C2-B wt

value: WT


title: ChIP-seq of H3K27ac in Homo sapiens: U87-Erastin 10 μM 72 h-input

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

library_source: genomic

data_processing:
Clean reads of RNA-seq were mapped to hg38 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with featureCounts (2.0.4)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with padj < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to hg38 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP were mapped to hg38 with HIC-Pro (2.11.4)
HiChIP loops was called by hichipper(0.7.7)
Assembly: hg38
Supplementary files format and content: gene count text files; chip peak bigwig files; HiChIP interaction matrix files

molecule: genomic DNA

source_name: brain

growth_protocol: The glioma cell lines U87 was cultured in DMEM (GIBCO), supplemented with 10% fetal bovine serum (BI) and 1% penicillin/streptomycin (GIBCO).

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.  2. For Chip-seq: Cells were cross-linked with 1% formaldehyde at RT for 10 min and quenched in 125 mM glycine for 5 min. Cells were resuspended in SDS lysis buffer for 5 min and sonicated to generate DNA fragments averaging 100–500 bp in length. After centrifugation, chromatin fragments were immunoprecipitated with antibodies overnight (H3K27ac, H3K4me1, Abcam). The precipitated DNA and input DNA were purified and then sequenced at Novogene (Tianjin city, China).                                                                                3. For HiChIP: Briefly,  cells were cross-linked and chromatin was digested using MboI restriction enzyme (NEB). Then biotin-14-dATP was used to fill in the restriction fragment overhangs and mark the DNA ends. After ligation and sonication, the genomic DNA was incubated with H3K27ac antibody at 4 °C overnight. Immunocomplexes were captured by protein A magnetic beads. Beads were subsequently washed three times with low salt wash buffer, high salt wash buffer and LiCl wash buffer. DNA was eluted and purified with AMPure XP Beads (Beckman). Biotinylated DNA beads were captured by Streptavidin C-1. QIAseq FX DNA Library Kits (QIAGEN) was used to generate the sequencing library according to the manufacturer’s protocol. The libraries were validated for size distribution of 300–700 bp using AMPure XP beads (Beckman). The DNA was subjected to 2 × 150 bp paired-end sequencing at Novogene (Tianjin city, China).
RNA-seq Library: Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.                                                                                2. ChIP-seq:  DNA libraries were generated using a FS DNA Library Prep Kit (QIAGEN). The precipitated DNA and input DNA were purified and then sequenced on Illumina HiSeq XTen sequencer. Bowtie2 was used to map ChIP-seq raw reads to the hg38 human reference genome. MACS2 program was used to call peaks of ChIP-seq data with the corresponding input data as control with default parameters. 3. HiChIP: QIAseq FX DNA Library Kits (QIAGEN) was used to generate the sequencing library according to the manufacturer’s protocol. The libraries were validated for size distribution of 300–700 bp using AMPure XP beads (Beckman). The DNA was subjected to 2 × 150 bp paired-end sequencing. The respective paired-end reads were aligned to the hg38 genome by HiC-Pro pipeline. Default settings were used for removal of duplicated reads, assignment to MboI restriction fragments and filtering for valid interactions. For each cell type, we merged the valid read pairs of individual samples. Hichipper was applied to call loops with default parameter. Loops with FDR < 0.1 and supported by at least 2 paired-end tags (PETS) were kept for further analysis. HiC-Pro was used to generate the HiChIP interaction maps. HiChIP interaction maps was then visualized by JuicerBox software at 50, 10 and 5 kb resolution as indicated.

treatment_protocol: For Erastin treatment, U87 cells were treated with 10 μM Erastin for 72 h.

value: brain

tag: treatment

value: 10 microM Erastin treated 72 h


title: Mus03

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v2.2.0 using default parameters to obtain the gene expression matrices.
Genome_build: mm10 or Aco_one
Supplementary_files_format_and_content: mtx matrix files

source_name: ear

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

tag: age

value: Adult

value: ear

tag: cell type

value: macrophages


title: healthy donor - adipose stromal cells, Rep 3

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with parameters : --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using featureCounts from Subread package.
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts values for each Sample.

source_name: healthy donor, fat tissue

growth_protocol: not applicable

extract_protocol:
Lipoaspiration from 4 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells (Dynal, Dynabeads CD45) stromal cells were sorted by FACS based on their phenotype and RNA extraction (Macherey-Nagel, NucleoSpin RNA XS) was performed. Quality control was performed using the Agilent RNA 6000 Pico Kit.
RNA libraries were prepared (with 10ng of total RNA) for sequencing using standard Illumina protocols.

treatment_protocol: not applicable

value: native adipose stromal cells

tag: subject

value: healthy donor


title: LS200C2-A wt


title: ChIP-seq of H3K4me1 in Homo sapiens: U87-H3K4me1-Rep2

value: Normal growth condition


title: gastroc hypoxia replicate 08


title: healthy donor - adipose stromal cells, Rep 2


title: Mus00


title: gastroc normoxia replicate 03


title: gastroc normoxia replicate 11


title: LS200C13-B ko


title: ChIP-seq of H3K4me1 in Homo sapiens: U87-H3K4me1-Rep1


title: gastroc normoxia replicate 01


title: Gp38+ stromal cells - Ad5 infected - Day 2, Rep 18 [Mus_stromal_cells]

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mm10 whole genome using STAR with parameters : --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread.
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: *txt: Tab-delimited text files include counts values for each Sample.

source_name: Gp38+ stromal cells from salivary glands

extract_protocol:
Gp38pos stromal cells from salivary glands infected or not with Ad5 at different time point post infection were sorted by FACS based on their phenotype and RNA extraction (Macherey-Nagel, NucleoSpin RNA XS) was performed. Quality control was performed using the Agilent RNA 6000 Pico Kit.
RNA libraries were prepared (with 10ng of total RNA) for sequencing using standard Illumina protocols.

value: Balb/c

value: WT native Gp38+ stromal cells

value: Ad5 infected

tag: time point


title: ChIP-seq of H3K4me1 in Homo sapiens: U87-Erastin 10 μM 72 h-H3K4me1-Rep2


title: healthy donor - adipose stromal cells, Rep 1


title: Gp38+ stromal cells - Ad5 infected - Day 2, Rep 17 [Mus_stromal_cells]


title: ChIP-seq of H3K4me1 in Homo sapiens: U87-Erastin 10 μM 72 h-H3K4me1-Rep1


title: ChIP-seq of H3K27ac in Homo sapiens: U87-H3K27ac-Rep2


title: LS200C1-B wt

value: Glutamatergic Neurons


title: LS200C13-A ko

value: KO


title: TNFLT/GSKJ4 treated ASC, Rep 4 [Hum_ASC_GSKJ4]

description:
ASC16
mRNA

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with parameters : --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread.
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include counts values for each Sample.

source_name: fat tissue

growth_protocol: Adipose stromal cells (ASC) were obtained from the stromal vascular fraction of adipose tissue and were maintained in a modified Minimum Essential Medium Eagle (Gibco) supplemented with 10% fetal calf serum (FCS) (Biosera) and 1 ng/mL of basic fibroblast growth factor (bFGF) (Cellgenix). These cells were used between passages 1 and 3 for experiments in the same medium without supplementation in bFGF.

extract_protocol:
RNA was extracted from human ASC by using NucleoSpin RNA Plus Kit (Macherey-Nagel).
RNA libraries were prepared (with 500ng of mRNA) for sequencing using standard Illumina protocols.

treatment_protocol: ASC were treated by using tumor necrosis factor alpha (TNFα) (5 ng/mL) / lymphotoxin αlpha1 beta2 (LTα1β2) (50 ng/mL) (R&D Systems). When indicated ASC were concomitantly treated with the KDM6 inhibitor GSK-J4 (20uM) or DMSO (MOCK control) for 6 hours before RNA extraction.

value: adipose stromal cells

tag: treatment 1

value: treated with TNFLT

tag: treatment 2

value: treated with GSKJ4

value: healthy donor 4


title: GSKJ4 treated ASC, Rep 4 [Hum_ASC_GSKJ4]

description:
ASC15
mRNA

value: untreated


title: LS200C1-A wt

value: WT


title: TNFLT treated ASC, Rep 4 [Hum_ASC_GSKJ4]

description:
ASC14
mRNA


title: ChIP-seq of H3K27ac in Homo sapiens: U87-H3K27ac-Rep1

value: brain


title: Gp38+ stromal cells - Ad5 infected - Day 1, Rep 14 [Mus_stromal_cells]


title: TNFLT/GSKJ4 treated ASC, Rep 3 [Hum_ASC_GSKJ4]

description:
ASC12
mRNA

value: healthy donor 3


title: ChIP-seq of H3K27ac in Homo sapiens: U87-Erastin 10 μM 72 h-H3K27ac-Rep2

value: 10 microM Erastin treated 72 h


title: Gp38+ stromal cells - Ad5 infected - Day 1, Rep 13 [Mus_stromal_cells]


title: ChIP-seq of H3K27ac in Homo sapiens: U87-Erastin 10 μM 72 h-H3K27ac-Rep1


title: Gp38+ stromal cells - not infected - Hour 0, Rep 12 [Mus_stromal_cells]

value: not infected at H0


title: NPC_DNA_rep3

city: Kyoto

first: Xun

last: Chen

address: Faculty of Medicine Building B, Yoshidatachibanacho, Sakyo Ward

department: Institute for the Advanced Study of Human Biology (ASHBi)

country: Japan

institute: Kyoto University

description: NPC replication 3 DNA library

library_source: other

data_processing:
The optimized MPRAflow pipeline was used to associate every insert sequence and barcodes
An in-house python script "ConvertPickleToCsv.py" was used to convert the output files from "pickle" to "csv" format
The optimized MPRAflow pipeline was used to count barcodes per sequence in DNA and RNA libraries
Assembly: hg19, panTro4, and macFas5
Supplementary files format and content: text files include raw DNA and RNA counts per barcode for each library

molecule: other

growth_protocol: WTC11 human iPSCs were maintained on matrigel in mTeSR plus medium (Stemcell technologies) and passaged using ReLeSR (Stemcell technologies).

extract_protocol:
Genomic DNA and total RNA were purified from the infected cells using an AllPrep DNA/RNA mini kit (Qiagen). To remove contaminating DNA, RNA was treated with Turbo Dnase (Thermo Fisher Scientific).
120 ug total RNA samples were reverse-transcribed with SuperScript II (Invitrogen) using a barcode-specific primer, which has a 16-bp unique molecular identifier (UMI). The cDNA and 48 μg genomic DNA from each sample were used for 3-cycle PCR with specific primers that add sample index and UMI. A second round PCR (21 and 26 cycles for DNA and RNA barcode samples, respectively) was performed using P5 and P7 primers. PCR products were size-selected with an agarose gel, purified with AmPure XP beads (Beckman coulter) and pooled.
Custom DNA sequencing; 15-cycle paired-end reads, 16-cycle index read1 for UMI, and 10-cycle index read2 for sample index.

treatment_protocol: iPSCs were infected with the MPRA library using ViroMag R/L reagent (OZ Biosciences) and incubated for 24 hours. The infected cells were cultured for additional 3 days with a daily change of the mTeSR plus media, or induced into neural lineage for 3 days by following dual-Smad inhibition protocol (Chambers et al., 2009; Inoue et al, 2019).

value: iPSC-derived NPCs

value: MPRA library infection and NPC differentiation


title: NPC_RNA_rep2

description: NPC replication 2 RNA library


title: NPC_RNA_rep1

description: NPC replication 1 RNA library


title: TNFLT treated ASC, Rep 3 [Hum_ASC_GSKJ4]

description:
ASC10
mRNA


title: RNA-Seq of Homo sapiens: U87-Erastin 10 μM 72 h-Rep2


title: NPC_DNA_rep2

description: NPC replication 2 DNA library


title: Gp38+ stromal cells - Ad5 infected - Day 2, Rep 16 [Mus_stromal_cells]

value: Balb/c


title: RNA-Seq of Homo sapiens: U87-Erastin 10 μM 72 h-Rep1


title: Gp38+ stromal cells - Ad5 infected - Day 1, Rep 15 [Mus_stromal_cells]

value: WT native Gp38+ stromal cells


title: Gp38+ stromal cells - not infected - Hour 0, Rep 10 [Mus_stromal_cells]


title: NPC_DNA_rep1

description: NPC replication 1 DNA library


title: Gp38+ stromal cells - not infected - Hour 0, Rep 11 [Mus_stromal_cells]


title: RNA-Seq of Homo sapiens: U87-WT-Rep2

value: Normal growth condition


title: TNFLT/GSKJ4 treated ASC, Rep 2 [Hum_ASC_GSKJ4]

description:
ASC8
mRNA

value: healthy donor 2


title: DMSO treated ASC, Rep 3 [Hum_ASC_GSKJ4]

description:
ASC9
mRNA


title: RNA-Seq of Homo sapiens: U87-WT-Rep1


title: NPC_RNA_rep3

description: NPC replication 3 RNA library


title: Gp38+ stromal cells - Ad5 infected - Day 23, Rep 8 [Mus_stromal_cells]

value: Ad5 infected


title: GSKJ4 treated ASC, Rep 2 [Hum_ASC_GSKJ4]

description:
ASC7
mRNA

value: adipose stromal cells


title: iPSC_RNA_rep2

description: iPSC replication 2 RNA library

value: iPSCs

value: MPRA library infection


title: DMSO treated ASC, Rep 4 [Hum_ASC_GSKJ4]

description:
ASC13
mRNA

value: healthy donor 4


title: Gp38+ stromal cells - Ad5 infected - Day 23, Rep 9 [Mus_stromal_cells]


title: MDA-MB-468 cells, shTopBP1, vehicle, biol rep 4

city: Houston

first: Weei-Chin

last: Lin

state: TX

address: R410, One Baylor Plaza

department: Medicine and Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Sequenced reads in FASTQ files were mapped to hg19 whole genome using STAR (v2.5), and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MDA-MB-468 cell line was from the American Type Culture Collection (ATCC). Cell were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc. (Sacramento, CA USA). The datasets were processed and analyzed using Illumina NovaSeq 6000 Sequencing System.

treatment_protocol: Cells were treated with 5D4 (5mM), Calcein AM (5mM) or vehicle control for 6 hours.

value: triple-negative breast cancer

value: TopBP1 knockdown

value: DMSO vehicle control

tag: time

value: 6 hours


title: GSKJ4 treated ASC, Rep 3 [Hum_ASC_GSKJ4]

description:
ASC11
mRNA

value: untreated

value: treated with GSKJ4

value: healthy donor 3


title: MDA-MB-468 cells, shTopBP1, vehicle, biol rep 3


title: DMSO treated ASC, Rep 2 [Hum_ASC_GSKJ4]

description:
ASC5
mRNA


title: iPSC_RNA_rep1

description: iPSC replication 1 RNA library

value: WT


title: iPSC_DNA_rep3

description: iPSC replication 3 DNA library


title: MDA-MB-468 cells, shTopBP1, vehicle, biol rep 2


title: Gp38+ stromal cells - Ad5 infected - Hour 3, Rep 5 [Mus_stromal_cells]

value: Balb/c


title: TNFLT/GSKJ4 treated ASC, Rep 1 [Hum_ASC_GSKJ4]

description:
ASC4
mRNA

value: treated with TNFLT

value: healthy donor 1


title: iPSC_DNA_rep2

description: iPSC replication 2 DNA library


title: MDA-MB-468 cells, shTopBP1, vehicle, biol rep 1


title: iPSC_RNA_rep3

description: iPSC replication 3 RNA library


title: GSKJ4 treated ASC, Rep 1 [Hum_ASC_GSKJ4]

description:
ASC3
mRNA


title: Gp38+ stromal cells - Ad5 infected - Hour 3, Rep 4 [Mus_stromal_cells]

value: WT native Gp38+ stromal cells


title: MDA-MB-468 cells, shScr, Calcein AM, biol rep 4

value: Calcein AM


title: Gp38+ stromal cells - Ad5 infected - Day 8, Rep 3 [Mus_stromal_cells]

value: Ad5 infected


title: TNFLT treated ASC, Rep 1 [Hum_ASC_GSKJ4]

description:
ASC2
mRNA

value: adipose stromal cells


title: iPSC_DNA_rep1

description: iPSC replication 1 DNA library

value: iPSCs

value: MPRA library infection


title: MDA-MB-468 cells, shScr, Calcein AM, biol rep 3

value: triple-negative breast cancer


title: TNFLT treated ASC, Rep 2 [Hum_ASC_GSKJ4]

description:
ASC6
mRNA

value: healthy donor 2


title: Gp38+ stromal cells - Ad5 infected - Day 23, Rep 7 [Mus_stromal_cells]


title: MDA-MB-468 cells, shScr, Calcein AM, biol rep 2


title: Gp38+ stromal cells - Ad5 infected - Day 8, Rep 1 [Mus_stromal_cells]


title: Gp38+ stromal cells - Ad5 infected - Day 8, Rep 2 [Mus_stromal_cells]


title: Not treated ASC, Rep 3 [Hum_ASC_TNFLT]

description:
ASC5
mRNA

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters : --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using featureCounts from Subread package.
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include counts values for each Sample.

treatment_protocol: ASC were treated by using tumor necrosis factor alpha (TNFα) (5 ng/mL) / lymphotoxin αlpha1 beta2 (LTα1β2) (50 ng/mL) (R&D Systems) and collected 3 days after treatment.

value: No treatment


title: MDA-MB-468 cells, shScr, Calcein AM, biol rep 1

value: 6 hours


title: ASFV-ASFV PPI network

city: Wuhan

first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
Data filtering:  The semi-global alignment algorithm and unique alignment algorithm were used to obtain the protein interaction information between Prey library and Bait library in RLL-Y2H sequencing data.The raw sequencing reads without complete MmeI-ATTL-MmeI site “gttggaTAGCGTGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGGCGTTGACtccgac” were excluded by the tool RLLNP (https://github.com/thxie/RLLNP).  Reads with adapters sequences was also excluded.
Trimming: retained the reads containing about 13 bp DNA flanking both sides of MmeI-ATTL-MmeI
Aligning: The two subreads libraries were aligned to bait library and prey library respectively using RLLNP. Only unambiguously aligned reads without mismatch were retained.
Frequency counting: Interaction frequency of a protein pair was calculated by counting the sequencing pairs that could be aligned to them.
Supplementary files format and content: text files include PPI for each Sample

organism: Saccharomyces cerevisiae

source_name: Y2HGold, Y188

growth_protocol: Clontech Yeast Protocols Handbook

extract_protocol:
All the colonies on SD/-AHLT selective plates were pooled for plasmid extraction, according to Clontech yeast plasmid extraction protocol
The plasmid were amplified, and then harvested for MmeI digestion.These digested products were ligated with Illumina P5 and P7 adaptors to generate a high throughput sequencing library.
The libraries were constructed into the pmAD/pmBD vector in yeast Y187 and Y2HGoldstrain strain by recombilation.

treatment_protocol: Yeast plasmids were extracted using the Yeast Plasmid Kit

value: Y2HGold, Y187

value: MATa, MAT&alpha

value: RLL-Y2H screening and library construction

value: recombined bait and prey fragments


title: MDA-MB-468 cells, shScr, 5D4, biol rep 4

value: WT


title: Gp38+ stromal cells - Ad5 infected - Hour 3, Rep 6 [Mus_stromal_cells]

value: Balb/c


title: TNFLT treated ASC, Rep 2 [Hum_ASC_TNFLT]

description:
ASC4
mRNA

value: TNFLT treatment


title: Rac1 cKO 3

city: Porto

first: Tiago

last: Almeida

address: Rua Alfredo Allen

country: Portugal

institute: i3s - Instituto de Investigação e Inovação em Saúde da Universidade do Porto

description: Targeted RNAseq

data_processing:
Thermo Fisher Torrent Suite V5.12 used for basecalling
Thermo Fisher Torrent Suite V5.12 used for alignment
Thermo Fisher ampliSeqRNA V5.12 in Torrent Suite V5.12 used for reads counting and normalization
Assembly: AmpliSeq_Mouse_Transcriptome_v1_designed
Supplementary files format and content: .chp files

source_name: Brain

extract_protocol:
Brains from PBS-perfused mice were collected and microglia was isolated through MACS (CD11b+ selection). Total RNA was extracted using the Quick-RNATM MiniPrep kit (Zymo Research) according to the manufacturer's instructions.
Ion Torrent sequencing libraries were prepared according to AmpliSeq™ Transcriptome Mouse Gene Expression Kit protocol following manufacturer's instructions.Briefly,1 ng of total RNA was reverse transcribed, the resulting cDNA was amplified for 16 cycles by adding PCR MasterMix and theAmpliSeq Mouse transcriptome gene expression primer pool.Amplicons were digested with the proprietary FuPa enzyme, then barcoded adapters were ligated onto the target amplicons. The library amplicons were bound to magnetic beads, and residual reaction components were washed off. Libraries were amplified, re-purified and individuallyquantified using Agilent TapeStation High Sensitivity tape. Individual libraries were diluted to a 50 pM concentration and pooled equally. Emulsion PCR, templating and 550 chip loading was performed with an Ion Chef Instrument (Thermo-Fisher). Sequencing was performed on an Ion S5XL™ sequencer (Thermo-Fisher).

value: Brain

value: Microglia

value: Cx3cr1CreER+/:Rac1fl/fl (Rac1 cKO)


title: CT 3

description: Targeted RNAseq

value: Rac1fl/fl (CT)


title: MDA-MB-468 cells, shScr, 5D4, biol rep 3


title: ASFV-host PPI network

source_name: Y2HGold, Y187


title: DMSO treated ASC, Rep 1 [Hum_ASC_GSKJ4]

description:
ASC1
mRNA

value: adipose stromal cells

value: untreated

value: healthy donor 1


title: MDA-MB-468 cells, shScr, 5D4, biol rep 2

value: triple-negative breast cancer


title: Rac1 cKO 2

description: Targeted RNAseq


title: TNFLT treated ASC, Rep 3 [Hum_ASC_TNFLT]

description:
ASC6
mRNA

value: healthy donor 3


title: TNFLT treated ASC, Rep 1 [Hum_ASC_TNFLT]

description:
ASC2
mRNA


title: Rac1 cKO 1

description: Targeted RNAseq


title: MDA-MB-468 cells, shScr, 5D4, biol rep 1

value: 6 hours


title: Acomys15

organism: Acomys cahirinus

value: Adult

value: ear

value: macrophages


title: Acomys10

description: 10X-Seifert-Acomys10-WT-20181217-3v2am_S3


title: CT 1

description: Targeted RNAseq


title: Not treated ASC, Rep 2 [Hum_ASC_TNFLT]

description:
ASC3
mRNA

value: No treatment

value: healthy donor 2


title: 136 - 1m_KO_rep5

city: Rehovot

first: Avraham

last: Yaron

address: Herzl st. 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a ADAPTER1 -A ADAPTER2 -a “A{10}” -a “T{10}” –times 2 -q 20 -m 25)
Reads were mapped to mm10 genome using STAR (DOI:10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Counting was done using STAR & Gencode GTF.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI:10.1186/s13059-014-0550-8)
FDR was calculated using fdrtool_1.2.15  R pakage (fdrtool function, statistic = "normal").
Assembly: mm10
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

source_name: Dorsal root ganglia

extract_protocol:
TRIzol® Reagent, Life Technologies, according to manufacturer’s instruction.
the poly(A) fraction (mRNA) was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation, and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).

value: Dorsal root ganglia

value: Kif2a fl/fl; Avil cre

value: 1 month


title: Acomys05


title: MDA-MB-468 cells, shScr, vehicle, biol rep 4

value: WT

value: DMSO vehicle control


title: 135 - 1m_WT_rep5

value: Kif2a fl/fl


title: KN99a_time_24h_replicate_4

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

data_processing:
Read quality was measured with FastQC
Fastq files were aligned to the KN99a genome ASM14924v2 using Hisat2 version 2.2.1 with the default parameters plus --max-intronlen 2200
SAM files were converted to bam, reads were sorted and indexed, and read duplicates were removed from the final bam files using SAMtools 1.7
d and indexed, and read duplicates were removed from the final bam files using SAMtools 1.7.
The number of reads mapped per gene was calculated using featureCounts from the package Subread 2.0.0
Assembly: Differential gene expression was analyzed with DESeq2, using the IHW (independent hypothesis weighting) package to calculate adjusted p-values
Supplementary files format and content: C8.24_KN99.24.csv
Supplementary files format and content: Table containing comparison of gene expression between C8 and KN99a (C8/KN99a) after growth for 24 hours in RPMI + 10% mouse serum (37°C, 5% CO2)

organism: Cryptococcus neoformans

source_name: cell Culture

growth_protocol: Strains were streaked from storage at -80 °C onto YPD plates, incubated for two days at 30 °C, inoculated from single colonies into YPD liquid cultures, and grown at 30 °C with shaking (220 rpm)

extract_protocol:
Approximately 2 × 10^8cells were collected by centrifugation, suspended in TRIzol reagent (from Invitrogen), and subjected to mechanical lysis by bead beating at 4°C with 0.5-mm glass beads for 1 min, followed by a 2-min rest, for a total of 5 cycles. Following lysis, total RNA was extracted according to the manufacturer's instructions. Residual DNA was removed from the RNA preparation by treatment with the Turbo DNA-free kit (from Ambion) according to the manufacturer's instructions.
We used the NEBNext Ultra Directional RNA Library Prep Kit for Illumina protocol according to the manufacturer's instruction.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: RNA was isolated from  strains before or after growth for 24 hours in RPMI + 10% mouse serum (37°C, 5% CO2)

value: cell Culture

value: Yeast


title: MDA-MB-468 cells, shScr, vehicle, biol rep 3


title: KN99a_time_24h_replicate_3


title: Acomys03

description: 10X-Seifert-Acomys03-WT-20181217-3v2am_S2


title: CT 2

description: Targeted RNAseq

value: Brain

value: Microglia

value: Rac1fl/fl (CT)


title: 133 - 1m_WT_rep4

value: Kif2a fl/fl;


title: MDA-MB-468 cells, shScr, vehicle, biol rep 2

value: triple-negative breast cancer

value: 6 hours


title: Acomys00

description: 10X-Seifert-Acomys00-WT-20181217-3v2am_S1

value: Adult

value: ear

value: macrophages


title: KN99a_time_24h_replicate_2


title: 132 - 1m_KO_rep3

value: Dorsal root ganglia


title: Pollen_WT_3

first: Xuemei

last: Zhou

address: 182 Minyuan Road, Hongshan district

institute: South-Central University for Nationalities

description: Extracted by MiniBEST Plant RNA Extration Kit (TaKaRa)

data_processing:
Base-calling was performed using a propriety Sub-pixel Registration algorithm.
Reads contained adaptors and low quality reads were removed by SOAPnuke.
Clean reads were then mapped to the tobacco genome and reference transcript sequences using the HISAT2 and Bowtie 2.
The expression level of each gene in the transcriptome as quantified as fragments per kilobase of transcript per million mapped reads using RSEM.
Differentially expressed genes were identified using DESeq2.
Genome_build: Ntab-TN90 reference Annotation Release 100
Supplementary_files_format_and_content: Excel file includes FPKM vaule of each gene

organism: Nicotiana tabacum

source_name: Pollen

growth_protocol: All plants were grown under 12 h of daylight at 25 ± 2 °C in a glasshouse

extract_protocol:
RNA was extracted  using MiniBEST Plant RNA Extration Kit (TaKaRa).
Sequencing libraries were then generated using MGIEasy RNA Library Prep Kit.

value: Pollen

tag: developmental stage

value: Bicellular pollen

value: WT plants


title: MDA-MB-468 cells, shScr, vehicle, biol rep 1

value: WT

value: DMSO vehicle control


title: KN99a_time_24h_replicate_1

value: cell Culture


title: Not treated ASC, Rep 1 [Hum_ASC_TNFLT]

description:
ASC1
mRNA

value: adipose stromal cells

value: No treatment

value: healthy donor 1


title: 131 - 1m_WT_rep3

value: 1 month


title: 125 - 1m_KO_rep2

value: Kif2a fl/fl; Avil cre


title: KN99a_time_0h_replicate_4

value: Yeast


title: Pollen_WT_1


title: 134 - 1m_KO_rep4


title: Pollen_ATG5_3

value: ATG5 RNAi plants


title: 124 - 1m_WT_rep2

value: Kif2a fl/fl


title: KN99a_time_0h_replicate_2


title: ORG-PT_cut-and-run_IgG (HNF4A control)

city: St. Louis

first: Yasuhiro

last: Yoshimura

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

data_processing:
FASTQ files were trimmed with Trim Galore (Cutadapt [v2.8]) and aligned with Bowtie2 (parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700) using hg38.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Kidney organoid-derived proximal tubular cells

growth_protocol: Kidney organoids were generated by Takasato et al., 2016 (PMID: 27560173) with slight modifications. Proximal tubular cells were sorted as an LTL-positive population by flow cytometry and filtered through a 40-μm cell strainer.

extract_protocol:
Frozen human adult kidney cortex was cut into < 1 mm pieces, homogenized using a dounce tissue homogenizer, and incubated on ice for 3 min in chilled Nuclei EZ lysis buffer supplemented with protease inhibitor cocktail. The homogenate was filtered through a 40-μm cell strainer and centrifuged at 500 g for 5 minutes at 4°C. The pellet was resuspended and washed with chilled lysis buffer, and further incubated on ice for 3 minutes. Following centrifugation, the pellet was resuspended in XL wash buffer, and filtered through a 5-μm cell strainer. 500,000 isolated nuclei were fixed with 0.5% formalin for one minute at room temperature, followed by addition of glycine.  Sorted kidney organoid-derived proximal tubular cells were fixed with 0.5% formalin for one minute at room temperature. After inactivating unreacted aldehyde by adding glycine, 100,000 cells were treated with chilled multiome lysis buffer on ice for 5 minutes to obtain nuclei.
Libraries were generated with the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048). Fixed nuclei were incubated with Concanavalin A (ConA) conjugated paramagnetic beads and stained with 0.5 µg of antibodies. The remaining steps were performed according to manufacturer’s instructions. Library preparation was performed using the NEBNext Multiplex Oligos for Illumina with manufacturer’s instructions, including minor modifications indicated by CUTANA described above. CUT&RUN libraries were sequenced on a NovaSeq instrument (Illumina, 150 bp paired-end reads).

value: AN1.1 hiPSC


title: Pollen_WT_2


title: 120 - 1m_KO_rep1


title: Pollen_ATG5_1


title: HNF4A/4G-DKO_d26_rep6

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software. The count matrices were then input to edgeR51 for data normalization and differential gene analysis.
Assembly: hg38
Supplementary files format and content: The processed files are the raw read counts and CPM for each gene/sample in txt format.

source_name: Kidney organoid

growth_protocol: Kidney organoids were generated by Takasato et al., 2016 (PMID: 27560173) with slight modifications. Briefly, on the next day of passage, pluripotent stem cells were treated with 8 µM CHIR99021 in basal medium that were comprised APEL2 supplemented with 1.5% Protein Free Hybridoma Medium II and 1x antibiotic-antimycotic solution for 4 days. On day4, medium was switched to 200 ng/mL FGF9 and 1 μg/mL heparin in the basal medium. On day 7, cells were dissociated into single cells using Accutase and diluted 5-fold with the basal medium with 10 µM Y27632. 200,000 cells were spun down at 300 g for 2 minutes (twice with 180° flip) to make cell aggregates in a 1.5-ml low-cell-binding tube and transferred onto a 0.4-µm pore polyester membrane transwell. Pellets were incubated with 5 µM CHIR99021 in the basal medium for 1 hour, and then cultured with 200 ng/mL FGF9 and 1 µg/mL heparin in the basal medium for 5 days. From day 12 to day 26, organoids were grown in the basal medium. Medium were changed every other day.

extract_protocol:
RNA was extracted with a RNeasy Plus Micro Kit (Qiagen) and total RNA integrity was determined using a 4150 TapeStation (Agilent).
Libraries were prepared using a SMARTer cDNA synthesis kit (Takara) according to manufacturer’s instruction, and then indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

value: Kidney organoid

value: HNF4A/4G-DKO iPSC


title: Pollen_ATG5_2

value: Pollen


title: KN99a_time_0h_replicate_1


title: 121 - 1m_WT_rep1

value: Dorsal root ganglia

value: Kif2a fl/fl;


title: ORG-PT_cut-and-run_HNF4A

value: Kidney organoid-derived proximal tubular cells


title: KN99a_time_0h_replicate_3


title: HAK_cut-and-run_HNF4A

source_name: Human adult kidney cortex

value: Human adult kidney cortex

tag: Sex

value: Female

tag: serum creatinine


title: HAK_cut-and-run_IgG (HNF4A control)


title: C8_time_24h_replicate_4

value: cell Culture

tag: strain


title: HNF4A/4G-DKO_d26_rep5

tag: genotype


title: 130 - 6m_KO_rep3

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a ADAPTER1 -A ADAPTER2 -a “A{10}” -a “T{10}” –times 2 -q 20 -m 25)
Reads were mapped to mm10 genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Counting was done using STAR & Gencode GTF.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8)
FDR was calculated using fdrtool_1.2.15  R pakage (fdrtool function, statistic = "normal").
Assembly: mm10
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

tag: tissue

value: 6 months


title: Pollen_ATG2_2

value: Bicellular pollen

value: ATG2 RNAi plants


title: 129 - 6m_WT_rep3


title: Pollen_ATG2_3


title: C8_time_24h_replicate_3


title: HNF4A/4G-DKO_d26_rep4


title: C8_time_24h_replicate_2


title: Pollen_ATG2_1


title: 128 - 6m_KO_rep2

value: Kif2a fl/fl; Avil cre


title: HNF4A/4G-DKO_d26_rep3


title: C8_time_24h_replicate_1

value: Yeast


title: control, rep 3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description:
ctr-wt 3
all_counts.tsv:ctr_3

data_processing:
fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with FastQC
reads were mapped to dm6 with  bowtie2.3.5.1
differentially expressed genes were  identified with edgeR 3.26.8
Assembly: dm6
Supplementary files format and content: tsv file with header and 17676 data lines, with mapped read numbers; one column per sample

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Drosophila melanogaster larvae were raised under standard non-crowdings conditions at 25°

extract_protocol:
brains were manually dissected from 96h-old larvae & dissociated into individual cells; total RNA from GFP-positive cells (type 2 neuroblasts & their descendents) was sorted by FACS, RNA was isolated using Agilent Technologies’ Absolutely RNA Nanoprep Kit (including DNase I digestion) and RNA concentration and quality were determined on a 2100 Bioanalyzer Instrument (Agilent Technologies) using the Agilent RNA 6000 Pico Kit (Agilent Technologies)
Library preparation was performed using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and the NEBNext Ultra II Directional RNA library Prep Kit for Illumina (New England Biolabs). For library amplification 17 or 24 PCR cycles were used. Library size distribution and concentration were analyzed on the Fragment Analyzer (Agilent Technologies) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: larval brain

value: type 2 neuroblast clones

value: control


title: 127 - 6m_WT_rep2

value: Kif2a fl/fl


title: HNF4A/4G-DKO_d26_rep2

value: Kidney organoid

value: HNF4A/4G-DKO iPSC


title: control, rep 2

description:
ctr-wt 2
all_counts.tsv:ctr_2


title: 125 - 6m_KO_rep1

value: Dorsal root ganglia


title: C8_time_0h_replicate_4


title: HNF4A/4G-DKO_d26_rep1


title: HNF4G-KO_d26_rep5

value: HNF4G-KO iPSC


title: HNF4G-KO_d26_rep6


title: 156 - 3m_WT_rep3

source_name: Dorsal Root Ganglia

value: Dorsal Root Ganglia

value: 3 months


title: C8_time_0h_replicate_2


title: C8_time_0h_replicate_1


title: 123 - 6m_WT_rep1


title: 154 - 3m_KO_rep2

value: Kif2a fl/fl; Avil Cre


title: brat-KD Spt5-KD, rep 1

description:
tum-kd 1
all_counts.tsv:brat_Spt5_1

value: brat-KD Spt5-KD


title: 153 - 3m_WT_rep2


title: brat-KD Spt5-KD, rep 2

description:
tum-kd 2
all_counts.tsv:brat_Spt5_2


title: control, rep 1

description:
ctr-wt 1
all_counts.tsv:ctr_1


title: HNF4G-KO_d26_rep4


title: HNF4G-KO_d26_rep3


title: brat-KD, rep3

description:
tum-wt 3
all_counts.tsv:brat_3

value: brat-KD


title: 152 - 3m_KO_rep1


title: 151 - 3m_WT_rep1


title: brat-KD, rep1

description:
tum-wt 1
all_counts.tsv:brat_1


title: C8_time_0h_replicate_3

value: cell Culture


title: HNF4A-KO_d26_rep6

value: HNF4A-KO iPSC


title: brat-KD, rep2

description:
tum-wt 2
all_counts.tsv:brat_2


title: MD58_WT_MIWI IP

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads from small RNA libraries were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200) with only sequences of at least 15 nucleotides left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards).  The reads were then mapped to the mouse genome (GRCm38: Ensembl release 95) using STAR(Dobin et al., 2013) (with parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000) and length distributions of the reads were plotted. Read counts were normalized to library sizes.  To see whether any piRNAs are produced from the reporters, the reads were mapped by bowtie(Langmead et al., 2009) (with parameters: -v 0 -a --best --strata) to the Ythdc2 transcript sequence containing individual reporters: 1xPerf,1xBulge,10xPerf,10xBulge.
Reads from long RNA-seq libraries were mapped to the mouse genome (GRCm39 - Ensembl release 104) using salmon(Patro et al., 2017) (salmon quant with options -l A –validateMappings–gcBias). Further analysis was performed using R(R Core Team, 2017) and Bioconductor(Huber et al., 2015). The DESeq2(Love et al., 2014) package was used to obtain normalized read counts for individual genes.
Assembly: GRCm38(small RNA libraries) and GRCm39 (total RNA libraries)
Supplementary files format and content: The bigwig files contain piRNA coverages along the genome. The csv file contains gene expression data.

source_name: Testes

growth_protocol: The reporters were created by inserting one or ten complementary binding sites for piR-A in the 3ʹ UTR of the Ythdc2 gene (MGI: 2448561; NCBI Gene: 240255). Binding sites were perfectly complementary or contained two mismatches at the 10th and 11th position relative to the guide RNA. Mismatched sites are referred to bulges. The first line contains one perfect complementary binding site (1XPerf), the second line contains one bulge binding site (1xBulge), the third line contains ten perfect complementary binding sites (10xPerf) and the fourth line contains ten bulge binding sites (10xBulge). Ythdc2 locus of the B6D2F1/J hybrid line (also called B6D2; The Jackson Laboratory, stock no. 100006) was targeted using CRISPR/Cas9 system.

extract_protocol:
Total RNA was extracted from adult testes using TRIzol™ Reagent (Thermo Scientific, Cat. No.  15596026).   Immunoprecipitation was conducted with Mili (PMID: 19465913) or Miwi antibodies (PMID: 22121019) and Protein G Sepharose® 4 Fast Flow beads (GE Healthcare, No. 17-0618-01) and Mili and Miwi loaded piRNAs were extracted using phenol-chloroform.
piRNA sequencing libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Ref. E7300L) and sequenced by NextSeq 500 platform (Illumina) in GeneCore(Heidelberg).   The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation from total RNA with 500 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation (DNA High sensitivity chip). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads (iGE3 Genomics Platform, University of Geneva).

tag: immunoprecipitation

value: MIWI IP

value: WT

tag: mouse


title: MD57_WT_MILI IP

value: MILI IP


title: brat-KD, rep4

description:
tum-wt 4
all_counts.tsv:brat_4

value: larval brain

value: type 2 neuroblast clones


title: HNF4A-KO_d26_rep3

tag: cell line


title: MD56_WT_MIWI IP


title: MD55_WT_MILI IP


title: HNF4G-KO_d26_rep2


title: agonistic anti-CD40 (S3)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: NOT PROVIDED

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted out the beads and immobilized on the cartridge for data collection.

data_processing: The raw code counts were normalized by the trimmed mean of M-values normalization method (TMM).

label: NOT PROVIDED

source_name: oral squamous cell carcinoma

label_protocol: NOT PROVIDED

extract_protocol: Total RNA was extracted from the formalin-fixed paraffin-embedded (FFPE) specimens of primary tumors by using Qiagen’s miRNeasy FFPE Kit (Qiagen, Valencia, CA, USA).

value: 4NQO-indued OSCC mice

tag: treatment

value: agonistic anti-CD40


title: AN1.1_d26_rep6

value: Kidney organoid

value: AN1.1 hiPSC

value: wild type


title: HNF4A-KO_d26_rep1


title: MD54_10xBulge_MIWI IP


title: agonistic anti-CD40 (S1)


title: agonistic anti-CD40 (S2)


title: HNF4A-KO_d26_rep4


title: HNF4A-KO_d26_rep2


title: MD53_10xBulge_MILI IP


title: Vehicle (A2)

value: Vehicle


title: Vehicle (A3)


title: AN1.1_d26_rep5


title: 4T1NA replicate3

city: Trivandrum

first: Radhika

last: Nair

state: Kerala

address: Poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Centre for Biotechnology

description:
Loosely adherent, round morphology, low proliferation rate, less aggressive
H3

data_processing:
Base calls performed using sanger/illumina 1.9
After trimming adaptors and removing poor quality reads, the sequence reads were aligned top mouse reference genome mm10 using TopHat2 tool, a widely used spice aware aligner for RNA-Seq experiments
After alignment, read counts were obtained using HTSeq-count tool
The obtained read counts were normalized and differential gene expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text normalized count file obtained from DESeq2 that uses median of ratios as normalization

source_name: Mammary tumor

growth_protocol: The 4T1A population displayed adherent epithelial morphology. 4T1NA cells displayed round morphology and were lossely adherent. Both the cells were cultured in DMEM/F-12 media supplemented with 10% FBS and Penicilin/streptomycin solution. The Since the 4T1NA cells are loosely adherent, it is not trypsinized and are subcultured like suspension culture.

extract_protocol:
Total RNA was extracted from cell pellets using the Qiagen Rneasy minikit using manufacturer's protocol
RNA libraries were prepared for sequencing using modified Illumina TruSeq RNA Sample Preparation V2 protocol (RS1222001)

value: BALB/c

value: Mammary tumor

tag: cancer cell marker

value: GFP

tag: injected cell line


title: HNF4A-KO_d26_rep5


title: MD51_10xBulge_MILI IP


title: Vehicle (A1)


title: AN1.1_d26_rep4


title: AN1.1_d26_rep3


title: 4T1NA replicate1

description:
Loosely adherent, round morphology, low proliferation rate, less aggressive
H1


title: 4T1NA replicate2

description:
Loosely adherent, round morphology, low proliferation rate, less aggressive
H2


title: AN1.1_d26_rep2


title: 4T1A replicate1

description:
Low GFP, adherent, epithelial morphology, High proliferation rate, aggressive invivo phenotype
N1


title: AN1.1_d26_rep1


title: MD49_10xPerf_MILI IP


title: MD47_10xPerf_MILI IP


title: MD52_10xBulge_MIWI IP


title: A673_si1_siRREB1_set3

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

description: Set 3

data_processing:
Initial processing of reads, QC assessment, and gene counts were performed using Nextflow(v19.04.0), rna-seq pipeline v3.1.8 (https://github.com/bioinfo-pf-curie/RNA-seq).
Reads were aligned to the hg19 human genome build, with gencode.v19 annotations, using STAR v2.6.1a_08-27
Read counts generated by STAR were analyzed further; non-expressed/ very low expression genes were filtered (gene row sums < 6, across 6 samples), and  differential gene expression analysis was carried out using DESeq2 (v1.34.0)
Assembly: hg19, gencode.v19 annotations
Supplementary files format and content: CSV file with raw gene counts from STAR alignment
Supplementary files format and content: CSV file with gene ID (gencode.v19) to gene name annotations

source_name: Ewing sarcoma

extract_protocol:
72 hours after transfection, cells were collected, and RNA was extracted (Machery-Nagel total RNA extraction kit).
RNA-Seq libraries were prepared from 1 μg of RNA using Truseq Stranded mRNA library preparation kit (Illumina, ref 20020594).

treatment_protocol: 75,000 A673 cells were first seeded in each well of a 6 well plate. The following day, siRNA against RREB1 (Dharmacon ON-TARGETplus Human RREB1 siRNA J-019150-05-0005, referred to as siRREB1 #1) (Dharmacon/ Horizon Discovery), and control siRNA (siCT, Dharmacon/ Horizon Discovery) were transfected using lipofectamine RNAiMAX (Thermo Fisher/ Invitrogen) (50nM siRNA, lipofectamine ratio 1), using manufacturers protocols.

value: Ewing sarcoma

tag: cell type


title: A673_siCT_set3

description: Set 3

value: siCT


title: Mut_PA_3

city: Changsha

first: Zhongfan

last: Zheng

address: No. 27 Tianma Road

institute: Hunan university

data_processing:
Illumina Casava1.8 software used for basecalling.
The clean reads were mapped to the C. elegans genome sequence using Hisat2 v2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of three biological replicates per condition was performed using the DESeq R package (1.18.0).
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all Samples.

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1 worms were placed onto NGM plates seeded with OP50 and grown at 20oC till L4 stage.

extract_protocol:
Animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01-01). Total RNA was obtained using the kit (Transgen, ER501-01) and 1 ug total RNA from each sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: L4 stage animals were collected and washed with M9 solution before being transferred to modified NGM plates containing OP50 or PA14 for 24 h at 25oC.

value: L4 animal

tag: infection

value: PA

value: L4 animal exposed for 24 h


title: 4T1A replicate3

description:
Low GFP, adherent, epithelial morphology, High proliferation rate, aggressive invivo phenotype
N3


title: brat-KD Spt5-KD, rep 3

description:
tum-kd 3
all_counts.tsv:brat_Spt5_3

value: brat-KD Spt5-KD


title: MD46_1xBulge_MIWI IP

value: MIWI IP


title: MD45_1xBulge_MILI IP

value: MILI IP


title: Mut_PA_2


title: 155 - 3m_KO_rep3

value: Dorsal Root Ganglia

value: Kif2a fl/fl; Avil Cre

tag: age

value: 3 months


title: A673_si1_siRREB1_set2

description: Set 2


title: Mut_PA_1


title: Mut_OP_3

value: control (OP)


title: MD42_1xPerf_MIWI IP


title: MD43_1xBulge_MILI IP


title: A673_siCT_set1

description: Set 1


title: A673_siCT_set2

description: Set 2


title: A673_si1_siRREB1_set1

description: Set 1


title: MD41_1xPerf_MILI IP


title: MD48_10xPerf_MIWI IP


title: Mut_OP_1


title: 3C42B

city: Toledo

first: Shang

last: Su

address: 3000 Transverse Dr

department: Cell and Cancer Biology

institute: The University of Toledo

data_processing:
We applied a customed species-specific pipeline by integrating three different methods, Xenome, Xenofilter, and Kallisto, to extract human- and mouse- specific reads from the RNA-Seq data from the mixed co-culture samples. For Xenome and Xenofilter, read alignment was performed based on reference genome (GRCh38 for human and GRCm38 for mouse) and human/mouse-only reads were sorted with default settings and the species-specific reads were used for downstream differential expression (DE) analyses. For Kallisto, a combined human-mouse transcriptome was created by joining human transcriptome and mouse transcriptome (downloaded from Gencode) and then the FastQ reads were mapped to the joint transcriptome. Human/mouse-specific transcript counts were extracted for downstream DE analyses. DE analyses were performed with DESeq2 in R and DE gene thresholds were set at |log2FC| >=1 & padj < 0.05.
Assembly: GRCh38/GRCm38
Supplementary files format and content: CSV file containing log2FC results from DESeq2

source_name: cell line

growth_protocol: All the cells were maintained in alpha-MEM supplemented with 10% FBS.

extract_protocol:
Total RNAs were extracted from cells cultured alone or the mixed co-culture using RNeasy kit and were decontaminated of the DNA using RNase-Free DNase Set (Qiagen, Hilden, Germany). 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA stranded mRNA kit (v4.16) (Kapa Biosystems, Wilmington, MA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina UDI adapters (IDT, Coralville, IA). Quality and quantity of the libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA) and QuantiFluor® dsDNA System (Promega). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq 6000 sequencer using 100 cycle sequencing kit (Illumina Inc., San Diego, CA) to a minimum read depth of 40 M reads/library.

value: cell line

value: human prostate cancer cells

value: WT

value: Cultured alone


title: Mut_OP_2


title: 4T1A replicate2

description:
Low GFP, adherent, epithelial morphology, High proliferation rate, aggressive invivo phenotype
N2

value: BALB/c

value: Mammary tumor

value: GFP


title: MD40_1xPerf_MIWI IP


title: 2C42B


title: MD50_10xPerf_MIWI IP


title: MD39_1xPerf_MILI IP


title: 1C42B


title: HNF4G-KO_d26_rep1

value: Kidney organoid

value: HNF4G-KO iPSC


title: WT_PA_2

value: L4 animal

value: PA

value: L4 animal exposed for 24 h


title: 3C4MC

organism:
Homo sapiens
Mus musculus

value: human prostate cancer cells; mouse osteoblasts

value: Co-culture in 1:30 ratio


title: ChIP NLS-GFP rep 3

city: Singapore

first: Dennis

last: Kappei

address: 14 Medical Drive, #11-01 (Bench 11), Centre for Translational Medicine

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

data_processing:
ChIP-seq reads were aligned to human reference genome version GRCh38 using Bowtie2 version 2.3.5.1 with default settings
Reads having a mapping quality of 40 or more were filtered using samtools version 1.12
peaks were called using MACS version 2.2.7.1 in paired-  end mode with default q‐value cut‐off (0.05)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig generated using deeptools version 3.5.0, shows coverage in CPM with binsize 6, smoothlength 30 and reads centered

source_name: U2OS NLS-GFP

growth_protocol: U2OS cells were cultivated in 4.5 g/l glucose, 4 mM glutamine, 1 mM sodium pyruvate containing Dulbecco's Modified Eagle's Medium (D-MEM) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco) in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Subconfluent U2OS cells were washed twice with cold PBS and cross-linked with 1% formaldehyde (Life Technologies) in DMEM for 20 min at RT. The formaldehyde was quenched with glycine (0.125 M final concentration) for 5 min at RT, cells were scraped with a plastic scraper and washed once in PBS. For lysis, cells were resuspended in lysis buffer 1 (50 mM Tris-HCl pH 8.0, 250 mM sucrose, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 0.5% IGEPAL-630 (Sigma-Aldrich), 0.25% Triton X-100, 0.25% Tween20) for 15 min, pelleted and subsequently resuspended in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min both at 4 ºC. Sonication was performed in 1.5 ml sonication buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.0) with a EpiShear probe sonicator (Active Motif)  for 6.25 min (30% amplitude, 15 sec ON, 30 sec OFF) to obtain fragments of 200-400bp.
DNA fragments were repaired, A-tailed and then ligated with Illumina adapters. After size selection and PCR amplification, the sequencing library was checked for size distribution using the 2100 Bioanalyzer System (Agilent), quantified using real-time PCR and the Qubit dsDNA HS Assay kit on a Qubit 2.0 fluorometer (Thermo Scientific). The quantified libraries were pooled in equimolar ratio and sequenced on a Illumina NovaSeq 6000.

treatment_protocol: U2OS cells were cultivated in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 300 ng/mL doxycycline (Sigma, D9891) for 48h.

tag: genotype/variation

value: NLS-GFP

value: 300 ng/mL doxycycline

tag: chip antibody

value: gtma-100 GFP-Trap® Magnetic Agarose


title: MD44_1xBulge_MIWI IP

value: MIWI IP


title: WT_OP_3

tag: developmental stage

value: control (OP)

tag: time


title: ChIP NLS-GFP rep 2


title: ChIP NLS-GFP rep 1


title: 2C4MC

value: cell line

value: WT


title: 1C4MC


title: WT_PA_1


title: WT_OP_2


title: Sacral-derived cells, post-umbilical gut replicate 2

city: Pasadena

first: Jessica

last: Jacobs-Li

state: California

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-3-2

library_source: transcriptomic single cell

data_processing:
Fastq raw data as aligned to standard ENSEMBL galgal6 reference database. Single-cell level gene quantification was then performed using Cellranger v3.1.023 and kallisto 0.46.2 & bustools 0.40.0 pipelines24 with default parameters. Gene count matrices from all the samples were combined and only cells with more than 200 genes detected were kept for the downstream analysis.
DoubletFinder 2.0.3 package was used to remove doublets.
Cells with greater than 2 transcripts of the RIA retrovirus promotor mRNA were then selected for further analysis
The first 30 principal components from PCA analysis were used to find neighbors with Findneighbors function before cell clustering with FindClusters function (resolution = 0.3). UMAP dimensionality reduction was performed using RunUMAP function with uwot-learn selected for the parameter umap.method.
Assembly: galgal6
Supplementary files format and content: R Data Serialization

molecule: polyA RNA

organism: Gallus gallus

source_name: E10 post-umbilical gut and associated ganglion

extract_protocol:
At embryonic day 10, the gastrointestinal tract, including the associated Nerve of Remak and pelvic plexuses , was dissected from chick embryos and washed with Ringer’s solution. Pre- and post-umbilical regions were separated, broke into pieces in chilled DPBS and loose-fit homogenized in Accumax solution (EMD Millipore). 400ml of Accumax-tissue mixture was aliquoted into 1.7 ml Eppendorf tubes and shaken at 37 °C for 12mins. After dissociation, chilled Hanks Buffered Saline Solution (HBSS) supplemented by BSA (125mg in 50ml, Sigma; 0.2% w/v) and 1M HEPES (500ml in 50ml, PH7.5, ThermoFisher) was added to quench the reaction. The dissociated cells were passed through a 70mm cell strainer (Corning) and collected by centrifuging at 500g for 11mins at 4 °C. The cells were resuspended in HBSS-BSA, supplemented 7-AAD Viability Staining Solution (Biolegend # 420404, 500 TESTS), and sorted for YFP+, viable single cells using Sony SY3200 cell sorter at the Caltech Flow Cytometry Facility.
Library contrusted per manufacturers instructions. The library was sequenced on NovaSeq S4 lane with 2x150bp reads by Fulgent Therapeutic

treatment_protocol: Viral solution was supplemented with 0.3ml of 2% food dye (Spectral Colors, Food Blue 002, C.A.S# 3844-45-9) as an indicator, injected to fill the neural tube between somite 1-7 at HH10 to label vagal neural crest and/or posterior to somite 28 at HH17 to label sacral neural crest in ovo. Embryos were supplied with Ringer’s Solution (0.9% NaCl, 0.042%KCl, 0.016%CaCl2 · 2H2O wt/vol, pH7.0), sealed with surgical tape, and incubated at 37 °C until embryonic day 10.

value: sacral chick neural crest

value: Wildtype

value: Replication incompetent avian retrovirus carrying nuclear (H2B) YFP, injected into the neural tube at somite level 1-7 at  embryonic day 1.5. FAC sorted for YFP+ cells


title: ChIP ZNF524-GFP ZF2 mut rep 2

source_name: U2OS ZNF524-GFP ZF2 mut

value: ZNF524-GFP ZF2 mut


title: ChIP ZNF524-GFP ZF2 mut rep 1


title: WT_OP_1


title: ChIP ZNF524-GFP WT rep 3

source_name: U2OS ZNF524-GFP WT

value: ZNF524-GFP WT


title: H2AZmCherry,Decitabine,rep1

city: Rochester

first: Fanju

last: Meng

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Raw reads were aligned to zebrafish genome build Zv11 using Bismark (v0.23.1) according to the published method (Chapin at al, Communications Biol, 2022), bismark -p 4 --parallel 6 -q --pbat -o -1 reads1.fastq.gz -2 reads2.fastq.gz
PCR duplicates were removed using deduplicate_bismark
Mapped reads were further filtered based on MAPQ score 20 using samtools view -h -q 20
methylated cytosines were extracted using bismark_methylation_extractor --parallel 10 --no_overlap --gzip --bedGraph --zero_based --cytosine_report
DNA methylation genomic tracks were generated using bedgraphtobigwig, with site coverage less than 10 filtered out.
Assembly: Zv11
Supplementary files format and content: bigWig files

organism: Danio rerio

source_name: whole embryo

growth_protocol: Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle

extract_protocol:
Genomic DNA was extracted using phenol:chloroform from 6 hour post fertilization developing zebrafish embryos after either DMSO or DAC treatment.
Extracted genomic DNA was used to generate sequencing library based on anchor-based bisulfite sequencing protocol (Chapin et al, Communications Biology, 2022)

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM Decitabine (DAC) , or with 0.1% DMSO as control group.

value: whole embryo

value: 6hour post fertilization

value: H2A.Z overexpression

value: Decitabine


title: H2AZmCherry,Decitabine,rep2


title: Vagal-derived cells, pre-umbilical gut replicate 2

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-1-2

source_name: E10 pre-umbilical gut and associated ganglion

value: vagal chick neural crest


title: H2AZmCherry,DMSO,rep2

value: DMSO


title: Vagal-derived cells, pre-umbilical gut replicate 1

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-1-1

value: E10 pre-umbilical gut and associated ganglion


title: ChIP ZNF524-GFP WT rep 2

value: 300 ng/mL doxycycline

value: gtma-100 GFP-Trap® Magnetic Agarose


title: H2AZmCherry,DMSO,rep1


title: Vagal-derived cells, post-umbilical gut replicate 2

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-2-2

value: E10 post-umbilical gut and associated ganglion


title: Input DNA - NLS-GFP

value: NLS-GFP


title: WT,Decitabine,rep2

value: wild type


title: top1_treated_rep2 [RNA-seq]

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Quality controls for FASTQ files using FastQC
Trim of low quality read bases from FASTQ files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2  genone reference using STAR
Confirmation that no coverage biases are present in the aligned data according to genomic reference file using QualiMap2
Read count overlapping Schizosaccharomyces pombe ASM294v2 genomic features using htseq-count
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: tab-separated .txt table of DEseq2 Normalized counts for all the samples

organism: Schizosaccharomyces pombe

growth_protocol: WT (972) and top1 strain were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
Hot phenol extraction
TrueSeq Stranded mRNA sample Prep kit v2 following manufacterer's instructions

treatment_protocol: 1mM H2O2 during 30 minutes

value: 30 min 1mM H2O2


title: Input DNA - ZNF524-GFP ZF2 mut


title: WT,DMSO,rep2


title: WT,Decitabine,rep1


title: top1_treated_rep1 [RNA-seq]


title: WT,DMSO,rep1


title: Vagal-derived cells, post-umbilical gut replicate 1

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-2-1

value: Wildtype


title: ChIP ZNF524-GFP ZF2 mut rep 3


title: top1_untreated_rep2 [RNA-seq]

value: untreated


title: Input DNA - ZNF524-GFP WT


title: Sacral-derived cells, post-umbilical gut replicate 1

description:
10X Genomics; cells with >2 counts of viral promoter transcript were used for downstream analysis (single_cell_cellranger_RIA_pos.rds)
WEIYI-3-1

value: sacral chick neural crest

value: Replication incompetent avian retrovirus carrying nuclear (H2B) YFP, injected into the neural tube at somite level 1-7 at  embryonic day 1.5. FAC sorted for YFP+ cells


title: WT_PA_3

value: L4 animal

value: PA

value: L4 animal exposed for 24 h


title: brain_brat_IgG_rep1

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
CUTandRUN_47
brain_brat_IgG_total.bw

data_processing:
library strategy: CUT&RUN
Raw CUT&RUN reads were trimmed to remove adapter sequences using NGmerge version 0.3
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded.
Peak calling was performed using MACS2 with parameters –broad -f BAMPE –keep-dup all -g dm.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-scoore normalized read depth of merged replicates

source_name: brain

growth_protocol: Flies were raised on standard fly food at 25 °C

extract_protocol:
CUT&RUN was performed using EpiCypher reagents according to the manufacturer protocol. 50 brains were used for each CUT&RUN reaction. Overnight incubation with antibodies was performed in antibody buffer containing 0.05% digitonin. 0.5 µL anti-Zld antibody was used for CUT&RUN.
Libraries were prepared using the NEBNext Ultra II kit (NEB). During library preparation, cleanup steps were performed using a 1.1X ratio of Axygen paramagnetic beads, as recommended by EpiCypher. PCR amplification was performed with the following conditions: 98°C for 45 seconds, then 14 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and a final extension of 72°C for 1 minute.

treatment_protocol: Larvae were grown at 18°C until reaching the L3 stage, then shifted to 33°C for 24 hours to induce Zld overexpression

value: brain

value: L3 larvae

value: Type II neuroblast

tag: antibody

value: IgG


title: brain_brat_IgG_rep2

description:
CUTandRUN_48
brain_brat_IgG_total.bw


title: top1_untreated_rep1 [RNA-seq]

tag: strain


title: U87shOGTS2

city: Al Ain

first: Suraiya

last: Ansari

address: Tawam

country: United Arab Emirates

institute: United Arab Emirates University

data_processing:
StringTie was used for alignment and transcripts quantification
For 6 samples, if more than one Count value was 0, it was not included in the analysis. Therefore, from total of 46,427 genes, 24,799 were excluded and only 21,628 genes were used for statistic analysis
Fold Change, exactTest using edgeR, Hierarchical Clustering
Assembly: Human genome assembly GRCh38 was used

source_name: Brain

extract_protocol:
Total RNA was isolated using MasterPure RNA isolation Kit.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit
Ribosomal RNA was depleted.

value: Brain


title: WT_treated_rep2 [RNA-seq]


title: ChIP ZNF524-GFP WT rep 1

value: ZNF524-GFP WT

value: 300 ng/mL doxycycline

value: gtma-100 GFP-Trap® Magnetic Agarose


title: WT_treated_rep1 [RNA-seq]


title: U87shOGTS1


title: U87shOGAS1


title: U87shOGAS2


title: U8737S2


title: WT_untreated_rep1 [RNA-seq]


title: R microplus fed on vaccinated cattle replicate 3

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

hyb_protocol: Equivalent picomoles (20 pmol) of Cy3-labelled cDNA from the common reference pool were hybridised with Cy5-labelled individual test cDNA. Overnight hybridisation at 65°C (rotation speed of 10), washing and post-processing were performed at the ACGT Microarray Facility (University of Pretoria, South Africa). Prior to slide scanning with the Axon GenePix 4000B scanner (Molecular Devices), slides were washed and dried by centrifugation

scan_protocol: Scanned on an Axon GenePix 4000B scanner (Molecular Devices) Images were measured, recorded, analysed and spots were inspected using Axon GenePix Pro 6.0 software (Molecular Devices)

data_processing: Axon GenePix Pro 6.0 software (Molecular Devices) and the linear model for microarray data analysis (LIMMA) within the R statistical environment (http://cran.r-project.org/) was employed. Adaptive background correction (offset = 50) was followed by within-array normalisation (Robust Spline) and between-array normalisation (G quantile). Fold change was determined between all transcripts using the empirical Bayesian statistics, which were subsequently expressed as P- values (corrected for false discovery rate).

organism: Rhipicephalus microplus

source_name: R microplus midgut tissue fed on vaccinated cattle

label_protocol:
First-strand cDNA synthesis was performed by incubating 4 µg RNA (from each biological replicate and the reference pool) with 250 pmol oligo(dT25) and 775 pmol random primer 9 for 10 minutes at 70˚C, followed by cooling on ice for 10 minutes. Reverse transcription and aminoallyl-dUTP (5-(3-aminoallyl)-2’deoxyuridine-5’ triphosphate) incorporation were performed simultaneously using 340 units SuperScript® III reverse transcriptase (Invitrogen™ life technologies, USA).
cDNA samples were coupled to 75 picomol Cy3 (reference pool) and Cy5 (samples) fluorescent dyes (GE Healthcare Life Sciences)at pH 9 dissolved in DMSO. Unincorporated dye was then removed.

extract_protocol: Total RNA was isolated using TRI-reagent fractionation (Sigma-Aldrich) and the RNeasy mini kit (QIAGEN, Germany) following the manufacturer’s instructions. Contaminating genomic DNA was removed with a DNase I treatment (QIAGEN, Germany).

treatment_protocol: Twenty semi-engorged female ticks from each of the three cattle allocated in the vaccinated and control groups respectively, were collected 20 days post infestation. Midgut tissues were collected by dissection and homogenized in TRI Reagent® (Sigma-Aldrich, Germany), frozen in liquid nitrogen and stored at -80°C until RNA isolation was performed.

value: Midgut

source_name: Pooled R microplus midgut tissue from all samples


title: WT_untreated_rep2 [RNA-seq]


title: U8737S1


title: R microplus fed on vaccinated cattle replicate 2


title: R microplus fed on vaccinated cattle replicate 1


title: R microplus fed on unvaccinated cattle replicate 1

source_name: R microplus midgut tissue fed on unvaccinated cattle


title: R microplus fed on unvaccinated cattle replicate 3


title: R microplus fed on unvaccinated cattle replicate 2


title: dermis_35yrs [2020_165_35_D]

status: Public on Oct 22 2023

type: genomic

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

description: genomic DNA from dermis of 2020_165_35

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned with an iScan Reader (Illumina) using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v. 2011.1 (Illumina)

label: Cy5 and Cy3

source_name: dermis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

value: 35 yrs

tag: gender

value: male

value: dermis

tag: ethnicity

value: Korean-Asian


title: epidermis_56yrs [2020_25_56_E]

description: genomic DNA from epidermis of 2020_25_56

source_name: epidermis

value: 56 yrs

tag: tissue

value: epidermis


title: muscle_35yrs [2020_165_35_M]

description: genomic DNA from muscle of 2020_165_35

source_name: muscle

value: muscle


title: muscle_78yrs [2020_17_78_M]

description: genomic DNA from muscle of 2020_17_78

value: 78 yrs


title: epidermis_66yrs [2020_8_66_E]

description: genomic DNA from epidermis of 2020_8_66

value: 66 yrs


title: muscle_56yrs [2020_25_56_M]

description: genomic DNA from muscle of 2020_25_56


title: epidermis_35yrs [2020_165_35_E]

description: genomic DNA from epidermis of 2020_165_35


title: muscle_66yrs [2020_8_66_M]

description: genomic DNA from muscle of 2020_8_66


title: muscle_43yrs [2020_7_43_M]

description: genomic DNA from muscle of 2020_7_43

value: 43 yrs


title: muscle_77yrs [2020_16_77_M]

description: genomic DNA from muscle of 2020_16_77

value: 77 yrs


title: dermis_78yrs [2020_17_78_D]

description: genomic DNA from dermis of 2020_17_78


title: epidermis_41yrs [2020_157_41_E]

description: genomic DNA from epidermis of 2020_157_41

value: 41 yrs

value: female


title: dermis_77yrs [2020_16_77_D]

description: genomic DNA from dermis of 2020_16_77


title: epidermis_77yrs [2020_16_77_E]

description: genomic DNA from epidermis of 2020_16_77


title: epidermis_78yrs [2020_17_78_E]

description: genomic DNA from epidermis of 2020_17_78


title: muscle_41yrs [2020_157_41_M]

description: genomic DNA from muscle of 2020_157_41


title: epidermis_74yrs [2020_93_74_E]

description: genomic DNA from epidermis of 2020_93_74

value: 74 yrs


title: dermis_74yrs [2020_93_74_D]

description: genomic DNA from dermis of 2020_93_74


title: muscle_74yrs [2020_93_74_M]

description: genomic DNA from muscle of 2020_93_74


title: dermis_47yrs [2020_23_47_D]

description: genomic DNA from dermis of 2020_23_47

value: 47 yrs


title: epidermis_56yrs [2020_15_56_E]

description: genomic DNA from epidermis of 2020_15_56


title: muscle_63yrs [2020_147_63_M]

description: genomic DNA from muscle of 2020_147_63

value: 63 yrs


title: epidermis_47yrs [2020_23_47_E]

description: genomic DNA from epidermis of 2020_23_47


title: muscle_47yrs [2020_23_47_M]

description: genomic DNA from muscle of 2020_23_47


title: muscle_56yrs [2020_15_56_M]

description: genomic DNA from muscle of 2020_15_56


title: dermis_66yrs [2020_8_66_D]

description: genomic DNA from dermis of 2020_8_66


title: dermis_56yrs [2020_25_56_D]

description: genomic DNA from dermis of 2020_25_56


title: epidermis_43yrs [2020_7_43_E]

description: genomic DNA from epidermis of 2020_7_43


title: dermis_63yrs [2020_147_63_D]

description: genomic DNA from dermis of 2020_147_63


title: dermis_43yrs [2020_7_43_D]

description: genomic DNA from dermis of 2020_7_43


title: epidermis_63yrs [2020_147_63_E]

description: genomic DNA from epidermis of 2020_147_63


title: dermis_41yrs [2020_157_41_D]

description: genomic DNA from dermis of 2020_157_41


title: epidermis_50yrs [2020_138_50_E]

description: genomic DNA from epidermis of 2020_138_50

value: 50 yrs


title: dermis_48yrs [2020_14_48_D]

description: genomic DNA from dermis of 2020_14_48

value: 48 yrs


title: muscle_48yrs [2020_14_48_M]

description: genomic DNA from muscle of 2020_14_48

value: male


title: dermis_50yrs [2020_138_50_D]

description: genomic DNA from dermis of 2020_138_50

value: dermis


title: muscle_50yrs [2020_138_50_M]

description: genomic DNA from muscle of 2020_138_50

value: Korean-Asian


title: dermis_56yrs [2020_15_56_D]

description: genomic DNA from dermis of 2020_15_56

value: 56 yrs


title: muscle_46yrs [2020_13_46_M]

description: genomic DNA from muscle of 2020_13_46

value: 46 yrs


title: dermis_18yrs [2020_131_18_D]

description: genomic DNA from dermis of 2020_131_18

value: 18 yrs


title: epidermis_18yrs [2020_131_18_E]

description: genomic DNA from epidermis of 2020_131_18

value: epidermis


title: dermis_38yrs [2020_127_38_D]

description: genomic DNA from dermis of 2020_127_38

value: 38 yrs


title: muscle_38yrs [2020_127_38_M]

description: genomic DNA from muscle of 2020_127_38

value: muscle


title: epidermis_46yrs [2020_13_46_E]

description: genomic DNA from epidermis of 2020_13_46


title: epidermis_38yrs [2020_127_38_E]

description: genomic DNA from epidermis of 2020_127_38


title: muscle_39yrs [2020_120_39_M]

description: genomic DNA from muscle of 2020_120_39

value: 39 yrs


title: muscle_18yrs [2020_131_18_M]

description: genomic DNA from muscle of 2020_131_18


title: epidermis_48yrs [2020_14_48_E]

description: genomic DNA from epidermis of 2020_14_48


title: muscle_77yrs [2020_118_77_M]

description: genomic DNA from muscle of 2020_118_77

value: 77 yrs


title: dermis_39yrs [2020_120_39_D]

description: genomic DNA from dermis of 2020_120_39


title: epidermis_52yrs [2020_109_52_E]

description: genomic DNA from epidermis of 2020_109_52

value: 52 yrs

value: female


title: dermis_46yrs [2020_13_46_D]

description: genomic DNA from dermis of 2020_13_46


title: dermis_77yrs [2020_118_77_D]

description: genomic DNA from dermis of 2020_118_77


title: dermis_52yrs [2020_115_52_D]

description: genomic DNA from dermis of 2020_115_52


title: epidermis_77yrs [2020_118_77_E]

description: genomic DNA from epidermis of 2020_118_77


title: epidermis_52yrs [2020_115_52_E]

description: genomic DNA from epidermis of 2020_115_52


title: liver_74yrs [2020_93_74_Li]

description: genomic DNA from liver of 2020_93_74

source_name: liver

value: 74 yrs

value: liver


title: lung_66yrs [2020_8_66_Lu]

description: genomic DNA from lung of 2020_8_66

source_name: lung

value: 66 yrs

value: lung


title: muscle_52yrs [2020_109_52_M]

description: genomic DNA from muscle of 2020_109_52


title: muscle_52yrs [2020_115_52_M]

description: genomic DNA from muscle of 2020_115_52

value: male


title: kidney_74yrs [2020_93_74_K]

description: genomic DNA from kidney of 2020_93_74

source_name: kidney

value: kidney


title: liver_43yrs [2020_7_43_Li]

description: genomic DNA from liver of 2020_7_43

value: 43 yrs

value: Korean-Asian


title: kidney_66yrs [2020_8_66_K]

description: genomic DNA from kidney of 2020_8_66


title: dermis_52yrs [2020_109_52_D]

description: genomic DNA from dermis of 2020_109_52

value: dermis


title: kidney_43yrs [2020_7_43_K]

description: genomic DNA from kidney of 2020_7_43


title: kidney_56yrs [2020_25_56_K]

description: genomic DNA from kidney of 2020_25_56

value: 56 yrs


title: lung_43yrs [2020_7_43_Lu]

description: genomic DNA from lung of 2020_7_43


title: liver_78yrs [2020_17_78_Li]

description: genomic DNA from liver of 2020_17_78

value: 78 yrs


title: lung_47yrs [2020_23_47_Lu]

description: genomic DNA from lung of 2020_23_47

value: 47 yrs


title: kidney_47yrs [2020_23_47_K]

description: genomic DNA from kidney of 2020_23_47


title: lung_78yrs [2020_17_78_Lu]

description: genomic DNA from lung of 2020_17_78


title: liver_47yrs [2020_23_47_Li]

description: genomic DNA from liver of 2020_23_47


title: kidney_78yrs [2020_17_78_K]

description: genomic DNA from kidney of 2020_17_78


title: liver_56yrs [2020_25_56_Li]

description: genomic DNA from liver of 2020_25_56


title: lung_77yrs [2020_16_77_Lu]

description: genomic DNA from lung of 2020_16_77


title: lung_35yrs [2020_165_35_Lu]

description: genomic DNA from lung of 2020_165_35

value: 35 yrs


title: kidney_35yrs [2020_165_35_K]

description: genomic DNA from kidney of 2020_165_35


title: kidney_41yrs [2020_157_41_K]

description: genomic DNA from kidney of 2020_157_41

value: 41 yrs


title: lung_41yrs [2020_157_41_Lu]

description: genomic DNA from lung of 2020_157_41


title: liver_41yrs [2020_157_41_Li]

description: genomic DNA from liver of 2020_157_41


title: liver_56yrs [2020_15_56_Li]

description: genomic DNA from liver of 2020_15_56


title: lung_63yrs [2020_147_63_Lu]

description: genomic DNA from lung of 2020_147_63

value: 63 yrs


title: kidney_56yrs [2020_15_56_K]

description: genomic DNA from kidney of 2020_15_56


title: liver_35yrs [2020_165_35_Li]

description: genomic DNA from liver of 2020_165_35


title: liver_77yrs [2020_16_77_Li]

description: genomic DNA from liver of 2020_16_77

value: 77 yrs


title: kidney_48yrs [2020_14_48_K]

description: genomic DNA from kidney of 2020_14_48

value: 48 yrs


title: kidney_63yrs [2020_147_63_K]

description: genomic DNA from kidney of 2020_147_63


title: liver_48yrs [2020_14_48_Li]

description: genomic DNA from liver of 2020_14_48


title: kidney_77yrs [2020_16_77_K]

description: genomic DNA from kidney of 2020_16_77


title: kidney_50yrs [2020_138_50_K]

description: genomic DNA from kidney of 2020_138_50

value: 50 yrs


title: lung_56yrs [2020_15_56_Lu]

description: genomic DNA from lung of 2020_15_56

value: female


title: lung_48yrs [2020_14_48_Lu]

description: genomic DNA from lung of 2020_14_48


title: liver_50yrs [2020_138_50_Li]

description: genomic DNA from liver of 2020_138_50

value: liver


title: epidermis_39yrs [2020_120_39_E]

description: genomic DNA from epidermis of 2020_120_39

value: 39 yrs

value: epidermis


title: lung_18yrs [2020_131_18_Lu]

description: genomic DNA from lung of 2020_131_18

value: 18 yrs

value: male

value: lung


title: liver_66yrs [2020_8_66_Li]

description: genomic DNA from liver of 2020_8_66

value: 66 yrs

value: Korean-Asian


title: liver_18yrs [2020_131_18_Li]

description: genomic DNA from liver of 2020_131_18


title: kidney_18yrs [2020_131_18_K]

description: genomic DNA from kidney of 2020_131_18

value: kidney


title: lung_74yrs [2020_93_74_Lu]

description: genomic DNA from lung of 2020_93_74

value: 74 yrs


title: lung_50yrs [2020_138_50_Lu]

description: genomic DNA from lung of 2020_138_50


title: lung_46yrs [2020_13_46_Lu]

description: genomic DNA from lung of 2020_13_46

value: 46 yrs


title: liver_63yrs [2020_147_63_Li]

description: genomic DNA from liver of 2020_147_63


title: liver_46yrs [2020_13_46_Li]

description: genomic DNA from liver of 2020_13_46


title: lung_38yrs [2020_127_38_Lu]

description: genomic DNA from lung of 2020_127_38

value: 38 yrs


title: liver_38yrs [2020_127_38_Li]

description: genomic DNA from liver of 2020_127_38


title: lung_39yrs [2020_120_39_Lu]

description: genomic DNA from lung of 2020_120_39


title: kidney_38yrs [2020_127_38_K]

description: genomic DNA from kidney of 2020_127_38


title: kidney_46yrs [2020_13_46_K]

description: genomic DNA from kidney of 2020_13_46


title: lung_77yrs [2020_118_77_Lu]

description: genomic DNA from lung of 2020_118_77


title: liver_39yrs [2020_120_39_Li]

description: genomic DNA from liver of 2020_120_39


title: kidney_77yrs [2020_118_77_K]

description: genomic DNA from kidney of 2020_118_77


title: kidney_52yrs [2020_109_52_K]

description: genomic DNA from kidney of 2020_109_52

value: 52 yrs


title: liver_52yrs [2020_109_52_Li]

description: genomic DNA from liver of 2020_109_52


title: lung_52yrs [2020_115_52_Lu]

description: genomic DNA from lung of 2020_115_52


title: liver_52yrs [2020_115_52_Li]

description: genomic DNA from liver of 2020_115_52


title: lung_52yrs [2020_109_52_Lu]

description: genomic DNA from lung of 2020_109_52


title: liver_77yrs [2020_118_77_Li]

description: genomic DNA from liver of 2020_118_77

value: 77 yrs


title: heart_66yrs [2020_8_66_H]

description: genomic DNA from heart of 2020_8_66

source_name: heart

value: heart


title: kidney_52yrs [2020_115_52_K]

description: genomic DNA from kidney of 2020_115_52


title: lung_56yrs [2020_25_56_Lu]

description: genomic DNA from lung of 2020_25_56

value: 56 yrs


title: kidney_39yrs [2020_120_39_K]

description: genomic DNA from kidney of 2020_120_39


title: heart_74yrs [2020_93_74_H]

description: genomic DNA from heart of 2020_93_74


title: blood_56yrs [2020_25_56_Bl]

description: genomic DNA from blood of 2020_25_56

source_name: blood

value: blood


title: brain_66yrs [2020_8_66_Br]

description: genomic DNA from brain of 2020_8_66

value: brain


title: heart_56yrs [2020_25_56_H]

description: genomic DNA from heart of 2020_25_56


title: blood_66yrs [2020_8_66_Bl]

description: genomic DNA from blood of 2020_8_66


title: brain_74yrs [2020_93_74_Br]

description: genomic DNA from brain of 2020_93_74


title: heart_47yrs [2020_23_47_H]

description: genomic DNA from heart of 2020_23_47

value: 47 yrs

value: female


title: blood_43yrs [2020_7_43_Bl]

description: genomic DNA from blood of 2020_7_43

value: 43 yrs


title: brain_56yrs [2020_25_56_Br]

description: genomic DNA from brain of 2020_25_56

value: male


title: brain_43yrs [2020_7_43_Br]

description: genomic DNA from brain of 2020_7_43


title: blood_74yrs [2020_93_74_Bl]

description: genomic DNA from blood of 2020_93_74


title: heart_43yrs [2020_7_43_H]

description: genomic DNA from heart of 2020_7_43


title: brain_47yrs [2020_23_47_Br]

description: genomic DNA from brain of 2020_23_47


title: blood_47yrs [2020_23_47_Bl]

description: genomic DNA from blood of 2020_23_47


title: blood_78yrs [2020_17_78_Bl]

description: genomic DNA from blood of 2020_17_78

value: 78 yrs


title: brain_78yrs [2020_17_78_Br]

description: genomic DNA from brain of 2020_17_78


title: heart_35yrs [2020_165_35_H]

description: genomic DNA from heart of 2020_165_35

value: 35 yrs


title: blood_35yrs [2020_165_35_Bl]

description: genomic DNA from blood of 2020_165_35

value: Korean-Asian


title: brain_35yrs [2020_165_35_Br]

description: genomic DNA from brain of 2020_165_35


title: heart_77yrs [2020_16_77_H]

description: genomic DNA from heart of 2020_16_77


title: brain_41yrs [2020_157_41_Br]

description: genomic DNA from brain of 2020_157_41

value: 41 yrs


title: heart_78yrs [2020_17_78_H]

description: genomic DNA from heart of 2020_17_78


title: blood_41yrs [2020_157_41_Bl]

description: genomic DNA from blood of 2020_157_41


title: heart_56yrs [2020_15_56_H]

description: genomic DNA from heart of 2020_15_56


title: brain_77yrs [2020_16_77_Br]

description: genomic DNA from brain of 2020_16_77


title: heart_63yrs [2020_147_63_H]

description: genomic DNA from heart of 2020_147_63

value: 63 yrs


title: blood_63yrs [2020_147_63_Bl]

description: genomic DNA from blood of 2020_147_63


title: blood_56yrs [2020_15_56_Bl]

description: genomic DNA from blood of 2020_15_56


title: heart_41yrs [2020_157_41_H]

description: genomic DNA from heart of 2020_157_41


title: brain_63yrs [2020_147_63_Br]

description: genomic DNA from brain of 2020_147_63


title: blood_77yrs [2020_16_77_Bl]

description: genomic DNA from blood of 2020_16_77


title: brain_56yrs [2020_15_56_Br]

description: genomic DNA from brain of 2020_15_56


title: amniotic fluid AF70996-750knsp

city: Fuzhou

first: Xiaorui

last: Xie

address: No. 18 Daoshan Road

institute: Fujian Provincial Maternity and Children’s Hospital

description: Hybridized to CytoScan750K_Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

source_name: amniotic fluid AF70996

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: amniotic fluid

tag: ultrasound abnormality classification

value: Isolated TE

tag: bilateral or unilateral

value: Bilateral


title: blood_50yrs [2020_138_50_Bl]

description: genomic DNA from blood of 2020_138_50

value: 50 yrs


title: brain_48yrs [2020_14_48_Br]

description: genomic DNA from brain of 2020_14_48

value: 48 yrs