title: P21uSC_H3K4me1_CutnRun_2

data_processing:
Library strategy: CutnRun
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For ChIPseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10 using STAR. PCR duplcates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count text files for RNAseq, peak region narrowPeak files for ATACseq, ChIPseq and CUT&RUN.

source_name: Utricle

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P21 utricles into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

value: postnatal day 21


title: RNA-Seq of  SGBS treated with ROSIGLITAZONE at 2uM concentration B_7_01

status: Public on Jul 09 2021

type: SRA

city: Los Angeles

first: Brunilda

last: Balliu

state: CA

address: 621 Charles Young Drive South

department: Computational Medicine

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Reference genome (hg19) and gene model annotation files were downloaded from the UCSC genome browser website directly.
Indexes of the reference genome were built using STAR3 and paired-end clean reads were aligned to the reference genome using STAR (v2.6.0; with default option mismatch = 10).
Bam files were filtered for uniquely mapped reads, sorted, and indexed using SAMtools4 (v1.4.1).
HTSeq5 (v0.11.0) was used to count the read numbers mapped to each gene (with option -m union).
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: adipose

growth_protocol: HepG2, terminally differentiated SGBS, and HCML-7304 cells were starved for 6 hours in EMEA with no FBS (HepG2), DMEM/F12 supplemented with pan/bio and penicillin/streptomycin but no FBS (SGBS adipocytes) or HCML growth medium (PromoCell) without supplements. For the glucose condition DMEM no glucose medium (Thermo) was used.

extract_protocol: none provided by the submitter

treatment_protocol: After starvation and washing with PBS, the cells were exposed for 2 hours to the different compounds or the respective control media.

tag: tissue

value: adipose

tag: cell type

value: adipocyte

tag: cell line

value: SGBS

tag: treatment

value: ROSIGLITAZONE


title: case_renal biopsy [BIOS-03-0056]

type: RNA

city: Dijon

first: Baptiste

last: Lamarthée

address: Bd du Mal De Lattre de Tassigny

department: RIGHT

country: France

institute: Inserm U1098

data_processing:
The normalization and all the data analysis were performed using Expression Suite software version 1.0.3. Assays with a cycle threshold (CT) values >35 were considered to be not expressed
For the normalization it uses the average of two housekeeping genes: RNU44 and RNU48
Target miRNA signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
All deltaCt based fold-change calculations from the uploaded raw threshold cycle data were calculated using R Studio.
The normalized_data.txt reports normalized signal (against housekeeping genes).

label: TaqMan

source_name: case_renal biopsy

label_protocol: Specific reverse transcription of 150 ng of total RNA was performed using Megaplex™ RT Primers Human Pool A v2.1 (Thermo Fisher Scientific, Les Ulis, France), on a Veriti Thermal Cycler (Applied Biosystems™, Thermo Fisher Scientific). No complementary (c)DNA preamplification was required.  MiRNA expression was assessed by qPCR, using TaqMan® Array Cards (Applied Biosystems™, Thermo Fisher Scientific), where the primers and probe of each miRNA were spotted and dried in duplicate wells of a microfluidic card. We used TaqMan® Array Human MicroRNA A+B Card Sets v3.0 (Thermo Fisher Scientific)

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV). The quantity (absorbance at 260 nm) and purity (ratio of the absorbance at 230, 260, and 280 nm) of the isolated RNA were measured using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific/Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated with the Eukaryote nano/pico RNA Kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument (Agilent Technologies BelgiumNV)

value: renal, endothelial and immune cells

tag: outcome

value: MVI

tag: type of biopsy

value: Post kidney transplantation


title: tx-j+PCA+Choline_H3K27ac_6

city: Davis

first: Valentina

last: Medici

address: 451 E. Health Sciences Dr.

department: Department of Internal Medicine, Division of Hepatology/Gastroenterology

institute: University of California, Davis

library_source: genomic

data_processing:
The raw read data was filtered using HTStream (version 1.2.0) which included screening for contaminants (such as PhiX), removal of PCR duplicated reads, overlapping paired reads, quality-based trimming, and adapter trimming.
BWA MEM (version 0.7.16a) was used to align the processed data to the mouse genome (GRCm38).
Calling peaks was done using phantompeakqualtools (version 1.2.2). Bioconductor (version 3.11) package DiffBind (version 2.12.0) was used to combine raw count data for all peaks across replicates using R (version 3.6.3).
Bioconductor packages edgeR (version 3.26.8) and limma (version 3.40.6) were then used to perform differential expression analysis across the called peaks.
Finally, GREAT (version 4.0.4) was used to find the regulatory domains for the peaks and the genes within those domains.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

extract_protocol:
After 24 weeks, Liver were removed, flash frozen in liquid nitrogne. Liver tissue lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were generated  by using KAPA Hyper Prep Kit (Kapa Biosystems, Wilmington MA, catalog. # KK8502) which included end repair, A-tailing, and adapter ligation with the KAPA Unique Dual-Indexed Adapter Kit (Kapa Biosystems, Wilmington, MA, catalog # KK8727) according to the manufacturer’s instructions.

treatment_protocol: From 12 to 24 weeks of age, Penicillamine (PCA )(Sigma, catalog #P4575;) was administered orally in the drinking water (100 mg/kg body weight/day) to a subgroup of tx-j control and choline-supplemented mice. Mice were euthanized at 24 weeks of age.

tag: strain

value: Liver

tag: treatment group

value: Untreated tx-j+PCA+Choline

tag: genotype

value: Mutant (Atp7btx-J)

tag: age

value: 24 weeks

tag: chip antibody

value: H3K27ac (Abcam, Catalog-ab177178)


title: case_renal biopsy [BIOS-03-0054]


title: C3H_H3K9ac_2

value: Wild type

value: H3K9ac (Active Motif, Catalog-39918)


title: tx-j+PCA+Choline_H3K27ac_5


title: C3H_H3K9ac_1


title: RNA-Seq of  SGBS treated with IL-6 at 20ng/ml concentration B_6_03


title: RNA-Seq of  SGBS treated with IL-6 at 20ng/ml concentration B_6_02


title: P21uSC_ATACseq_2

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For ChIPseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10 using STAR. PCR duplcates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools,  and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count text files for RNAseq, peak region narrowPeak files for ATACseq, ChIPseq and CUT&RUN.

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P21 utricles into 500μL PBS supplemented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers

tag: developmental stage

value: supporting cells

tag: marker

value: Lfng-GFP


title: case_renal biopsy [BIOS-03-0052]


title: tx-j+PCA+Choline_H3K27ac_4


title: control_renal biopsy [BIOS-03-0051]

source_name: control_renal biopsy

value: No MVI


title: P21uSC_ATACseq_1

value: postnatal day 21


title: P21uSC_H3K4me1_CutnRun_1


title: tx-j+PCA+Choline_H3K27ac_3


title: RNA-Seq of  SGBS treated with IL-6 at 20ng/ml concentration B_6_01

value: adipose

value: adipocyte


title: control_renal biopsy [BIOS-03-0039]


title: P21cSC_H3K4me1_CutnRun_2

source_name: Cochlea

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P21 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.


title: tx-j+PCA+Choline_H3K27ac_2


title: P21cSC_H3K4me1_CutnRun_1


title: P21cSC_ATACseq_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P21 cochleae into 500μL PBS supplemented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers


title: tx-j+PCA+Choline_H3K27ac_1


title: RNA-Seq of  SGBS treated with TNF-a at 10ng/ml concentration B_5_02

value: SGBS

value: TNF-a


title: RNA-Seq of  SGBS treated with TNF-a at 10ng/ml concentration B_5_01


title: control_renal biopsy [BIOS-03-0035]

value: renal, endothelial and immune cells


title: case_renal biopsy [BIOS-03-0033]

value: MVI

value: Post kidney transplantation


title: tx-j+Choline_H3K27ac_6

value: Liver

value: Untreated tx-j+Choline


title: P21cSC_ATACseq_1


title: RNA-Seq of  SGBS treated with INSULIN at 100mM concentration B_4_03

value: INSULIN


title: tx-j+Choline_H3K27ac_5

value: Mutant (Atp7btx-J)

value: 24 weeks

value: H3K27ac (Abcam, Catalog-ab177178)


title: P6SC_H3K4me3_CutnRun_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P6 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

value: postnatal day 6

value: supporting cells


title: case_renal biopsy [BIOS-03-0030]


title: RNA-Seq of  SGBS treated with INSULIN at 100mM concentration B_4_02


title: case_renal biopsy [BIOS-03-0026]


title: tx-j+Choline_H3K27ac_4


title: tx-j+Choline_H3K27ac_3


title: RNA-Seq of  SGBS treated with INSULIN at 100mM concentration B_4_01


title: P6SC_H3K4me1_CutnRun_2

value: Lfng-GFP


title: control_renal biopsy [BIOS-03-0038]

value: No MVI


title: control_renal biopsy [BIOS-03-0020]


title: control_renal biopsy [BIOS-03-0023]


title: RNA-Seq of  SGBS treated with GLUCOSE at 10mM concentration B_3_03

value: adipose

value: GLUCOSE


title: tx-j+Choline_H3K27ac_2


title: RNA-Seq of  SGBS treated with GLUCOSE at 10mM concentration B_3_02

value: adipocyte

value: SGBS


title: P6SC_H3K4me1_CutnRun_1


title: RNA-Seq of  SGBS treated with TNF-a at 10ng/ml concentration B_5_03

value: TNF-a


title: P1SC_Base_H3K4me1_CutnRun_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from the basal half of P1 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

value: postnatal day 1


title: tx-j+Choline_H3K27ac_1


title: tx-j+PCA_H3K27ac_6

value: Untreated tx-j+PCA


title: RNA-Seq of  SGBS treated with GLUCOSE at 10mM concentration B_3_01


title: RNA-Seq of  SGBS CONTROL FOR GLUCOSE B_2_03

description: RNA-Seq of  SGBS CONTROL FOR GLUCOSE

value: NO GLUCOSE (DMEM NO GLUCOSE)


title: control_renal biopsy [BIOS-03-0017]

value: renal, endothelial and immune cells

value: Post kidney transplantation


title: P1SC_Base_H3K4me1_CutnRun_1


title: case_renal biopsy [BIOS-03-0015]

value: MVI


title: P1SC_Apex_H3K4me1_CutnRun_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from the apical half of P1 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.


title: P6SC_H3K4me3_CutnRun_1


title: RNA-Seq of  SGBS CONTROL FOR GLUCOSE B_2_02

description: RNA-Seq of  SGBS CONTROL FOR GLUCOSE


title: tx-j+PCA_H3K27ac_4

value: Liver

value: Mutant (Atp7btx-J)

value: 24 weeks


title: control_renal biopsy [BIOS-03-0014]


title: tx-j+PCA_H3K27ac_3

value: H3K27ac (Abcam, Catalog-ab177178)


title: RNA-Seq of  SGBS CONTROL FOR GLUCOSE B_2_01

description: RNA-Seq of  SGBS CONTROL FOR GLUCOSE


title: control_renal biopsy [BIOS-03-0013]


title: RNA-Seq of  SGBS CONTROL B_1_03

description: RNA-Seq of  SGBS CONTROL

value: CONTROL (EMPTY EMEM MEDIUM) 1


title: P1SC_Apex_H3K4me1_CutnRun_1

value: supporting cells

value: Lfng-GFP


title: P1SC_H3K27me3_ChIPseq_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS, and purified cell were crosslinked by 1% formadehyde. Chromatin was sheared by sonication, and DNA ends were tagged by Tn5 transposase. Nucleosomes with particular histone modification were precipitated using specific antibody and dynabeads protein A.
Libraries were prepared by PCR with indexed primers


title: case_renal biopsy [BIOS-03-0008]


title: tx-j+PCA_H3K27ac_2


title: P1SC_H3K27me3_ChIPseq_1


title: tx-j+PCA_H3K27ac_1


title: P1SC_H3K27ac_CutnRun_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.


title: control_renal biopsy [BIOS-03-0019]

value: No MVI


title: RNA-Seq of  SGBS CONTROL B_1_01

description: RNA-Seq of  SGBS CONTROL

value: adipose

value: adipocyte


title: tx-j_H3K27ac_6

value: Untreated tx-j


title: P1SC_H3K27ac_CutnRun_1

value: postnatal day 1


title: case_renal biopsy [BIOS-03-0004]


title: P1SC_H3K4me3_CutnRun_2


title: tx-j+PCA_H3K27ac_5

value: Untreated tx-j+PCA


title: RSU3_USW

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

state: Barcelona

address: Carrer Jordi Girona, 20

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

description:
specific sampling site location:
scientific-technical unit of Polytechnic University of Catalonia (UPC) (“Agrópolis”, Viladecans (Barcelona), 41°17'19,1"N, 2°02'43,4"E).
RSU3

data_processing:
Library strategy: 16S rDNA metagenome-seq
Paired-end reads was assigned to samples based on their unique barcodes and truncated by cutting off the barcode and primer sequences. Paired-end reads were merged using FLASH (V1.2.7)[21] (see details http://ccb.jhu.edu/software/FLASH/), a very fast and accurate analysis tool, which was designed to merge paired-end reads when at least some of the reads overlap the read generated from the opposite end of the same DNA fragment, and the splicing sequences were called raw tags. Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags[22] according to the Qiime (V1.7.0)[23] (see details http://qiime.org/scripts/split_libraries_fastq.html) quality controlled process.
The tags were compared with the reference database (Gold database, see details http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, see details http://www.drive5.com/usearch/manual/uchime_algo.html)[24] to detect chimera sequences (see details https://drive5.com/usearch/manual/chimeras.html). And then the chimera sequences were removed[25]. Then the Effective Tags finally obtained.
OTU cluster and Taxonomic annotation: Sequences analysis were performed by Uparse software (Uparse v7.0.1001, see details http://drive5.com/uparse/)[26] using all the effective tags. Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
OTU cluster and Taxonomic annotation: For each representative sequence, Mothur software was performed against the SSUrRNA database of SILVA Database (see details http://www.arb-silva.de/)[27]for species annotation at each taxonomic rank (Threshold:0.8~1)[28] (kingdom, phylum, class, order, family, genus, species).
OTU cluster and Taxonomic annotation: To obtain the phylogenetic relationship of all OTUs representative sequences, the MUSCLE[29] (Version 3.8.31, see details http://www.drive5.com/muscle/) can compare multiple sequences rapidly.
OTU cluster and Taxonomic annotation: OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences. Subsequent analysis of alpha diversity and beta diversity were all performed basing on this output normalized data.
Genome_build: SILVA database
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values (normalized counts) for each sample.

organism: solid waste metagenome

source_name: AMENDMENT

growth_protocol: Soils were freezed at -20ºC prior to DNA extraction

extract_protocol:
DNeasy PowerSoil Kit (Qiagen Laboratories, Inc.)
Sequencing libraries were generated using NEBNext Ultra DNA Library Pre ®Kit for Illumina, following manufacturer's recommendations. Sequencing was carried out on an Illumina platform and 250 bp paired-end reads were generated

treatment_protocol: Soil directly added to the kit at a total amount of 0,25g following manufacturer´s indications

value: USW

tag: geographic location

tag: sampling date

tag: soil type

value: oil type not applicable. Sample is Raw USW


title: RNA-Seq of  SGBS CONTROL B_1_02

description: RNA-Seq of  SGBS CONTROL

value: SGBS


title: tx-j_H3K27ac_5


title: tx-j_H3K27ac_4


title: P1SC_H3K4me3_CutnRun_1


title: P1SC_H3K4me1_CutnRun_2


title: tx-j_H3K27ac_2


title: P1SC_H3K4me1_CutnRun_1


title: tx-j_H3K27ac_3


title: tx-j_H3K27ac_1


title: P1SC_ATACseq_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers


title: C3H_H3K27ac_6

value: Wild type


title: control_renal biopsy [BIOS-03-0005]

value: renal, endothelial and immune cells

value: Post kidney transplantation


title: M5a1 WT Nfix rep2

city: London

first: Martin

last: Buck

address: Imperial College Road, South Kensington

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Sequencing reads were trimmed to remove adapter sequences and filtered to remove duplicates
Reads were mapped to the ICL_KoM5aI template sequence (GenBank WGS accession: JAFHKG010000000; BioSample: SAMN17288411), resulting in binary alignment map (bam) files and a matrix of normalised gene counts (reads per kilobase per million; RPKM)
Differential gene expression analysis was performed using the R/Bioconductor statistical package DEseq2 (version 1.22.2), utilising settings of regularized logarithm (rlog) normalisation of read counts, Wald hypothesis testing and p-value adjustment using a False Discovery Rate threshold of 0.05. Log2 fold changes between conditions were calculated for differentially expressed genes (DEGs) with an adjusted p value of <0.05
Genome_build: Klebsiella oxytoca M5aI (GenBank WGS accession: JAFHKG010000000; BioSample: SAMN17288411)
Supplementary_files_format_and_content: M5aI_NfixNrich_processed_RPKM_DESeq.xls [xls file containing two tabs: Expression_matrix=a matrix of total mapped reads and RPKM values for all gene ids and samples; DESeq_DEGs=all differentially expressed genes (where FDR adjusted p-values <0.05) in Nfix samples compared to Nrich control, with log2 fold changes]; .bam files [Binary Alignment Map (BAM) for each sample. Read alignment to the ICL_KoM5aI template sequence (GenBank WGS accession: JAFHKG010000000; BioSample SAMN17288411)]

organism: Klebsiella oxytoca

source_name: bacterial cells_nitrogen starved

growth_protocol: M5aI cells were cultured in 100 mL Nitrogen-Free David and Mingioli (NFDM) medium [69 mM K2HPO4, 25 mM KH2PO4, 0.1 mM Na2MoO4, 90 μM FeSO4, 0.8 mM MgSO4, 2% w/v glucose] supplemented with NH4Cl (Nfix=0.5 mM; Nrich=10 mM) as a nitrogen source from an initial OD600 of 0.1. Culture vessels were sealed and flushed with N2 gas for 45 minutes to initiate micro-aerobic conditions, prior to incubation at 25°C and 200 rpm. Cultures were cultured for a further 3 hours following exhaustion of NH4 in the supernatant, measured by colorimetric assay.

extract_protocol:
Cell cultures were fixed with a 1/10 volume of 5% phenol/95% ethanol (v/v), harvested by centrifugation at 4000 x g and stored at -80°C. Cell pellet samples were shipped on ice to Vertis Biotechnologie AG (Freising, Germany) for RNA extraction and sample processing.Total RNA was isolated via lysozyme lysis and the mirVana microRNA isolation kit (Ambion). DNase was used to specifically remove contaminant DNA and ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina).
The primary RNA transcripts were fragmented using ultrasound (4 pulses of 30 s each at 4°C) prior to ligation of 3’ oligonucleotide adapters. First-strand cDNA synthesis via Moloney Murine Leukemia Virus (M-MLV) reverse transcriptase was primed using the 3’ adapter. Following purification of first-strand cDNA, a 5' Illumina TruSeq sequencing adapter (Illumina), inclusive of an 8 nt barcode sequence, was ligated to the 3' end of the antisense cDNA prior to PCR-amplification of double-stranded cDNA to about 10-20 ng/μl (12-13 thermocycles) using a high fidelity DNA polymerase. cDNA was purified, pooled in equimolar quantities and size-fractionated (200-500 bp) using the Agencourt AMPure XP kit (Beckman Coulter Genomics) prior to analysis by capillary electrophoresis. cDNA pools were quality checked on a Shimadzu MultiNA microchip electrophoresis system prior to strand-specific sequencing on an Illumina NextSeq 500 system, utilising a read length of 75 nt and a depth of 100 million reads.

tag: medium

value: NFDM + 0.5 mM NH4Cl

tag: illumina truseq i5 adapter barcode

value: GCCTCTAT


title: M5a1 WT Nfix rep1

value: AGGCTATA


title: REU4502A31 (RN124)

city: Bristol

first: Johannes

last: Reul

address: Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School

institute: University of Bristol

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA v2.7.7, Application Version: HD 3.4.0.38
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to the Rat genome Rnor_6.0, Ensembl release 81.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: exon_counts.txt: Gene expression counts using reads aligning to annotated exon features of 32546 genes
Supplementary_files_format_and_content: intron_counts.txt: Gene expression counts using reads aligning to intron features of 22971 genes
Supplementary_files_format_and_content: QC_Table.xlsx: Contains two excel sheets with Sheet 1 = sample information with information regarding sequencing depth and mapping QC metrics
Supplementary_files_format_and_content: QC_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1

organism: Rattus norvegicus

source_name: late afternoon baseline (BL PM)

extract_protocol:
RNA was extracted from hippocampus tissue using TRI reagent as per manufacturer's instructions. The resulting RNA pellets were dissolved in 50 μl of nuclease-free water (Ambion). Purified RNA was treated with DNase I (Qiagen, Germany) and incubated for 10 min at room temperature. DNase was inactivated by the addition of EDTA (Final conc. 5mM) for 10 min at 70°C and RNA was purified over MinElute spin column as per manufacturer’s instructions (Qiagen, Germany).
Total RNA was depleted of ribosomal RNA using Ribo-Zero rRNA Removal Kit (Epicentre/Illumina, Human/Mouse/Rat). Library preparation was completed using TruSeq Stranded Total RNA kit (Illumina).

tag: group

value: late afternoon baseline (BL PM)

tag: Sex

value: Male

value: Wistar

tag: tissue

value: Whole hippocampus

tag: conditions

value: Late afternoon baseline conditions


title: P1SC_RNAseq_3

molecule: polyA RNA

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from P1 cochleae into 300μL RNA lysis buffer (Zymo), and RNA was extracted using Quick RNA Microprep kit (Zymo).
Poly-A tail RNA were enriched, and libraries were prepared using Illumina True-Seq mRNA-seq kit.

tag: cell type

value: supporting cells

value: Lfng-GFP


title: REU4502A30 (RN123)

tag: strain


title: C3H_H3K27ac_4

value: Liver

tag: treatment group

value: 24 weeks

value: H3K27ac (Abcam, Catalog-ab177178)


title: C3H_H3K27ac_5

tag: genotype


title: P1SC_ATACseq_1

value: postnatal day 1


title: P1SC_RNAseq_2


title: REU4502A29 (RN120)


title: REU4502A28 (RN119)


title: P1SC_RNAseq_1


title: REU4502A27 (RN118)


title: C3H_H3K27ac_3

value: Wild type

tag: age


title: M5a1 WT Nrich

source_name: bacterial cells_nitrogen replete

value: NFDM + 10 mM NH4Cl

value: AGGATAGG


title: E17SC_H3K4me3_ChIPseq_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from E17.5 cochleae into 500μL PBS supplemented with 10% FBS, and purified cell were crosslinked by 1% formadehyde. Chromatin was sheared by sonication, and DNA ends were tagged by Tn5 transposase. Nucleosomes with particular histone modification were precipitated using specific antibody and dynabeads protein A.
Libraries were prepared by PCR with indexed primers

value: embryonic day 17.5


title: C3H_H3K27ac_2

tag: chip antibody


title: REU4502A26 (RN114)

value: 360 min following onset of FS


title: C3H_H3K27ac_1


title: E17SC_H3K4me3_ChIPseq_1

tag: developmental stage


title: REU4502A25 (RN113)


title: E17SC_H3K4me1_CutnRun_2

extract_protocol:
Lfng-GFP positive supporting cells were FACS-sorted from E17.5 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for CUT&RUN with specific antibody, and DNA fragments were extracted using phenol-chloroform method.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

tag: marker


title: REU4502A24 (RN111)


title: REU4502A23 (RN108)


title: E17SC_H3K4me1_CutnRun_1


title: tx-j+PCA+Choline_5

data_processing:
Raw reads (FASTQ) were processed through fastp (0.20.0), removing reads containing adapter and poly-N sequences and low-quality reads while simultaneously calculating Q20, Q30, and GC content
Paired-end clean reads were aligned to the reference genome(grcm38) using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d)
FeatureCounts(v1.5.0-p3) was used to count the reads mapped to each gene; RPKM of each gene was calculated based on the length of the gene and reads mapped to the gene.
Genome_build: grcm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited text files with raw gene counts for every gene and every sample

extract_protocol:
After 24 weeks, Liver were removed, flash frozen in liquid nitrogne, and  total RNA was extracted from frozen mouse liver  using the AllPrep DNA/RNA Mini Kit (Cat. No- 80204 QIAGEN).
Sequencing libraries were generated using with 1 ug of total RNA by NEBNext Ultra RNA Library Prep Kit for Illumina (Cat. no-E7530LNew England Biolabs).

value: Untreated tx-j+PCA+Choline

value: Mutant (Atp7btx-J)


title: tx-j+PCA+Choline_6


title: REU4502A22 (RN107)

value: Male


title: P1HC_H3K27me3_ChIPseq_2

extract_protocol:
Atoh1-GFP positive sensory hair cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS, and purified cell were crosslinked by 1% formadehyde. Chromatin was sheared by sonication, and DNA ends were tagged by Tn5 transposase. Nucleosomes with particular histone modification were precipitated using specific antibody and dynabeads protein A.
Libraries were prepared by PCR with indexed primers

value: hair cells


title: tx-j+PCA+Choline_3


title: P1HC_H3K27me3_ChIPseq_1


title: REU4502A21 (RN106)

value: Wistar

value: Whole hippocampus

value: 180 min following onset of FS


title: P1HC_H3K27ac_ChIPseq_2


title: tx-j+PCA+Choline_1


title: tx-j+PCA+Choline_2


title: P1HC_H3K27ac_ChIPseq_1


title: REU4502A19 (RN104)


title: REU4502A20 (RN105)


title: tx-j+Choline_6

value: Untreated tx-j+Choline


title: P1HC_H3K4me3_ChIPseq_2


title: REU4502A18 (RN102)


title: P1HC_H3K4me3_ChIPseq_1


title: REU4502A17 (RN098)


title: tx-j+Choline_4

value: Liver


title: tx-j+Choline_3

value: 24 weeks


title: REU4502A16 (RN096)

value: 120 min following onset of FS


title: P1HC_H3K4me1_CutnRun_1

extract_protocol:
Atoh1-GFP positive sensory hair cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS. Purified cells were used for Cut&Run with H3K4me1 antibody (Active Motif). DNA fragments were purified using  phenol-chloroform.
Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit with single-indexed and UMI adaptors.

value: postnatal day 1


title: P1HC_H3K4me1_CutnRun_2


title: tx-j+Choline_5


title: REU4502A15 (RN093)


title: tx-j+Choline_2


title: P1HC_ATACseq_2

extract_protocol:
Atoh1-GFP positive sensory hair cells were FACS-sorted from P1 cochleae into 500μL PBS supplemented with 10% FBS. Nuclei was extracted from sorted cells, and Tn5 transposation was carried out at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were prepared by PCR with indexed primers


title: tx-j+Choline_1


title: REU4502A14 (RN092)


title: REU4502A13 (RN091)


title: tx-j+PCA_6

value: Untreated tx-j+PCA


title: tx-j+PCA+Choline_4


title: REU4502A12 (RN089)


title: tx-j+PCA_5


title: P1HC_RNAseq_2

extract_protocol:
Atoh1-GFP positive sensory hair cells were FACS-sorted from P1 cochleae into 300μL RNA lysis buffer (Zymo), and RNA was extracted using Quick RNA Microprep kit (Zymo).
Poly-A tail RNA were enriched, and libraries were prepared using Illumina True-Seq mRNA-seq kit.


title: tx-j+PCA_3


title: REU4502A11 (RN088)

value: 60 min following onset of FS


title: P1HC_RNAseq_1


title: tx-j+PCA_4


title: REU4088A12 (RN087)


title: tx-j+PCA_2


title: D2 Sus 3 input

city: Phoenix

first: Hee-Dae

last: Kim

state: AZ

address: 425 N 5th St

department: Basic Medical Sciences

institute: University of Arizona College of Medicine

description: Total RNA from NAc tissue

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Several database sources were referenced for enrichment analysis, including Interpro, NCBI, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Genome_build: mm10

source_name: Nucleus accumbens (NAc)

extract_protocol:
Six NAc tissue punches (2 mm) from two RT; D1-Cre or RT; D2-Cre mice are homogenized in 1 ml of homogenization buffer (Sanz et al., 2009) for each sample (2 mice, pooled for each sample). Samples are then centrifuged at 4°C, 10,000 g for 10 min and 750 μl of clear supernatants are mixed with 5 μg of HA-antibody (Abcam, #ab9110), and incubated on a gentle rotator at 4°C overnight. Remaining supernatants are saved for input samples at -80°C until RNA purification. The next day, 200 μl of magnetic beads (Dynabeads anti-rabbit IgG; Life technology) are added and incubated overnight with constant rotation. The following day, magnetic beads are washed 3 times in the magnetic rack for 10 min with a high salt wash buffer. Each RNA sample was extracted using Direct-zol miniprep kit (Zymo Research) and subjected to RNA-seq. For quality control, RNA integrity (RIN) values were measured and samples with RIN < 7 were excluded.
Purified RNA samples from RiboTag immunoprecipitation (500 ng of RNA for each) were prepped for libraries after poly-A selection (KAPA Stranded mRNA-Seq Kit, Roche) and the libraries were sequenced in NextSeq500 (Illumina).

treatment_protocol: Test mice (RT;D1-Cre & RT;D2-Cre) were exposed to an unfamiliar and aggressive male CD1 retired breeder mouse for 10 min per day for up to 10 days. Following direct interaction with the CD1 aggressor, animals were placed in an adjacent compartment of the same cage for the next 24 hrs with sensory, but not physical contact. Control animals were housed in equivalent cages but with members of the same strain. 24 hrs following the last social defeat, animals were assayed on the social interaction test and sorted into either susceptible or unsusceptible (resilient) phenotypes based on interaction scores.

value: Brain

value: 8-12 weeks old

value: RT; D2-Cre

tag: stress condition

value: Susceptible


title: P1HC_RNAseq_3


title: D2 Sus 1 input

description: Total RNA from NAc tissue


title: REU4088A11 (RN085)


title: REU4088A10 (RN083)


title: D2 Sus 2 input

description: Total RNA from NAc tissue


title: REU4502A9 (RN082)


title: tx-j+PCA_1

value: Mutant (Atp7btx-J)


title: D2 Res 3 input

description: Total RNA from NAc tissue

value: Resilient


title: tx-j_6

value: Untreated tx-j


title: P1HC_ATACseq_1

value: hair cells


title: D2 Res 2 input

description: Total RNA from NAc tissue


title: REU4088A9 (RN078)

value: Male

value: Wistar

value: Whole hippocampus

value: 30 min following onset of FS


title: D2 Res 1 input

description: Total RNA from NAc tissue


title: tx-j_4

value: Liver

value: 24 weeks


title: REU4502A8 (RN077)


title: D2 Con 3 input

description: Total RNA from NAc tissue

value: Control


title: REU4502A10 (RN086)


title: tx-j_2


title: REU4088A8 (RN076)


title: D2 Con 2 input

description: Total RNA from NAc tissue


title: REU4088A7 (RN074)


title: tx-j_1


title: REU4502A7 (RN073)


title: tx-j_5


title: D1 Sus 3 input

description: Total RNA from NAc tissue

value: RT; D1-Cre


title: C3H_6

value: Wild type


title: D1 Sus 2 input

description: Total RNA from NAc tissue

value: Brain


title: D2 Con 1 input

description: Total RNA from NAc tissue

value: 8-12 weeks old


title: C3H_5


title: C3H_4


title: REU4502A6 (RN072)


title: REU4502A5 (RN070)

source_name: early morning baseline (BL AM)

value: early morning baseline (BL AM)

value: Early morning baseline conditions


title: D1 Sus 1 input

description: Total RNA from NAc tissue

value: Susceptible


title: D1 Res 3 input

description: Total RNA from NAc tissue

value: Resilient


title: REU4502A4 (RN068)


title: REU4502A3 (RN067)


title: C3H_3


title: REU4502A2 (RN063)


title: D1 Res 2 input

description: Total RNA from NAc tissue


title: D1 Res 1 input

description: Total RNA from NAc tissue


title: tx-j_3

value: Untreated tx-j

value: Mutant (Atp7btx-J)


title: C3H_2


title: REU4502A1 (RN062)

value: Male


title: C3H_1


title: D1 Con 3 input

description: Total RNA from NAc tissue


title: Input_replicate-R

description: R-I

data_processing:
Sequencing adapters and primers still present in unmapped reads were trimmed using Skewer (version 0.1.125).
Reads were mapped to the reference genome using BWA (version 0.7.15).
Bamtools (version 2.3.0) was used to filter out reads with poor quality, not properly paired and with too long insert size.
Since samples were sequenced across 5 lanes, their mapped / filtered reads were merged and deduplicated using Picard (version 1.111).
Mapped reads were analysed for standard ChIP-Seq quality metrics; in particular, for each sample, the Normalized Strand Cross-correlation and the Relative Strand Cross-correlation was calculated.
Peaks were called using the software MACS2 (version 2.1.1.20160309) with default parameters for narrow regions. Input samples (named “*-I”) were used as controls for the corresponding IP samples (named “*-GR” or “*-MR”) from the same animal and experimental condition.
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: narrowPeak files (BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue)

source_name: Late afternoon baseline_Input_ChIPSeq

extract_protocol:
Whole hippocampus were dissected, snap frozen in liquid N2 and stored at -80C until processing. Hippocampi from 2 rats were cross-linked in 1% formaldehyde containing inhibitors and sonicated  to extract chromatin. Chromatin was immunoprecipitated using antibodies against MR (MR H-300, sc11412x, Santa Cruz) or GR (GR H-300, sc8992x, Santa Cruz) and inputs were prepared from original chromatin sample in the absence of antibody.
Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (WaferGen PrepX Complete ILMN 32i) using an Apollo system for end-repair, A-tailing, and ligation. The adapter-ligated samples were then single-indexed and PCR amplified.

value: Wistar

value: Late afternoon baseline conditions

value: whole hippocampus


title: D2 Sus 4

description: mRNA from D2-MSNs only

value: RT; D2-Cre


title: ChIP-GR_replicate-R

description: R-GR

source_name: Late afternoon baseline_GR_ChIPSeq

value: GR (GR H-300, sc8992x, Santa Cruz)


title: D1 Con 2 input

description: Total RNA from NAc tissue

value: Control


title: ChIP-MR_replicate-Q

description: Q-MR

source_name: Acute stress_MR_ChIPSeq

value: Acute stress conditions

value: MR (MR H-300, sc11412x, Santa Cruz)


title: Input_replicate-Q

description: Q-I

source_name: Acute stress_Input_ChIPSeq


title: D1 Con 1 input

description: Total RNA from NAc tissue

value: Brain

value: RT; D1-Cre


title: D2 Sus 3

description: mRNA from D2-MSNs only

value: 8-12 weeks old


title: ChIP-GR_replicate-Q

description: Q-GR

source_name: Acute stress_GR_ChIPSeq


title: Input_replicate-P

description: P-I

source_name: Early morning baseline_Input_ChIPSeq

value: Early morning baseline conditions


title: D2 Sus 2

description: mRNA from D2-MSNs only

value: Susceptible


title: D2 Sus 1

description: mRNA from D2-MSNs only


title: ChIP-MR_replicate-P

description: P-MR

source_name: Early morning baseline_MR_ChIPSeq


title: ChIP-GR_replicate-P

description: P-GR

source_name: Early morning baseline_GR_ChIPSeq


title: D2 Res 5

description: mRNA from D2-MSNs only

value: Resilient


title: ChIP-MR_replicate-R

description: R-MR

source_name: Late afternoon baseline_MR_ChIPSeq


title: Input_replicate-K

description: K-I


title: D2 Res 3

description: mRNA from D2-MSNs only


title: D2 Res 2

description: mRNA from D2-MSNs only


title: D2 Sus 5

description: mRNA from D2-MSNs only


title: Epithelial_fraction_irradiated_96h_rep1

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: Epithelial fraction small intestine, irradiated, t=96h

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina Totalprep RNA amplification kit for Illumina arrays

growth_protocol: Mice were housed in specific pathogen free conditions, fed regular chow.

extract_protocol: RNA was isolated using TRI-reagent

treatment_protocol: Mice were exposed to 12 gy whole-body ionizing gamma-irradiation, in half of the mice the epithelial fraction was isolated from the small intestine with EDTA.

tag: condition

value: Irradiated

tag: time point

value: 96 hours

tag: tissue type

value: Epithelial fraction from small intestinal tissue (EDTA)


title: Epithelial_fraction_irradiated_96h_rep2


title: Epithelial_fraction_irradiated_48h_rep4

source_name: Epithelial fraction small intestine, irradiated, t=48h

value: 48 hours


title: Epithelial_fraction_irradiated_48h_rep5


title: Epithelial_fraction_irradiated_96h_rep5


title: ChIP-MR_replicate-I

description: I-MR

value: Wistar

value: Male


title: Epithelial_fraction_irradiated_48h_rep2


title: Epithelial_fraction_irradiated_96h_rep4


title: ChIP-MR_replicate-K

description: K-MR

value: Late afternoon baseline conditions

value: whole hippocampus


title: Epithelial_fraction_irradiated_24h_rep5

source_name: Epithelial fraction small intestine, irradiated, t=24h

value: 24 hours


title: ChIP-GR_replicate-I

description: I-GR

value: Acute stress conditions

value: GR (GR H-300, sc8992x, Santa Cruz)


title: Epithelial_fraction_irradiated_96h_rep3


title: Input_replicate-I

description: I-I


title: D2 Res 1

description: mRNA from D2-MSNs only

value: Brain

value: RT; D2-Cre


title: D2 Con 3

description: mRNA from D2-MSNs only

value: 8-12 weeks old

value: Control


title: Epithelial_fraction_irradiated_48h_rep1


title: Input_replicate-G

description: G-I

value: Early morning baseline conditions


title: Epithelial_fraction_irradiated_24h_rep4


title: Epithelial_fraction_irradiated_24h_rep2


title: Epithelial_fraction_irradiated_48h_rep3


title: ChIP-GR_replicate-K

description: K-GR


title: Epithelial_fraction_irradiated_24h_rep1


title: Epithelial_fraction_irradiated_24h_rep3


title: D2 Res 4

description: mRNA from D2-MSNs only

value: Resilient


title: D2 Con 2

description: mRNA from D2-MSNs only


title: ChIP-GR_replicate-G

description: G-GR


title: ChIP-MR_replicate-G

description: G-MR

value: MR (MR H-300, sc11412x, Santa Cruz)


title: D2 Con 4

description: mRNA from D2-MSNs only


title: D2 Con 1

description: mRNA from D2-MSNs only


title: Input_replicate-F

description: F-I


title: D1 Sus 4

description: mRNA from D1-MSNs only

value: RT; D1-Cre

value: Susceptible


title: D1 Sus 5

description: mRNA from D1-MSNs only


title: D2 Con 5

description: mRNA from D2-MSNs only


title: D1 Sus 3

description: mRNA from D1-MSNs only


title: ChIP-MR_replicate-E

description: E-MR


title: D1 Res 4

description: mRNA from D1-MSNs only


title: ChIP-GR_replicate-F

description: F-GR


title: Input_replicate-E

description: E-I


title: D1 Sus 2

description: mRNA from D1-MSNs only


title: D1 Sus 1

description: mRNA from D1-MSNs only


title: Epithelial_fraction_control_0h_rep4

source_name: Epithelial fraction small intestine, control, t=0h

value: 0 hours

value: Epithelial fraction from small intestinal tissue (EDTA)


title: Epithelial_fraction_control_0h_rep3


title: Epithelial_fraction_control_0h_rep2


title: Epithelial_fraction_control_0h_rep1


title: Small_intestine_irradiated_96h_rep5

source_name: Small intestine, irradiated, t=96h

value: Irradiated

value: 96 hours

value: Small intestinal tissue


title: ChIP-GR_replicate-E

description: E-GR

value: Wistar

value: Male

value: whole hippocampus


title: Epithelial_fraction_control_0h_rep5


title: Input_replicate-D

description: D-I


title: D1 Res 2

description: mRNA from D1-MSNs only

value: Brain


title: ChIP-MR_replicate-D

description: D-MR


title: Small_intestine_irradiated_96h_rep3


title: ChIP-MR_replicate-F

description: F-MR

value: Late afternoon baseline conditions


title: D1 Res 1

description: mRNA from D1-MSNs only

value: 8-12 weeks old


title: D1 Con 4

description: mRNA from D1-MSNs only

value: Control


title: ChIP-GR_replicate-D

description: D-GR

value: Early morning baseline conditions

value: GR (GR H-300, sc8992x, Santa Cruz)


title: Small_intestine_irradiated_96h_rep2


title: Small_intestine_irradiated_48h_rep5

source_name: Small intestine, irradiated, t=48h

value: 48 hours


title: Small_intestine_irradiated_96h_rep4


title: Small_intestine_irradiated_48h_rep4


title: Small_intestine_irradiated_48h_rep3


title: D1 Con 3

description: mRNA from D1-MSNs only

source_name: Nucleus accumbens (NAc)

value: RT; D1-Cre


title: D1 Con 2

description: mRNA from D1-MSNs only


title: ChIP-GR_replicate-C

description: C-GR


title: D1 Con 1

description: mRNA from D1-MSNs only


title: Input_replicate-B

description: B-I

value: Acute stress conditions


title: ChIP-MR_replicate-C

description: C-MR

value: MR (MR H-300, sc11412x, Santa Cruz)


title: ChIP-MR_replicate-B

description: B-MR


title: C-L-3

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: Gene expression data from pUC9 inoculated leaves

data_processing:
Base calling and adapter trimming was performed automatically by Torrent Suite software.
Residual rRNA and ERCC reads were identified and filtered out using bbsplit and filterbyname scripts from BBTools suite (Brian Bushnell).
Reads were aligned to genome using TMAP 5.0.13. with soft clipping from both ends and returning all the mappings with the best score. Other settings were set according to Torrent Suite defaults. Unaligned reads were aligned with BBMap (Brian Bushnell).
Quantitation to ITAG3.2 transcripts and differential expression analysis was performed in Partek Flow (Partek Inc.) using Partek GSA algorithm.
Genome_build: ITAG3
Supplementary_files_format_and_content: gene read counts - Table with raw read counts derived from Partek E/M Quantification Algorithm. Genes are in rows, samlples - in columns
Supplementary_files_format_and_content: differential expression table - table containing results of GSA differential gene expression analysis. For each comparison (Contrast), values of p-value, q-value,FDR, ratio and fold change are presented in column for each gene (in rows)

organism: Solanum lycopersicum

source_name: Solanum lycopersicum leaves inoculated with pUC9

growth_protocol: Inoculated tomato plants were maintained in a greenhouse at 28-30ºC for 16 h and at 25ºC for 8 h in the dark.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit according to manufacturer’s instruction (Qiagen). Contaminating DNA was removed from the extracted RNA using TURBO DNase-free TM Kit (Ambion).
ERCC RNA Spike-In Mix 1 (Thermo Fisher) was added as internal control to each sample. Ribosomal RNA was removed using RiboMinus Plant Kit (Thermo Fisher). Libraries were prepared with Ion Total RNA-Seq Kit v2 and Ion Xpress RNA-Seq Barcode 1-16 Kit according to user guide. Sequencing template was generated with Ion PI™ Template OT2 200 Kit v3 on Ion OneTouch™ 2 System. Sequencing was performed on Ion PI™ chip v2 and Ion Proton™ sequencer using Ion PI™ Sequencing 200 Kit v2

treatment_protocol: Two μg of purified plasmids containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control were mechanically inoculated into  tomato seedling leaves. Tomato leaves were collected at 17 days post inoculation.

tag: organ

value: leaves

tag: infecious variants


title: C-L-2


title: D1 Res 3

description: mRNA from D1-MSNs only

value: Resilient


title: ChIP-GR_replicate-B

description: B-GR

tag: Sex


title: C-L-1


title: Input_replicate-C

description: C-I

source_name: Late afternoon baseline_Input_ChIPSeq

tag: tissue


title: S23-L-2

description: Gene expression data from PSTVd-S23 inoculated leaves

source_name: Solanum lycopersicum leaves inoculated with PSTVd-S23


title: Input_replicate-A

description: A-I

tag: conditions


title: Small_intestine_irradiated_96h_rep1

value: Irradiated

value: 96 hours


title: Small_intestine_irradiated_48h_rep2

value: Small intestinal tissue


title: S23-L-3


title: ChIP-MR_replicate-A

description: A-MR

value: Wistar

value: Male


title: Small_intestine_irradiated_48h_rep1


title: ChIP-GR_replicate-A

description: A-GR

value: whole hippocampus


title: Small_intestine_irradiated_24h_rep3

source_name: Small intestine, irradiated, t=24h

value: 24 hours


title: Small_intestine_irradiated_24h_rep5


title: Small_intestine_irradiated_24h_rep4


title: Patient1-library 3

city: Shenzhen

first: Chao

last: Chen

state: Outside the US or Canada

address: Shenzhen,china

country: China

institute: Peking University Shenzhen Hospital

data_processing:
Quality control
Converted to a Cell Ranger-specific FASTQ file using an in-house Perl script
Aligned reads with the GRCH38 human reference using STAR software (v2.5.3)
The mapped reads were then filtered out for valid cell barcodes and UMIs
Generate a gene-cell matrix for downstream analysis
Genome_build: GRCH38(hg38)
Supplementary_files_format_and_content: count_mtx.tsv.gz, the UMI counts of each cell in the sample.

source_name: Colorectum

extract_protocol:
The concentration of single-cell suspension was adjusted to 1000 cells/uL by using cell resuspension buffer. Single cell suspension was then loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer's instructions (MGI DNBelab C4 system).
An scRNA-seq library was prepared using the DNBelab C4 system as previously described. Briefly, the single-cell suspension was transformed into the scRNA-seq library of barcodes through the steps of droplet encapsulation, emulsification and fragmentation, mRNA capture bead collection, reverse transcription, cDNA amplification and purification. An indexed sequencing library was constructed according to the manufacturer's instructions. The sequencing library was quantified using the Qubit SSDNA Assay Kit (Thermo Fisher Scientific).

value: female

value: MSI-H


title: S23-L-1


title: Small_intestine_control_0h_rep5

source_name: Small intestine, control, t=0h

value: Control

value: 0 hours


title: Patient1-library 1


title: Patient1-library 2


title: Small_intestine_irradiated_24h_rep1


title: Suffolk_natural_follicular_rep9

status: Public on Jul 08 2021

city: Dunsany

first: Paul

last: Cormican

address: Grange

department: Bioscience

country: Ireland

institute: Teagasc

data_processing:
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence, then mapped to OAR V3.1  genome version  using STAR (v2.6.1b)
Read counts per gene for each sample were estimated using featurCounts from the subread package (v.1.6.3).
Genome_build: OAR v3.1
Supplementary_files_format_and_content: Individual matrix tables with raw gene counts for every gene in a sample

organism: Ovis aries

source_name: Cervical post mortem

extract_protocol:
Cervical samples were taken, flash frozen before subsequent RNA extraction in TRIzol reagent. Total RNA concentration was quantified using the Nanodrop ND-1000 UV-Vis Spectophotometer. Quality of RNA was ascertained with the use of 2100 Agilent Bioanalyzer .
RNA libraries were prepared for sequencing using Illumina® TruSeq® Stranded mRNA Library preparation Kits

tag: sheep breed

value: Suffolk

tag: cycle

value: Natural

tag: phase

value: Follicular

value: cervix


title: M-L-3

description: Gene expression data from PSTVd-M inoculated leaves

source_name: Solanum lycopersicum leaves inoculated with PSTVd-M

value: leaves

value: PSTVd-M


title: M-L-1


title: Small_intestine_control_0h_rep1


title: Suffolk_natural_follicular_rep6


title: Suffolk_natural_follicular_rep8


title: Small_intestine_control_0h_rep3


title: Small_intestine_control_0h_rep2


title: Suffolk_natural_follicular_rep3


title: Suffolk_natural_follicular_rep7


title: Small_intestine_irradiated_24h_rep2

value: Irradiated


title: Suffolk_natural_follicular_rep2


title: Suffolk_induced_luteal_rep9

value: Induced

value: Luteal


title: Suffolk_induced_luteal_rep6


title: Suffolk_induced_luteal_rep7


title: Suffolk_induced_luteal_rep4


title: Suffolk_induced_luteal_rep3


title: Suffolk_natural_follicular_rep5


title: Small_intestine_control_0h_rep4

value: Small intestinal tissue


title: Suffolk_natural_follicular_rep1


title: Suffolk_induced_luteal_rep10


title: Suffolk_natural_follicular_rep4


title: Suffolk_induced_luteal_rep8


title: Suffolk_induced_luteal_rep5


title: M-L-2


title: Suffolk_induced_luteal_rep2


title: Suffolk_induced_luteal_rep1


title: Suffolk_induced_follicular_rep11


title: Suffolk_induced_follicular_rep6


title: Suffolk_induced_follicular_rep5


title: Suffolk_induced_follicular_rep10


title: Suffolk_induced_follicular_rep9


title: Norwegian_natural_follicular_rep9

value: Norwegian


title: Suffolk_induced_follicular_rep4


title: Suffolk_induced_follicular_rep7


title: Suffolk_induced_follicular_rep1


title: Suffolk_induced_follicular_rep3


title: Norwegian_natural_follicular_rep7


title: Suffolk_induced_follicular_rep8


title: Norwegian_natural_follicular_rep6


title: Norwegian_natural_follicular_rep10


title: Norwegian_natural_follicular_rep2


title: Norwegian_natural_follicular_rep4


title: Norwegian_natural_follicular_rep1


title: Norwegian_natural_follicular_rep5


title: Norwegian_natural_follicular_rep8


title: Norwegian_induced_luteal_rep4


title: Norwegian_natural_follicular_rep3


title: Norwegian_induced_luteal_rep5


title: Norwegian_induced_luteal_rep7


title: Norwegian_induced_luteal_rep6


title: Norwegian_induced_luteal_rep8


title: Norwegian_induced_luteal_rep1


title: Suffolk_induced_follicular_rep2


title: Norwegian_induced_follicular_rep10


title: Norwegian_induced_follicular_rep8


title: Norwegian_induced_follicular_rep9


title: Norwegian_induced_luteal_rep2


title: Norwegian_induced_follicular_rep7


title: Norwegian_induced_follicular_rep4


title: Norwegian_induced_follicular_rep5


title: Norwegian_induced_follicular_rep3


title: Norwegian_induced_follicular_rep1


title: Norwegian_induced_follicular_rep2


title: FUR_natural_follicular_rep10

value: FUR


title: FUR_natural_follicular_rep7


title: FUR_natural_follicular_rep4


title: FUR_natural_follicular_rep8


title: FUR_natural_follicular_rep6


title: FUR_natural_follicular_rep1


title: Norwegian_induced_luteal_rep3


title: FUR_natural_follicular_rep2


title: FUR_natural_follicular_rep9


title: FUR_induced_luteal_rep9


title: FUR_natural_follicular_rep3


title: FUR_induced_luteal_rep6


title: FUR_natural_follicular_rep5


title: FUR_induced_luteal_rep4


title: FUR_induced_luteal_rep3


title: FUR_induced_luteal_rep5


title: FUR_induced_luteal_rep2


title: Norwegian_induced_follicular_rep6


title: FUR_induced_follicular_rep7


title: FUR_induced_follicular_rep8


title: FUR_induced_follicular_rep4


title: FUR_induced_follicular_rep6


title: FUR_induced_follicular_rep3


title: Belclare_natural_follicular_rep10

value: Belclare


title: FUR_induced_follicular_rep2


title: Belclare_natural_follicular_rep9


title: FUR_induced_luteal_rep7


title: FUR_induced_follicular_rep1


title: FUR_induced_luteal_rep8


title: Belclare_natural_follicular_rep7


title: Belclare_natural_follicular_rep8


title: Belclare_natural_follicular_rep5


title: Belclare_natural_follicular_rep4


title: Belclare_natural_follicular_rep6


title: Belclare_natural_follicular_rep3


title: Belclare_natural_follicular_rep1


title: Belcare_induced_Luteal_rep9


title: Belcare_induced_Luteal_rep10


title: Belcare_induced_Luteal_rep8


title: Belclare_natural_follicular_rep2


title: Belcare_induced_Luteal_rep7


title: FUR_induced_luteal_rep1


title: Belcare_induced_Luteal_rep6


title: Belcare_induced_Luteal_rep5


title: Belcare_induced_Luteal_rep4


title: Belcare_induced_Luteal_rep2


title: Belcare_induced_Luteal_rep3


title: Belcare_induced_Luteal_rep1


title: FUR_induced_follicular_rep5


title: Belclare_induced_Follicular_rep10


title: Belclare_induced_Follicular_rep8


title: Belclare_induced_Follicular_rep7


title: Belclare_induced_Follicular_rep5


title: Belclare_induced_Follicular_rep6


title: Belclare_induced_Follicular_rep9


title: Belclare_induced_Follicular_rep4


title: Belclare_induced_Follicular_rep3


title: Belclare_induced_Follicular_rep2


title: High intramuscular fat rep1

city: Beijing

first: Pan

last: Zhang

address: No. 2, Yuanmingyuan West Road, Beijing

institute: China Agricultural University

description:
FPKM.txt
MG01

data_processing:
The Illumina Novaseq6000 (Illumina, San Diego, CA, USA) platform is used for transcriptome sequencing
Clean reads were mapped to the reference pig genome version scrofa.Sscrofa11.1by using HISAT2（V2.0.5）tool software for alignment.
We used Cufflinks (V2.2.1) software to calculate FPKM (Fragments per Kilobase Millon Mapped Reads) values to represent gene expression levels.
DESeq2 (V1.25.9) was used to analyze the differences between group
Genome_build: ss11.1
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Sus scrofa

source_name: Longissimus dorsi

extract_protocol:
Total RNA was extracted from the LD muscle and back subcutaneous fat tissues according to the TRIzol method. RNase-free DNase was added to total RNA to remove DNA contamination. The integrity of RNA was checked by 1.2% agarose gel electrophoresis and the quality of RNA and the amount of total RNA were determined by Nanodrop 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Dingyuan

value: 300 days old

value: High intramuscular fat


title: High intramuscular fat rep2

description:
FPKM.txt
MG02

tag: age


title: Low intramuscular fat rep3

description:
FPKM.txt
MD04

value: Low intramuscular fat


title: High back fat rep3

description:
FPKM.txt
BG03

source_name: Back subcutaneous fat

value: High back fat


title: Low intramuscular fat rep1

description:
FPKM.txt
MD02


title: High back fat rep1

description:
FPKM.txt
BG01


title: Low back fat rep3

description:
FPKM.txt
BD04

value: Low back fat


title: Low back fat rep1

description:
FPKM.txt
BD02


title: High back fat rep2

description:
FPKM.txt
BG02


title: Belclare_induced_Follicular_rep1

value: Follicular


title: Low intramuscular fat rep2

description:
FPKM.txt
MD03


title: Low back fat rep2

description:
FPKM.txt
BD03


title: High intramuscular fat rep3

description:
FPKM.txt
MG03


title: Sftpd_KO_Distal_small_intestine_1

city: Boston

first: Matthew

middle: K

last: Waldor

state: MA

address: 181 Longwood Avenue

department: Microbiology

institute: Harvard Medical School

description:
TRA00210823
GSE_Raw_Counts_Distal_Small_intestine.txt

data_processing:
Reads were trimmed using Trim Galore with automatic adapter sequence detection.
Trimmed reads were mapped to the mouse reference genome and annotation using RNA STAR.
Feature Counts was used to build a count matrix from mapped reads using the Ensembl annotation as a guide.
Genome_build: GRCm38
Supplementary_files_format_and_content: GSE_Raw_Counts_Proximal_Small_intestine.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: GSE_Raw_Counts_Distal_Small_intestine.txt: Tab-delimited text file includes raw counts.

source_name: Distal small intestine

growth_protocol: Infant P3 day old C57BL/6 mouse WT and Sftpd KO.

extract_protocol:
Proximal and distal small intestine tissues were harvested and preserved using Trizol reagent. Total RNA was extracted using the RNeasy mini kit (Qiagen).
mRNA libraries were prepared using KAPA mRNA HyperPrep kit (Roche).

treatment_protocol: Infected with V. cholerae.

tag: strain

tag: genotype

tag: treatment

value: Vibrio cholerae infection

value: Distal small intestine


title: WT_Distal_small_intestine_4

description:
TRA00210822
GSE_Raw_Counts_Distal_Small_intestine.txt

value: WT


title: WT_Proximal_small_intestine_4

description:
TRA00210814
GSE_Raw_Counts_Proximal_Small_intestine.txt

source_name: Proximal small intestine

value: Proximal small intestine


title: WT_Proximal_small_intestine_3

description:
TRA00210813
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: Sftpd_KO_Distal_small_intestine_4

description:
TRA00210826
GSE_Raw_Counts_Distal_Small_intestine.txt


title: Sftpd_KO_Proximal_small_intestine_1

description:
TRA00210815
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: WT_Distal_small_intestine_3

description:
TRA00210821
GSE_Raw_Counts_Distal_Small_intestine.txt


title: Sftpd_KO_Distal_small_intestine_3

description:
TRA00210825
GSE_Raw_Counts_Distal_Small_intestine.txt


title: Sftpd_KO_Proximal_small_intestine_2

description:
TRA00210816
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: Sftpd_KO_Distal_small_intestine_2

description:
TRA00210824
GSE_Raw_Counts_Distal_Small_intestine.txt


title: WT_Proximal_small_intestine_1

description:
TRA00210811
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: Sftpd_KO_Proximal_small_intestine_3

description:
TRA00210817
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: WT_Distal_small_intestine_2

description:
TRA00210820
GSE_Raw_Counts_Distal_Small_intestine.txt


title: Sftpd_KO_Proximal_small_intestine_4

description:
TRA00210818
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: WT_Distal_small_intestine_1

description:
TRA00210819
GSE_Raw_Counts_Distal_Small_intestine.txt


title: WT_Proximal_small_intestine_2

description:
TRA00210812
GSE_Raw_Counts_Proximal_Small_intestine.txt


title: SEP3-AG(API-I)  seq-DAP-seq rep3

city: Grenoble

first: Romain

last: BLANC-MATHIEU

address: 17 Avenue des martyrs

institute: CEA

description: Recombinant proteins were produced by TnT in vitro transcription translation system from Promega

data_processing:
Alignment to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Consensus peaks are reworked around maximum of peaks (+/-200 bp).
Consensus bedgraphs are computed by the mean of the replicates bedgraphs
Genome_build: TAIR10
Supplementary_files_format_and_content: Bed files contain position of consensus peaks centered around maximum
Supplementary_files_format_and_content: Bedgraphs files contain profiles of binding intensity (cpm)

organism: Arabidopsis thaliana

source_name: Sheared genomic DNA extracted from Arabidopsis thaliana.

growth_protocol: Grow on 0.5 Murashige and Skoog medium in long-day conditions for 2-weeks.

extract_protocol:
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index

tag: protein epitope tags


title: SEP3-AG(API-I)  seq-DAP-seq rep2


title: SEP3-AG(API-I)  seq-DAP-seq rep1


title: naive rep2 [K002000164_74491]

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

country: Germany

institute: University Medical Center Goettingen

data_processing:
alignment with STAR aligner
count quantification with featureCounts
normalization with RUV-seq
differential gene expression analysis with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 output list; Featurecounts quantification list for all the samples

growth_protocol: Patient-derived GSCs were cultured in Neurocult NS-A basal medium (STEMCELL technologies) supplemented with 10% BSA (STEMCELL technologies), L-Glutamin (Gibco, 25030081), Heparin (STEMCELL technologies), B27 without vitamin A (Gibco),  N2 (Gibco), 20ng/ml recombinant human epidermal growth factor (hEGF) (Peprotech), 20ng/ml basic fibroblast growth factor (bFGF) (Peprotech) (Xie et al, 2015) (Marziali et al., 2017). Cells were maintained at 37°C and 5% CO2 on poly-L-ornithine-coated (Sigma) and laminin-coated (Sigma) cell culture dishes. Cells were dissociated using Accutase (Thermo Fisher). GSCs were cultured in stem cell medium and analyzed for expression of stem cell markers such as, SOX2, PAX6, Nestin, and for the absence of differentiation markers such as TUJ1 and GFAP.

extract_protocol:
U3047MG (before ciliation) and U3047-Nek2-KD (after ciliation) cells were collected and washed once with cold PBS before adding to 300 µl Tri-Reagent (Sigma Aldrich, USA) by free-thawing, and total RNA was isolated and DNase-treated using the DirectZol RNA kit (Zymo Research). Approximately 2 μg of total RNA was used to subselect poly(A)+ transcripts and generate strandspecific cDNA libraries (TrueSeq kit; Illumina).
TruSeq RNA library kit (Illumina)

treatment_protocol: Constitutive overexpression of mCherry U3047MG lentiviral vectors was prepared using pSicoREf1a-mCh-Puro (Addgene plasmid 31845). For GSCs, stable lines generation inducible lentivectors were used pLix 603 Nek2-KD EGFP and pLix 603 Nek2-KD EGFP.  The lentiviral shRNA constructs pLKO.1-puro for CDC components (NDE1, OFD1, HDAC, Nek2 were kindly provided by Dr. Rajalingam. The cloned vectors were packed into lentivirus using second‐generation packaging plasmids (pMD2.G, Addgene #12259 and psPAX2, Addgene #12260). Briefly, target vectors and packaging plasmids were transfected into HEK293TS cells using calcium chloride. After 16 h, the medium was changed, and the virus was collected after 8 h. The freshly harvested virus was used to transduce target cells in a 1:1 ratio for 72–96 h. To generate GSCs lines stably expressing inducible GFP tagged-Nek2-WT and Nek2-KD, pLIX_403 lenti inducible gateway cloning vector (Addgene #41395) was used. The target cells were transduced with lentivirus containing pLIX‐NEK2-WT and pLIX‐NEK2-KD and selected with puromycin antibiotic 2µg/ml. For the expression of the transgenes, all the cell lines stably expressing inducible lenti vector were induced with 2-5 μg/ml of doxycycline (Sigma) for 24–96 h.

tag: cell line

tag: cell type

value: glioblastoma patient-derived GSC line

tag: genotype/variation

value: Control


title: NEK2-KD rep1 [K002000164_74477]


title: naive rep1 [K002000164_74489]


title: NEK2-KD rep2 [K002000164_74479]


title: Control_rep3 [K002000061_49540]

source_name: IMR90 derived normal neural organoids

growth_protocol: Human iPS cell lines IMR90 were cultured in mTeSR1 medium (Stem cell technologies) on Matrigel (Corning) coated cell culture dishes at 37°C and 5% CO2 and routinely checked for mycoplasma contamination with the MycoAlert Kit (Lonza). Cells were dissociated to small aggregates with ReLeSR (Stem cell technologies) every 5-7 days and splitted 1:5 onto fresh Matrigel coated dishes. Before inducing neural differentiation, iPS cells were dissociated to single cells with 1x wash with pre-warmed DMEM/F12 (Gibco) and then treated for 5 min. at 37°C with Accutase (Sigma-Aldrich). After cell collection, centrifuging and counting, cells were diluted in neural induction medium (NIM, Stem cell technologies) plus Rock-inhibitor (10 µM, Y-27632 2HCl, Selleck Chem) at a concentration of 1x105 cells per ml. 100 µl of this cell suspension was given into each well of a 96-well v-bottom low adherent plate and incubated at 37°C and 5% CO2. Half of the medium was changed every day for 5 days until neurospheres were formed. At day 5 of neural induction, the neurospheres were collected and transferred to a 100 mm petri dish containing “neurosphere medium” (Method table 1). Additionally, 0.1% Matrigel was added to the medium and neurospheres were incubated for 5 days at 37°C and 5% CO2. At day 3, 2 ml of “OVB-Organoid medium” (Method table 2) containing r60 nM etinol acetate was added. At day 5, neurospheres were transferred to spinner flasks containing 100 ml “OVB-Organoid medium” (Table 2) to let the neurospheres developing to OVB-Organoid.

extract_protocol:
Samples were collected in Trizol and RNA was purified with Direct-Zol RNA extraction kit (Zymo)
TruSeq RNA library kit (Illumina)

tag: cell type source

value: Normal lung fibroblast IMR90 derived organoids

tag: cell subtype

value: Neurospheres


title: OVB_rep3 [K002000207_84380]

source_name: IMR90 derived OVB organoids

value: OVB-organoids


title: OVB_rep2 [K002000207_84379]


title: OVB_rep1 [K002000207_84378]


title: P6PTD_2_Gamet_0min

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic R56. Processed reads were mapped to the P. beghei ANKA reference genome (release 40 in PlasmoDB- http://www.plasmoddb.org) using Hisat257 (V 2.1.0) with parameter “—rna-strandness FR”. Counts per feature were estimated using FeatureCounts. Raw read counts data were converted to counts per million (cpm) and genes were excluded if they failed to achieve a cpm value of 1 in at least one of the three replicates performed. Library sizes were scale-normalized by the TMM method using EdgeR software59 and further subjected to linear model analysis using the voom function in the limma package. Differential expression analysis was performed using DeSeq2.
Normalization of raw read counts was done using voom tmm method and differential gene expression analysis was carried out using DeSeq2
Genome_build: GCA_900002375
Supplementary_files_format_and_content: tab-delimited text file includes read count values for each Sample

organism: Plasmodium berghei

source_name: P. berghei strain ANKA

growth_protocol: Gametocytes (non-activated 0 min and activated 30 min-) were collected from PP1PTD and WT lines. Total RNA was isolated from purified parasites using an RNeasy purification kit (Qiagen). RNA was vacuum concentrated (SpeedVac) and transported using RNA stable tubes (Biomatrica).

extract_protocol:
Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies).
Strand-specific mRNA sequencing was performed of total RNA and using TruSeq stranded mRNA sample prep kit LT (Illumina), as previously described55.  Libraries were sequenced using an Illumina Hiseq 4000 sequencing platform with paired-end 150 bp read chemistry. The quality of the raw reads was assessed using FATSQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic R56. Processed reads were mapped to the P. beghei ANKA reference genome (release 40 in PlasmoDB- http://www.plasmoddb.org) using Hisat257 (V 2.1.0) with parameter “—rna-strandness FR”. Counts per feature were estimated using FeatureCounts. Raw read counts data were converted to counts per million (cpm) and genes were excluded if they failed to achieve a cpm value of 1 in at least one of the three replicates performed. Library sizes were scale-normalized by the TMM method using EdgeR software59 and further subjected to linear model analysis using the voom function in the limma package. Differential expression analysis was performed using DeSeq.  Genes with a fold-change greater than two and a false discovery rate corrected p-value (Benjamini-Hochberg procedure) < 0.05 were considered to be differentially expressed. Genes with fold change greater than 2 and p-value less than 0.05 were considered as significantly differentially expressed.
Stranded RNA-Seq

treatment_protocol: Gametocytes were activated by placing them in ookinete medium.

value: ANKA

value: Gametocytes

tag: cell status

value: non-activated


title: P6PTD_1_Gamet_0min


title: Control_rep2 [K002000061_49539]


title: WT_2_Gamet_0min


title: WT_1_Gamet_0min


title: M10L

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

description: M10 left

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

source_name: breast milk-derived epithelial cells

growth_protocol: DMEM/F12 (1:3) + 5% FBS + Hydrocortisone (0.4 µg/ml) + Insulin (5 µg/ml) + EGF (20 ng/ml) + Adenine phosphate salt (24 µg/ml) + ROCK inhibitor (Y-27632, 1mM) +1 μM of BMP inhibitor DMH-1 +1 μM of TGFβ inhibitor A-83-01

extract_protocol:
Total RNA was isolated using RNeasy Kit from Qiagen
TruSeq Stranded Total RNA LT(w/ Ribo-Zero™ Gold)

value: breast milk-derived epithelial cells

tag: location

value: left


title: WT_2_Gamet_30min

value: activated


title: Control_rep1 [K002000061_49538]


title: P6PTD_1_Gamet_30min


title: P6PTD_2_Gamet_30min


title: M10L-3

description: M10 left 3


title: M10R-3

description: M10 right 3

value: right


title: WT_1_Gamet_30min


title: M10L-2

description: M10 left 2


title: M5L-3

description: M5 left 3


title: M5R-2

description: M5 right 2


title: M10R

description: M10 right


title: M5R

description: M5 right


title: M4L-3

description: M4 left 3


title: M5L

description: M5 left


title: M4R-3

description: M4 right 3


title: M10R-2

description: M10 right 2


title: M4R-2

description: M4 right 2


title: M4L-2

description: M4 left 2


title: M4R

description: M4 right


title: M5L-2

description: M5 left 2


title: M5R-3

description: M5 right 3


title: M3R-3

description: M3 right 3


title: M3L-3

description: M3 left 3


title: M3L-2

description: M3 left 2


title: M3L

description: M3 left


title: M3R

description: M3 right


title: M2L-3

description: M2 left 3


title: M2R-3

description: M2 right 3


title: ZWT103 KO CAR 1

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: transferred CAR T cells sorted from spleens of B6 recipients

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: CD8+ CAR T cells were isolated by flow cytometric sorting of splenocytes based on reporters and congenical markers: WT CAR (mCherry+Thy1.1+Thy1.2+) and KO CAR T cells (Ametrine+Thy1.1–Thy1.2+) 21 days after co-transfer

extract_protocol: Total RNA samples were prepared according to the prototol of RNeasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from RNeasy Micro kit from Qiagen.

value: CAR transgenic mice were bred on a B6 background and then to Thy1.1 and Rosa26-Cas9 knockin mice.


title: ZWT105 KO CAR 3

value: KO CAR T cells (Ametrine+Thy1.1–Thy1.2+)


title: M2L-2

description: M2 left 2


title: ZWT104 KO CAR 2


title: ZWT101 WT CAR 2

value: WT CAR (mCherry+Thy1.1+Thy1.2+)


title: M4L

description: M4 left


title: M3R-2

description: M3 right 2


title: M2R

description: M2 right


title: ZWT100 WT CAR 1


title: ZWT102 WT CAR 3


title: ZWT048

growth_protocol: CD8+ CAR T cells were isolated by flow cytometric sorting of splenocytes based on reporters and congenical markers: WT CAR (mCherry+Thy1.1+Thy1.2+) and KO CAR T cells (Ametrine+Thy1.1–Thy1.2+) 7 days after co-transfer with or without tumor

tag: group

value: KO CAR without tumor


title: ZWT054

value: WT CAR without tumor


title: ZWT049


title: ZWT053


title: ZWT045

value: WT CAR with tumor


title: M2L

description: M2 left


title: M1R-3

description: M1 right 3


title: ZWT055


title: ZWT046


title: ZWT043


title: ZWT047


title: ZWT050


title: M2R-2

description: M2 right 2


title: ZWT044


title: ZWT051


title: M1L-3

description: M1 left 3


title: M1R-2

description: M1 right 2


title: ZWT042


title: M1L-2

description: M1 left 2


title: M1R

description: M1 right


title: ZWT040

value: KO CAR with tumor


title: M1L

description: M1 left


title: ZWT039


title: ZWT041


title: Mg-Ecs-IP

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
Sequence quality was examined using the FastQC software.
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human reference genome UCSC HG19 using BOWTIE (V2.1.0).
Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generating by MACS v1.4.2 (Model-based Analysis of ChIP-seq) software. The signal profile (at 10 bp resolution) with UCSC WIG file format was generated from ChIP-seq data, which can be visualized on UCSC genome browser or IGB browser (Integrated Genome Browser, Java Runtime Environment needed, http://www.bioviz.org/igb/).

source_name: Mg-ECs-IP

growth_protocol: All cell lines were cultured under an atmosphere of 5% CO2 at 37°C. Human Coronary Artery Endothelial Cells (HCAEC) purchased from ScienCellTM (San Diego, California) were cultured in Endothelial Cell Medium (ScienCellTM). The medium package consists of 500 ml of basal medium, 25 ml of fetal bovine serum (ScienCellTM), 5 ml of endothelial cell growth supplement (ECGS, ScienCellTM) and 5 ml of penicillin/streptomycin solution (P/S, ScienCellTM).

extract_protocol:
Briefly, HCAEC were collected from seeding on Mg-based alloy discs after 2 days. Cells were then fixed with1% formaldehyde (Sigma) in medium for 10min at RT, and lysed in cell lysis buffer. Chromatin was sheared to approximately 200bp fragments by using ULTRASONIC PROCESSOR (Fisher Scientific, USA). For ChIP-seq, sheared chromatin was incubated with anti-YAP antibody overnight at 4°C. Antibody/antigen complexes were recovered with ProteinA-Dynabeads (Invitrogen) for 2 h at 4 °C. 10ng ChIP’d DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using HiSeq 3000/4000 PE Cluster Kit (Illumina). Sequencing was carried out by running 2× 150 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

treatment_protocol: HCAECs cultued on Magnesium-based alloy discs 24h, and static cultured HCAECs were used as control

tag: passages

tag: cell catalog

value: ScienCell #6020

value: Magnesium-based alloy discs 24h

tag: chip antibody


title: Mg-ECs-input

source_name: Mg-ECs-input

value: Human Coronary Artery Endothelial Cells (HCAEC)


title: Control-Ecs-IP

source_name: Control-IP

value: static cultured


title: ak_16_3

city: Jinan

first: Wenqiang

last: Chang

state: Shandong

address: No. 44 West Wenhua Road

institute: Shandong University

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. For the quantification of gene expression levels, we use feature Counts v1.5.0-p3 to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: GCF_000182965.3_ASM18296v3

organism: Candida albicans

source_name: Candida albicans

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Overnight grown C. albicans SC5314 were diluted to 1E7 cells per milliliter  RPMI1640 medium amd treated by 19ak (0.5 μg/mL or 2 μg/mL) for 6 h at 30℃.

value: C. albicans SC5314 cells were treated by 2 ug/mL of 19ak


title: contr_2

value: C. albicans SC5314 cells without drug treatment


title: Control-Ecs-input

source_name: Control-input


title: ak_16_2


title: ak_6_3

value: C. albicans SC5314 cells were treated by 0.5 ug/mL of 19ak


title: contr_3


title: ak_16_1


title: ZWT037


title: Du145 ZBC-260 24h-3

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

description: Time point: 24 hours of treatment

data_processing:
RNA-seq
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
Genome_build: Genome_build: GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: raw read count

extract_protocol:
polyA RNA
cDNA samples were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
RNA-seq using cDNA based on manufacturer's instructions (Illumina)

value: Prostate Adenocarcinoma

tag: passage

value: Passage 30-70

value: ZBC-260 Degrader 10nM


title: Du145 DMSO 24h-2

description: Time point: 24 hours of treatment

value: Thalidomide 10nM


title: Du145 ZBC-260 24h-2

description: Time point: 24 hours of treatment


title: Du145 DMSO 24h-3

description: Time point: 24 hours of treatment


title: ak_6_1


title: ZWT036

value: CAR transgenic mice were bred on a B6 background and then to Thy1.1 and Rosa26-Cas9 knockin mice.


title: Du145 DMSO 24h-1

description: Time point: 24 hours of treatment


title: Du145 ZBC-260 3h-3

description: Time point: 3 hours of treatment


title: 4-cell mouse embryos - Library 3

city: Santa Barbara

first: Siddharth

last: Dey

address: 3357 Engrg II UCSB

department: Chemical Engineering

institute: UCSB

data_processing:
Library strategy: scAba-seq (single-cell, genome-wide and strand-specific 5hmC sequencing technology, based on 5hmC glucosylation and glucosylation-dependent digestion of DNA)
For plates (P1-9) and libraries (L1-3), Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. 5hmCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
For scH&G, Fastq files are parsed for library barcodes. Read 1 was trimmed to  76 basepairs and mapped to the hg19 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. BseRI or AluI positions are obtained from the sequencing data using custom scripts in Perl identifying their respective recognition sequence in the hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Text files with 4 columns: Single Cell ID, chromosome, coordinate and strand

source_name: 4-cell mouse preimplantation embryos

extract_protocol:
Embryos were gently flushed out of the infidubulum of E2.5 pregnant mice using warm M2 medium. Embryos were then manipulated in 4-ring IVF dishes coated with RNase-free BSA because, once dissociated, cells stick to plastic. Embryos were washed in PBS-0 and in Tyrode’s acid to remove the zone pellucida, then placed in a 1/3 dilution of Tryple select GIBCO A12177-01 (stock solution is referred by Gibco as x10 concentrated) and placed on the warm plate for 2 minutes. We then used glass capillaries of different diameters to dissociate the embryo into 2-3 clusters. Cells were then progressively extracted from each cluster, one after the other, using glass capillaries. Every single cell that is released from the clusters is immediately placed into a well of a 384-well plate containing lysis buffer.
4 μL Vapor-Lock (Qiagen) is dispensed manually into each well of a 384 well plate using a multichannel pipet. 0.2 μL of lysis buffer (1x NEB buffer 4, 0.1 μg Qiagen protease) is dispensed at 12 psi pressure into each well using the NanoDrop II liquid-handling robot. Single cells are deposited  into each well and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of Glucosylation mix (1x NEB buffer 4, 2 U NEB T4-BGT, 1x NEB UDP-Glucose) is added and the plate is incubated at 37°C for 18 hours. Next, 0.2 μL of lysis buffer is added and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of AbaSI (1x NEB buffer 4, 2 U NEB AbaSI) is added and the plate is incubated at 25°C for 1 hour and 65°C for 20 min. 0.2 μL of 0.01 μM adapter is added, followed by 0.2 μL of ligation mix (80 U T4-Ligase, 2X T4-ligase buffer, 0.6 mM ATP) and the plate is incubated for 16 hours at 16°C. Contents of all the wells with different adapters are pooled and incubated with 0.8x Agencourt Ampure XP beads for 30 min, washed twice with 80% ethanol and resuspended in 6.4 μL nuclease free water. 9.6 μL of in vitro transcription mix is added (1.6 μL of each ribonucleotide, 1.6 μL T7 buffer, 1.6 μL T7 enzyme mix) and incubated at 37°C for 14 hours. After in vitro transcription, the aRNA  (amplified RNA) is size selected by incubating with 0.8x Agencourt RNAClean beads for 30 min, washed twice with 70% ethanol and resuspended in 16 μL nuclease-free water. Next, the aRNA is fragmented using fragmentation buffer (200mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc) at 94°C for 1.5 min and quenched by putting the reaction on ice and adding 2 μL 0.5 M EDTA. Fragmented aRNA is then purified using 1x Agencourt RNAClean beads as mentioned before and eluted in 16 uL nuclease-free water. After these steps, library preparation is performed as described in the scAba-seq protocol.
scAba-seq [Mooijman et al. 2016 Nature Biotechnology]

value: 4-cell mouse preimplantation embryos

tag: molecule subtype


title: 4-cell mouse embryos - Library 1

tag: strain


title: 4-cell mouse embryos - Library 2


title: contr_1


title: Du145 ZBC-260 3h-2

description: Time point: 3 hours of treatment


title: 8-cell mouse embryos - plate 8

source_name: 8-cell mouse preimplantation embryos

value: 8-cell preimplantation embryos


title: 8-cell mouse embryos - plate 9


title: ZWT038


title: Du145 ZBC-260 24h-1

description: Time point: 24 hours of treatment


title: ak_6_2


title: Du145 DMSO 3h-2

description: Time point: 3 hours of treatment


title: 22RVI ZBC-11 24 hr-2

description: Time point: 24 hours of treatment

value: ZBC-11 Inhibitor 150nM


title: Du145 DMSO 3h-1

description: Time point: 3 hours of treatment


title: 22RVI ZBC-246 24 hr-2

description: Time point: 24 hours of treatment

value: ZBC-246 Degrader 10nM


title: 8-cell and 16-cell mouse embryos - plate 7

source_name: 8-cell and 16-cell mouse preimplantation embryos

value: 8-cell and 16-cell preimplantation embryos


title: 8-cell mouse embryos - plate 6


title: 8-cell mouse embryos - plate 4


title: 22RVI DMSO 24 hr-2

description: Time point: 24 hours of treatment

value: DMSO


title: RNA_EMV2

city: Oxford

first: Adam

last: Mead

address: Headley Way

department: Radcliffe Department of Medicine

institute: University of Oxford

description: Condition: EMV

data_processing:
Raw sequencing reads were aligned to the reference genome using STAR v2.4.2a.
Aligned reads were sorted using samtools v0.1.19.
Raw counts were generated using subread v1.5.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Final_rpkm_table_2_Mar2021.txt: Tab-delimited text file includes RPKM values.

source_name: Hematopoietic stem cells

extract_protocol:
Bone marrow cells were retrieved and stained for FACS-purification of HSCs, followed by Smart-Seq2 protocol.
RNA libraries were prepared for sequencing using Illumina protocols and adapted for Smart-Seq2 (Picelli et al., 2014).

value: Hematopoietic stem cells

tag: genotype

value: Ezh2 loss


title: 22RVI ZBC-246 3 hr-1

description: Time point: 3 hours of treatment

tag: treatment


title: RNA_10_EMV

description: Condition: EMV


title: RNA_EMV4

description: Condition: EMV


title: RNA_EMV3

description: Condition: EMV


title: 22RVI ZBC-11 3 hr-1

description: Time point: 3 hours of treatment


title: 22RVI Thalido 3 hr-1

description: Time point: 3 hours of treatment


title: Du145 ZBC-260 3h-1

description: Time point: 3 hours of treatment


title: RNA_EMV6

description: Condition: EMV


title: Du145 DMSO 3h-3

description: Time point: 3 hours of treatment


title: RNA_23_EMV

description: Condition: EMV


title: 22RVI DMSO 3 hr-1

description: Time point: 3 hours of treatment


title: Du145-ZBC11 24hr-150nM-n=1

description: Time point: 24 hours of treatment


title: 8-cell mouse embryos - plate 5


title: 22RVI Thalido 24 hr-2

description: Time point: 24 hours of treatment


title: RNA_JMV1

description: Condition: JMV


title: Du145-ZBX 246 24hr-10nM-n=1

description: Time point: 24 hours of treatment


title: RNA_JMV3

description: Condition: JMV


title: Du145-Thalido 24hr-10nM-n=1

description: Time point: 24 hours of treatment


title: RNA_JMV5

description: Condition: JMV


title: RNA_EMV5

description: Condition: EMV


title: Du145-DMSO 24hr-n=1

description: Time point: 24 hours of treatment


title: RNA_JMV4

description: Condition: JMV


title: Du145-ZBC11 3hr-150nM-n=1

description: Time point: 3 hours of treatment


title: RNA_16_JMV

description: Condition: JMV


title: Du145-ZBX 246 3hr-10nM-n=1

description: Time point: 3 hours of treatment


title: RNA_JMV2

description: Condition: JMV


title: Du145-Thalido 3hr-10nM-n=1

description: Time point: 3 hours of treatment


title: A55

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

description: Gene expression in NN offspring

hyb_protocol: 600ng of Cy3-cRNA was then fragmented with a specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridization was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analyzed using the package limma from R.

organism: Oncorhynchus mykiss

source_name: Whole fry_condition NN

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

extract_protocol: Total RNA was extracted from liver from 12 whole fry per condition, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations. The concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

treatment_protocol: Whole fry from 4 different conditions : NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the high carbohydrate/low protein (HC/LP) diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet) were sampled before the first feeding.

tag: FISH identification

tag: tissue

value: Whole fry

tag: female nutritional history

value: NC

tag: male nutritional history

tag: offspring condition

value: NN

tag: Sex

value: male


title: A51

description: Gene expression in HN offspring

source_name: Whole fry_condition HN

value: HC/LP

value: HN


title: A8

description: Gene expression in HH offspring

source_name: Whole fry_condition HH

value: HH


title: A57

description: Gene expression in HH offspring


title: RNA_6_JMV

description: Condition: JMV

tag: cell type


title: A48

description: Gene expression in NN offspring


title: A49

description: Gene expression in NH offspring

source_name: Whole fry_condition NH

value: NH

value: female


title: A52

description: Gene expression in NN offspring


title: A56

description: Gene expression in HN offspring


title: A50

description: Gene expression in HH offspring


title: Du145-DMSO 3hr-n=1

description: Time point: 3 hours of treatment

tag: cell line

value: Prostate Adenocarcinoma

value: Passage 30-70


title: A7

description: Gene expression in NH offspring


title: A46

description: Gene expression in NH offspring


title: RNA_26_JEMV

description: Condition: JEMV

value: JAK2V17F + Ezh2 loss


title: A59

description: Gene expression in HN offspring


title: VCaP-ZBC11 24hr-150nM-n=2

description: Time point: 24 hours of treatment

source_name: VCaP

value: VCaP

value: ZBC-11 Inhibitor 150nM


title: RNA_24_JEMV

description: Condition: JEMV


title: VCaP-ZBX 246 24hr-10nM-n=2

description: Time point: 24 hours of treatment

value: ZBC-246 Degrader 10nM


title: A54

description: Gene expression in HH offspring


title: RNA_11_JEMV

description: Condition: JEMV

value: Hematopoietic stem cells


title: VCaP-Thalido 24hr-10nM-n=2

description: Time point: 24 hours of treatment

value: Thalidomide 10nM