title: YBX1

data_processing:
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq6000. Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length < 35 bp) and low-quality reads. Then FastQC is used to ensure high reads quality.
The clean reads were mapped to the reference genome (assembly GRCh38) using the Bowtie2 (v2.2.6) software.
Peak detection was performed using the MACS (v2.1.1) peak finding algorithm with 0.001 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
Briefly, S18 cells were fixed in 1% formaldehyde at room temperature for 10 min and quenched by 1 × glycine solution for 5 min. Afterward, nuclei were isolated, lysed and sonicated to yield chromatin fragments of about 200-1000 bp. The sheared chromatin was incubated with anti-YBX1 (Abcam, ab76149) or negative control IgG at 4℃ overnight, followed by immobilization on ChIP Grade Protein A/G Magnetic Beads. After extensive washing, immunoprecipitated DNA was eluted, de-crosslinked, purified
ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovotSeq 6000 with single-end 2x150 as the sequencing mode.

treatment_protocol: untreated


title: siSCR rep1

status: Public on Jul 26 2022

type: SRA

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

country: China

institute: Sun Yat-sen University Cancer Center

library_source: transcriptomic

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome (hg38) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

growth_protocol: S18 cells were maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was used to extract total RNA from S18 cell line.
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol: S18 cells were treated with circIPO7 siRNA or control siRNA using Lipofectamine 3000 reagent. The cells were harvested after transfection at 48h for assays.

tag: cell type

value: nasopharyngeal carcinoma cell

tag: cell line


title: K28BM, Luc

city: Singapore

first: Phyllis

last: Chong

address: 14 Medical Drive #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Trimming of adapter from
the sequencing fragments (raw data) was performed with Trip Galore
(version 0.3.7) with default settings. The trimmed data were mapped to
the human reference genome GRCh37 using STAR aligner
Basecalling and data filtering based on the BGI method.
Bowtie2 to map clean reads to reference gene and use HISAT to reference hg19 genome.
FPKM method is used in calculated expression level
Assembly: hg19
Supplementary files format and content: FPKM file

source_name: multiple myeloma

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (Qiagen)
sequenicng library was generated with 100ng total RNA using TruSeq RNA sample preparation kit v2 (Illumina)

tag: tissue

value: Bone marrow

value: plasma cell

tag: genotype

value: control


title: K18, KDPKCa

value: PKCalpha knockdown


title: 29_baseline_IFX_NR_RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts

source_name: Peripheral Whole-Blood

extract_protocol:
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
RNA Sequencing libraries were prepared from Paxgene™ Blood RNA Tubes (Qiagen) according to the Illumina TruSeq® messenger RNA (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2)
Paired-end sequencing (2x75bp) was performed on Illumina HiSeq 4000

tag: patient

tag: cohort

value: Discovery - Infliximab

tag: treatment

value: Infliximab

tag: remission at week 14

value: Non-remission

tag: time point

value: baseline

tag: diagnosis

value: UC


title: input

library_source: genomic

molecule: genomic DNA


title: Col_3h_21FR_1

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

country: Israel

institute: Volcani Institute

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build STAR (v2.5.4) (Dobin, Davis et al. 2013) with default parameter except --alignIntronMax 2000 and --outFilterMismatchNmax 2.
Mapped reads were counted by HTSeq (v0.6.0) with default parameters except "-m intersection-strict -s reverse" (Anders, Pyl et al. 2015) and differential expression was determined using edgeR (v3.16.5) (Robinson, McCarthy et al. 2010, Chen, Lun et al. 2016). Only genes with CPM (counts-per-million) values greater than 1 in at least two samples were kept for differential expression analysis. A design matrix was set up where each treatment (light conditions) at each time point is one group, and a generalized linear model was fitted to the read counts with this design matrix. For differential gene expression, contrasts were set up between 21WL and each of the light condition (21FR, 30WL or 30FR) at each time point.
Genome_build: TAIR10
Supplementary_files_format_and_content: HTSeqcounts_All_Samples: tab-delimited text files include counts for each gene in each sample based on HtseqCount
Supplementary_files_format_and_content: CPM_All_Samples: tab-delimited text files include normalized counts per million reads mapped  (cpm) generated using edgeR
Supplementary_files_format_and_content: LOG2_Fold_Change_relative_to_21WL: xlsx file include Log2 Fold Change between each of the conditions and 21WL at the same time point with FDR.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seedlings were grown vertically on 0.5X LS plates

extract_protocol:
The seedlings (~ 25 seedllings) were collected directly in the described condition and snap-frozen in liquid nitrogen.
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

treatment_protocol: Seedlings grown in constant LED white light (~70µE) at 21°C (21WL) for three days and moved to 21FR, 30WL, 30FR or left at 21WL for one, three, six, or 24 hours

value: Whole seedlings

tag: condition

value: 21C white light + Far-red

tag: ecotype

value: Columbia


title: iN, APP V717I, HuD wt, HuD tv2, biol rep3

city: Nijmegen

first: Geert

last: Poelmans

country: Netherlands

institute: Radboud UMC

description: 2x150 bp

data_processing:
Trimmomatic was used for trimming the beginning and ending bases from each read and identifying and trimming adapter sequences from the reads
For quantifying gene level transcript abundances, we (pseudo)aligned the trimmed reads to a human reference genome (GRCh38) using Kallisto
Detection of differentially expressed genes (DEGs) was performed with Limma-voom using the count data (transcripts per million) obtained from Kallisto
P-values were corrected for multiple testing using the false discovery rate (FDR) method
Assembly: GRCh38
Supplementary files format and content: tsv text files include TPM values for each Sample
Supplementary files format and content: xslx file includes differential gene expression data for all comparisons made

source_name: iPSC 153 fAD

growth_protocol: iPSCs were plated at 95K/cm2 in mTeSR1 media one-day prior to viral transduction. Ultrahigh titer lentiviruses were obtained from Alstem for plasmids FUdeltaGW-rtTA (Addgene #19780), pTet-O-Ngn2-puro (Addgene #52047), and DRH-307 (Addgene #112670), and were transduced at MOIs 5, 2, and 2, respectively. On day in vitro (DIV) 1, differentiation was induced by Doxycycline (2µg/ml). On DIV 2, puromycin (5 µg/ml) was added to select for cells expressing Ngn2. On DIV 4, iNs were plated on Poly-L-Ornithine laminin-coated plates and cultured in Neurobasal medium containing Glutamax, dextrose, NEAA, B27, Doxycycline, puromycin, BDNF, CNTF, and GDNF. Culturing media was conditioned starting at DIV 18, and media, protein, and RNA samples were harvested at DIV 21

extract_protocol:
RNA was harvested using PureLink RNA mini kits (ThermoFisher). 2 ug of total RNA was used for the construction of sequencing libraries.
Library preparation, Illumina, RNA with PolyA selection (executed by Genewiz)

treatment_protocol:
ELAVL4 KO was generated with CRISPR-Cas9 in iPSCs preceeding neuronal differentiation
ELAVL4 OE and rescue experiments were perfomed using lentivirus containing cDNA for ELAVL4 splice variant 1 (Origene #RC218612) or splice variant 2 (Genscript #OHu28682D)

value: iPSC 153 fAD

value: iPSC-derived neurons

tag: app genotype

tag: hud genotype

value: WT

tag: lentivirus

value: HuD tv2


title: Col_1h_30FR_2

value: 30C white light + Far-red


title: CVB5_5Y

city: Kunming

first: Wei

last: Chen

address: No. 727, Southern Jingming Road, Chenggong District

institute: Medical School

description: tumor cell

data_processing:
Library quality was assessed using Qubit2.0, Agilent 2100, while next-generation high throughput sequencing of samples was performed on the Illumina PE 150.
CPC2, CNCI, and PFAM tools were then used to predict the coding ability of the transcripts;
Differentially-expressed genes were defined as p<0.05 and/or fold change>2 times based on their FPKM values between the groups, which were calculated using Cuffdiff soft-ware
Genome_build: Homo sapiens GRCh38 (hg19)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: neuroblastoma-derived neuronal cell line SH-SY5Y

growth_protocol: RD and SH-SY5Y cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM)  supplemented with 10% fetal bovine serum (FBS)  or 2% FBS (maintenance medium) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
At 24 h post-infection (hpi) , discard the cell supernatant and wash with PBS, then collect cell pellets, total RNA were extracted from cells using RNAiso Plus according to the manufacturer’s instructions.
Ribosomal RNA was first eliminated, and first strand cDNA and second strand cDNA were synthesized using random hexamer primers ; followed by end repair, poly-A 3’ ends, ligation of adapters, and screening of DNA fragments in order to construct the RNA-seq library.

treatment_protocol: When RD and SH-SY5Y cells were cultured approximately to 80% confluency and then were infected with CV-B5 virus at multiplicity of infection (MOI) of 1.

value: neuroblastoma-derived neuronal cell

tag: infection

value: CV-B5 for 24h


title: CVB5_RD

description: tumor cell

source_name: rhabdomyosarcoma cell

value: rhabdomyosarcoma cell


title: K18, Luc

value: Bone marrow

value: plasma cell

value: control


title: s.alpha3

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: processed data: rcmat.txt 11th column

data_processing:
Illumina Casava ver 1.8.2 software used for basecalling.
Sequenced reads were mapped to hg38 human whole genome using Tophat2 v2.1.1 in the default settings.
Raw read counts were extracted using featureCounts with the default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: a single tab-delimited text file includes normalized counts for all samples

growth_protocol: The Jurkat cell lines were cultured with RPMI 1640 (Sigma) containing 2% fetal calf serum and antibiotics.

extract_protocol:
RNA was extracted from Jurkat T cell lines using Rneasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing in Medical & Biological Laboratories, co (Nagoya, Japan).

treatment_protocol: For the shaking treatment, cell cultures was kept on a Petit rocker Model-2230(Wakenyaku) placed in 37/5% CO2  incubator and was gently shaken at 40 movements per min. For IFN-alpha treatment, cell cultures were treated with IFN-alpha (100U/ml, Sigma) at 24h before collection.

value: Jurkat cell line

value: human CD4+ T cell line

tag: culture type

value: shaking cultured

value: IFN-alpha treated


title: Col_1h_30FR_1

value: Whole seedlings


title: Col_3h_21WL_2

value: 21C white light

value: Columbia


title: iN, APP V717I, HuD wt, HuD tv2, biol rep1

description: 2x150 bp

value: iPSC 153 fAD

tag: cell type

value: iPSC-derived neurons


title: iN, APP V717I, HuD wt, HuD tv2, biol rep2

description: 2x150 bp

tag: cell line

value: WT

value: HuD tv2


title: n3

description: processed data: rcmat.txt 10th column

value: static cultured

value: untreated


title: iN, APP V717I, HuD KO, media, biol rep1

description: 2x150 bp

value: KO

value: No


title: s3

description: processed data: rcmat.txt 9th column


title: Col_1h_30WL_1

tag: tissue

value: 30C white light


title: Col_3h_21WL_1

tag: genotype


title: n.alpha3

description: processed data: rcmat.txt 12th column


title: iN, APP V717I, HuD wt, empty vector, biol rep2

description: 2x150 bp

value: Empty vector


title: Col_1h_21FR_2

value: 21C white light + Far-red


title: Col_1h_30WL_2


title: iN, APP V717I, HuD wt, empty vector, biol rep3

description: 2x150 bp


title: Con_RD

description: tumor cell

value: rhabdomyosarcoma cell


title: Col_1h_21WL_2


title: Col_1h_21FR_1


title: E14 mESCs expressing high exogenous levels of Zmynd8 replicate#2 [WRH2c]

city: Worcester

first: Aimin

last: Yan

state: MA

address: 55 N Lake Ave

country: USA

institute: University of Massachusetts Medical School

data_processing:
Apply FASTP( v0.19.4) to the fastq files of the pair-end reads to perform adapter trimming and bad reads filtering by default parameters
Apply STAR(STAR_2.5.3a) to align the processed FASTQ files on GRCm38 ensembl reference genome and annotation to get SAM files with parameters(intronMotif --sjdbGTFfile --quantMode TranscriptomeSAM)
The SAM files are further converted to BAM files. We did not remove duplicates from the BAM files
Apply featureCounts(v1.6.2) to obtain the counts for each gene by  parameters (-T 13 -s 0 -p -g 'gene_id')
BigWig files are generated by bamCoverage(Version 3.1.3) using RPGC method with --binSize 10  --effectiveGenomeSize 2652783500(mm10 GRCm38)
Genome_build: mm10
Supplementary_files_format_and_content: raw count txt file(count.txt)

growth_protocol: E14 mESCs were maintained in Hyclone KO DMEM supplemented with 15% FBS, 2mM glutamine, 100uM Non-Essential Amino Acids, .1mM 2-mercaptoethanol, and 1000U/ml LIF

extract_protocol:
RNA was harvested using Trizol reagent.  NEB Next® Ultra™ RNA Library Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mESCs were plated in 6-well plates. 24 hours later, ESCs were treated with 5ug/ml of Doxycycline to induce exogenous expression of Zmynd8. 24 hours later, RNA was harvested with Trizol and subsequently treated with TurboDNAse

value: E14 Mouse Embryonic Stem Cells (mESCs)

tag: genotype/variation


title: iN, APP V717I, HuD wt, empty vector, biol rep1

description: 2x150 bp


title: E14 mESCs expressing high exogenous levels of Zmynd8 replicate#3 [WRH3c]


title: Con_5Y

description: tumor cell

value: neuroblastoma-derived neuronal cell


title: E14 mESCs expressing high exogenous levels of Zmynd8 replicate#1 [WRH1c]


title: s.alpha2

description: processed data: rcmat.txt 7th column

value: Jurkat cell line

value: human CD4+ T cell line

value: shaking cultured

value: IFN-alpha treated


title: n.alpha1

description: processed data: rcmat.txt 4th column


title: s.alpha1

description: processed data: rcmat.txt 3rd column


title: iN, APP wt, HuD KO, HuD tv1, biol rep3

description: 2x150 bp

source_name: iPSC 185 fADcorr

value: iPSC 185 fADcorr

value: iPSC-derived neurons

value: HuD tv1


title: n2

description: processed data: rcmat.txt 6th column

value: static cultured


title: s2

description: processed data: rcmat.txt 5th column

value: untreated


title: n.alpha2

description: processed data: rcmat.txt 8th column


title: iN, APP V717I, HuD wt, media, biol rep3

description: 2x150 bp

value: iPSC 153 fAD

value: WT


title: iN, APP wt, HuD KO, HuD tv1, biol rep1

description: 2x150 bp

value: KO


title: WT non- retinal ganglion cells sample 3

city: Boston

first: Dong Feng

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

data_processing:
RNa-seq: Alignments were carried out with STAR aligner (version 2.3) against the mm10 genome. RNA-seq quality metrics controls were accessed by the Broad Institute’s RNA-SeQC tool. Read quantification was carried out with featureCounts . Read normalization and Differential expression testing were performed with DESeq package in R, and sequence data quality was assessed based on FastQC package.
deseq files: basemean A = wild type and basemean B = Math5Cre;Ezh2f/fG9af/+ (dKO)
Genome_build: mm10

organism: Mus musculus

source_name: P0 other retinal cells (pooled together)

extract_protocol:
RNA-seq: Retinas were removed, dissociated with papain digestion system (worthington Biochem. Corporation. #LK003150) according to protocol. For separation of RGCs from non-RGCs, we continue with cell separation using magnetic microbeads labelled with anti-CD90-antibody (MACS Miltenyi Biotec, #130-094-523; 130-041-305). After centrifugation, cell pellet was used for RNA-Extraction using Qiagen RNEasy Mini Kit (Qiagen, #74104). 1ug of total RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain/genotype

value: retina


title: parental E14 mESCs repicate#3 [WRH3a]

source_name: parental E14 mESCs

value: parental


title: parental E14 mESCs repicate#1 [WRH1a]


title: E14 mESCs expressing low exogenous levels of Zmynd8 replicate#1 [WRH1b]


title: iN, APP wt, HuD KO, HuD tv1, biol rep2

description: 2x150 bp


title: iN, APP V717I, HuD wt, media, biol rep1

description: 2x150 bp

value: No


title: E14 mESCs expressing low exogenous levels of Zmynd8 replicate#3 [WRH3b]

value: E14 Mouse Embryonic Stem Cells (mESCs)


title: E14 mESCs expressing low exogenous levels of Zmynd8 replicate#2 [WRH2b]


title: n1

description: processed data: rcmat.txt 2nd column

tag: treatment


title: WT non- retinal ganglion cells sample 2


title: iN, APP V717I, HuD wt, media, biol rep2

description: 2x150 bp


title: iN, APP wt, HuD KO, HuD tv2, biol rep3

description: 2x150 bp

value: HuD tv2


title: parental E14 mESCs repicate#2 [WRH2a]


title: WT non- retinal ganglion cells sample 1


title: iN, APP wt, HuD KO, HuD tv2, biol rep1

description: 2x150 bp


title: Col_1h_21WL_1

value: Whole seedlings

value: 21C white light

value: Columbia


title: exonic KO replicate ΔE2.5

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

data_processing:
Illumina conventional base calls were performed.
A pseudo-castaneus genome was assembled by replacing available SNPs of cast (Sanger Center) into the BL6 mm10 reference genome.
RNA-seq reads were mapped using bowtie/v2.2.5 to the genome and transcriptome of both the BL6 and the pseudo-cast genomes. Only those reads that mapped uniquely and with a high-quality mapping score (MAPQ ≥ 30) to either the BL6 or pseudo-cast genomes were kept for further analyses.
The SNP-associated read counts were used to assess allelic expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each gene.

organism: Mus musculus musculus x Mus musculus castaneus

source_name: male

growth_protocol: Male and female ES cells were maintained in the presence of 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on a mono-layer of chemically inactivated mouse embryonic fibroblasts (MEF) in ES media containing high glucose DMEM media supplemented with 15% fetal bovine serum (FBS), 1% non-essential amino acids, 10 mg/ml APS, 0.1mM 2-mercaptoethanol and 25mM L-glutamine. ES cells were grown in a humidified incubator at 37ºC and 5% CO2. Plates were enriched for ES cells by incubation on 0.1% gelatin coated dishes for 1h to allow MEFs to attach, followed by transfer to fresh gelatin coated plates for overnight culture.

extract_protocol:
RNA was collected from ES cells followed by mRNA enrichemt and RNA-seq library construction.
RNA-seq libraries were made according to Illumina Truseq RNA sample preparation kit V2 according to manufacturer's protocol.

value: exonic KO

tag: Sex

value: male

value: embryonic stem cell

tag: strain

value: mus castaneus x Mus musculus


title: WT retinal ganglion cells sample 3

source_name: P0 retinal ganglion cells


title: exonic KO replicate ΔE2.7


title: WT retinal ganglion cells sample 2


title: iN, APP wt, HuD KO, empty vector, biol rep3

description: 2x150 bp

value: iPSC 185 fADcorr

value: iPSC-derived neurons

value: Empty vector


title: wt replicate 2_CB

value: wt


title: promoter KO replicate ΔP2.1

value: promoter KO


title: iN, APP wt, HuD KO, empty vector, biol rep2

description: 2x150 bp

value: WT

value: KO


title: WT retinal ganglion cells sample 1

value: retina


title: wt replicate 2_F

source_name: Female

value: Female

value: Mus musculus x mus castaneus


title: sKO non- retinal ganglion cells sample 2

value: Math5Cre; Ezh2f/f


title: sKO non- retinal ganglion cells sample 3


title: wt replicate 1_F


title: iN, APP wt, HuD KO, HuD tv2, biol rep2

description: 2x150 bp

value: HuD tv2


title: sKO non- retinal ganglion cells sample 1


title: promoter KO replicate ΔP4


title: iN, APP wt, HuD KO, media, biol rep2

description: 2x150 bp

value: No


title: iN, APP wt, HuD KO, media, biol rep1

description: 2x150 bp


title: Healthy PBMC child g

type: RNA

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

description: miRNA

hyb_protocol: Each sample was hybridized to a GeneChip® miRNA 3.0 Array for 18 h at 48°C and 60 rpm (Affymetrix, Santa Clara, CA, USA). Afterwards, the chips were washed and stained on Fluidics Station 450 (Fluidics script FS450-0002).

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G (both, Affymetrix, Santa Clara, CA, USA).

data_processing: Data were analyzed by using expression console software 1.4 (Affymetrix, Santa Clara, CA, USA). The expression values were normalized with robust multi-array average (RMA).miRNA calculations and statistical significances between two groups (paired Student’s t-test) were performed with Transcriptome Analysis Console (TAC) Software (ThermoFisher Scientific). Detected miRNAs whose expression levels were significantly different (FDR-p value < 0.01) and showed a linear-fold change of at least 3.0, were considered as differentially expressed.

label: biotin

source_name: Human mononuclear cells from healthy donors isolated from peripheral blood

label_protocol: 1.5 µg of total RNA containing low molecular weight RNA was labelled using the FlashTag™ Biotin HSR RNA Labeling Kit according to the manufacturer’s instructions (ThermoFisher Scientific).

growth_protocol: Human mononuclear cells from patients with JIA were isolated onto a Ficoll (PAN Biotech, Germany) gradient either from peripheral blood (PB) or synovial fluid (SF). Erythrocytes were lysed and cells were washed twice.  Peripheral blood mononuclear cells (PBMC) were isolated from healthy donors by the same procedure. SF was obtained by incubation with hyaluronidase for 30 min. Following centrifugation at 400 x g for 10 min.

extract_protocol: miRNA extraction kit preAnalytix plus DNase digstion

treatment_protocol: not applicable

value: mononuclear cells from peripheral blood

tag: disease state

value: healthy donor

tag: age

value: 14 years old

tag: developmental stage

value: children


title: Healthy PBMC child f

description: miRNA

value: 12 years old


title: Healthy PBMC child h

description: miRNA

value: 8 years old


title: exonic KO replicate ΔE3

value: exonic KO

value: male

value: embryonic stem cell


title: exonic KO replicate ΔE1


title: wt replicate 1_CB

value: wt

value: mus castaneus x Mus musculus


title: Healthy PBMC child e

description: miRNA

value: 16 years old


title: iN, APP wt, HuD KO, empty vector, biol rep1

description: 2x150 bp

value: iPSC 185 fADcorr

value: iPSC-derived neurons

tag: app genotype

value: WT

value: KO

value: Empty vector


title: Healthy PBMC child d

description: miRNA

value: mononuclear cells from peripheral blood

value: 10 years old


title: iN, APP wt, HuD wt, HuD tv1, biol rep3

description: 2x150 bp

tag: hud genotype

value: HuD tv1


title: sKO retinal ganglion cells sample 2

value: Math5Cre; Ezh2f/f

value: retina


title: iN, APP wt, HuD wt, HuD tv1, biol rep2

description: 2x150 bp

tag: lentivirus


title: Healthy PBMC child a

description: miRNA

value: healthy donor

value: 17years old

value: children


title: Healthy PBMC child b

description: miRNA

value: 3 years old


title: iN, APP wt, HuD KO, media, biol rep3

description: 2x150 bp

value: No


title: Healthy PBMC child c

description: miRNA


title: wt replicate 2_BC

value: wt

value: male

value: embryonic stem cell

value: Mus musculus x mus castaneus


title: iN, APP wt, HuD wt, HuD tv1, biol rep1

description: 2x150 bp

value: iPSC 185 fADcorr

value: iPSC-derived neurons

value: WT


title: wt replicate 1_BC


title: JIA SFMCs child9

description: miRNA

source_name: Human mononuclear cells from patients with JIA isolated from synovial fluid

value: mononuclear cells from synovial fluid

value: Juvenile idiopathic arthritis

value: 13-17 years old


title: dKO non- retinal ganglion cells sample 2

value: Math5Cre; Ezh2f/fG9af/+


title: iN, APP wt, HuD wt, HuD tv2, biol rep2

description: 2x150 bp

value: HuD tv2


title: iN, APP wt, HuD wt, HuD tv2, biol rep3

description: 2x150 bp


title: H3K27me3, KO replicate ΔE2.5

data_processing:
Illumina conventional base calls were performed.
A pseudo-castaneus genome was assembled by replacing available SNPs of cast (Sanger Center) into the BL6 mm10 reference genome.
ChIP-seq reads were mapped  to the BL6 genome and the pseudo-cast genome separately, using bwa/v0.7.12. Only those reads that mapped uniquely and with a high-quality mapping score (MAPQ ≥ 30) to either the BL6 or pseudo-cast genomes were kept for further analyses.
The SNP-associated read counts were used to assess allelic occupancy.
Assembly: mm10
Supplementary files format and content: bigWig file for reads mapped to either BL6 or pseudo-cast genomes.

source_name: ES cells

extract_protocol:
Cells were fixed in 1% formaldehyde and lysed. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Immunoprecipitated DNA was collected and libraries were constructed using the Illumina TruSeq V2 DNA preparation kit

value: embryonic stem cells

value: KO

tag: chip antibody


title: input, KO replicate ΔE2.5


title: iN, APP wt, HuD wt, HuD tv2, biol rep1

description: 2x150 bp


title: JIA SFMCs child8

description: miRNA

value: children


title: iN, APP wt, HuD wt, empty vector, biol rep3

description: 2x150 bp

value: Empty vector


title: input, wt replicate 1_CB


title: dKO  retinal ganglion cells sample 3

value: retina


title: sKO retinal ganglion cells sample 1

value: Math5Cre; Ezh2f/f


title: s1

description: processed data: rcmat.txt 1st column

value: Jurkat cell line

value: human CD4+ T cell line

tag: culture type

value: shaking cultured

value: untreated


title: JIA SFMCs child7

description: miRNA

tag: cell type


title: H3K27me3, wt replicate 1_CB

value: male

value: Mus musculus x mus castaneus


title: dKO retinal ganglion cells sample 2


title: dKO retinal ganglion cells sample 1


title: iN, APP wt, HuD wt, empty vector, biol rep2

description: 2x150 bp

tag: cell line

value: iPSC 185 fADcorr

value: iPSC-derived neurons

value: WT


title: input, KO replicate ΔE1


title: iN, APP wt, HuD wt, empty vector, biol rep1

description: 2x150 bp


title: JIA SFMCs child6

description: miRNA

value: mononuclear cells from synovial fluid

value: Juvenile idiopathic arthritis

value: 13-17 years old


title: dKO non- retinal ganglion cells sample 3

value: Math5Cre; Ezh2f/fG9af/+

tag: tissue


title: iN, APP wt, HuD wt, media, biol rep3

description: 2x150 bp

value: No


title: JIA SFMCs child5

description: miRNA

value: 13 years old

value: children


title: JIA SFMCs child4

description: miRNA

value: 18 years old


title: H3K27me3, KO replicate ΔE1

value: embryonic stem cells

tag: genotype

value: KO


title: dKO non- retinal ganglion cells sample 1

value: retina


title: epl1ab_rep3

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

state: Madrid

address: Autopista M-40, Km 38

country: Spain

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

description: Double mutant

data_processing:
FastQ files were mapped to Arabidopsis TAIR10 reference genome using for annotation ensembl release 41.
Mapped reads were quantified using SeqMonk software v1.45
Differential expression analysis was performed using DESeq2 module on SeqMonk software
Differential Expressed Genes (DEGs) when FDR≤0.05 and fold change (FC) was either FC≤0.5 (downregulated genes) or FC≥2 (Upregulated genes)
Genome_build: TAIR10 (annotation ensembl release 41)
Supplementary_files_format_and_content: A spreadsheet file providing gene ID, counts (reads) on each sample and fold change for each DEG

source_name: whole seedling

growth_protocol: Seeds were sown on petri dishes containing 1/2x Murashige & Skoog medium supplemented with 1% sucrose. After a 3-days stratification at 4ºC, plates were incubated for 14 days under long day photoperiod at 22ºC.

extract_protocol:
Total RNA was isolated using EZNA Plant RNA kit (Omega) following the manufacturer’s protocol. RNA samples were treated with DNase I (Roche) to remove genomic DNA contamination.
Total RNA was assayed for quality control using an Agilent Bioanalyzer 2100. Libraries were prepared using TrueSeq Stranded total RNA with Ribo-Zero Plant kit following manufacturer protocols. Then, libraries were sequenced on an Illumina HiSeq2000 sequencer generating a minimum of 40 million 50bp single-end reads.

treatment_protocol: Samples were taken at zeitgeber 8 (ZT8) from 14d-old seedlings  growing in control conditions (22ºC, long day photoperiod (16h light:8h dark), light intensity 100 umol m-2 s-1).

tag: ecotype

value: epl1a epl1b

value: 14-day-old seedling


title: epl1ab_rep2

description: Double mutant


title: input, wt replicate 1_BC

value: male

value: Mus musculus x mus castaneus


title: JIA SFMCs child3

description: miRNA

value: 5 years old


title: epl1ab_rep1

description: Double mutant


title: JIA SFMCs child2

description: miRNA


title: Col-0_rep2

description: Wild-type

value: WT


title: iN, APP wt, HuD wt, media, biol rep1

description: 2x150 bp

value: iPSC 185 fADcorr

value: iPSC-derived neurons


title: ATAC-seq, wt replicate 2_CB

data_processing:
Illumina conventional base calls were performed.
A pseudo-castaneus genome was assembled by replacing available SNPs of cast (Sanger Center) into the BL6 mm10 reference genome.
ATAC-seq reads were mapped  to the BL6 genome and the pseudo-cast genome separately, using bwa/v0.7.12. Only those reads that mapped uniquely and with a high-quality mapping score (MAPQ ≥ 30) to either the BL6 or pseudo-cast genomes were kept for further analyses.
The SNP-associated read counts were used to assess allelic occupancy.
Assembly: mm10
Supplementary files format and content: bigWig file for reads mapped to either BL6 or pseudo-cast genomes.

extract_protocol:
Cells were lysed in cold lysis buffer and nuclei were collected by centrifugation as described. (Buenrostro et al., 2013)
DNA was isolated and tagmented and amplified using the Illumina Nextra DNA prep kit according to the manufacturer's protocol.


title: JIA SFMCs child1

description: miRNA

value: mononuclear cells from synovial fluid

value: Juvenile idiopathic arthritis

value: 9 years old


title: iN, APP wt, HuD wt, media, biol rep2

description: 2x150 bp

value: No


title: Col-0_rep1

description: Wild-type


title: H3K27me3, wt replicate 1_BC


title: ATAC-seq, KO replicate ΔE2.5


title: Col-0_rep3

description: Wild-type


title: CRISPRi_perturb_seq,guide

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

description: 10x genomics

library_source: other

data_processing:
Alignment using Cell Ranger 10X Genomics CellRanger v3.1
Assembly: custom, based on GRCh38, SARS-CoV-2 and lentiviral sequences; viral_references.tar.gz
Supplementary files format and content: tar.gz containing Cellranger output files and cell identities
Supplementary files format and content: tar.gz containing viral fasta and gtf files
Library strategy: Perturb-seq

molecule: other

organism: synthetic construct

growth_protocol: Calu-3 CRISPRi cells were cultured in DMEM/F12 supplemented with 10% FCS, penicillin, streptomycin, glutamine and  non-essential amino acids. These CRISPRi cells were lentivirally transduced with the Perturb-seq library in the presence of polybrene, and puromycin selected.

extract_protocol:
After 24 hours, infected Calu-3 cells were washed with 1X PBS, dissociated with 10X TrypLE Select Enzyme (Thermofisher Scientific), washed, and resuspended in 1X PBS with 0.04% BSA.
Library prep was performed following manufacturer's instructions (10x Genomics Chromium NextGEM Single Cell V(D)J Reagents Kit v1.1); modifications to the manufacturer's single-cell sequencing protocol were made for direct guide capturing and library preparation as previously described (Replogle et al., 2020)

treatment_protocol: Cells were infected with an isolate of SARS-CoV-2.

value: viral infection


title: JIA PBMCs child8

description: miRNA

source_name: Human mononuclear cells from patients with JIA isolated from peripheral blood

value: mononuclear cells from peripheral blood

value: 13-17 years old

value: children


title: ATAC-seq, KO replicate ΔE1

value: embryonic stem cells

value: KO


title: JIA PBMCs child6

description: miRNA


title: sKO retinal ganglion cells sample 3

tag: strain/genotype

value: Math5Cre; Ezh2f/f

value: retina


title: ATAC-seq, wt replicate 1_BC

value: male

value: Mus musculus x mus castaneus


title: PIF7_30FR_2

description: Double side size selection during library preparation

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2 version 2.2.5 with with default parameters.
Peaks were called using HOMER (version 4.11.1) Findpeaks script with the following setting:  -style factor  -F 2 -P 0.001 -L 2 -LP 0.001 for samples #1 (and control_21FR) -F 4 -P 0.0001 -L 4 -LP 0.001 for samples #2 (and control_30FR)
IP from wild-type (Col-0) using anti-MYC antibody used as a background control.
Assembly: TAIR10
Supplementary files format and content: bedgraph.dtf report genome-wide ChIP created with HOMER.
Supplementary files format and content: Excel file with peaks and annotated genes for all samples.

growth_protocol: Seeds were sterilized and plated on 0.5× Linsmaier and Skoog medium (LS; Caisson Laboratories) with 0.8% phyta-agar (Caisson Laboratories). Stratified done in the dark at 4°C for four days.

extract_protocol:
Seedlings were collected into nylon socks, using a razor blade, and immediately fixed using formaldehyde. ChIP-seq experiments done as described in Kaufmann et al., 2010.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected aimed for 250bp insert length (control_30FR and samples #2, Samples #1 and control_21FR were  only size selected one sided (take out small fragments).

treatment_protocol: Seedlings grown in constant LED white light (~70µE) at 21°C (21WL) for three days and moved to 21FR, 30WL, 30FR or left at 21WL for two hours.

value: Whole seedlings

value: anti-MYC (9B11 , Cell siganling)

value: PIF7:PIF7-4xMYC (pif457)

tag: treatment

value: 2 hours 30°C white light + Far-red


title: PIF7_30FR_1

description: One side size selection during library preparation


title: JIA PBMCs child5

description: miRNA

value: Juvenile idiopathic arthritis

value: 13 years old


title: H2B8_seedling_Hi-C_rep2

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
ChIP-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. Mapped reads were sorted and indexed using SAMtools-1.9.
ChIP-seq: Bigwig files were generated by normalising IP bam files to respective inputs with the bamCompare tool from deepTools-3.1.1. Bigwig files of enrichment were generated at single base resolution (w1) and at 50 bp intervals (w50).
ChIP-seq: To generate peaks, H2B.8 enrichment was calculated over 50 bp windows and those with > 0.5 log2(IP/input) were retained. Windows within 501 bp were merged using BEDtools-2.28.0. Regions were filtered by size, with those < 201 bp removed from analysis. H2B.8 enrichment was then calculated over the new regions, those with < 0.5 log2(IP/input) were discarded. The remaining regions were defined as H2B.8 peaks.
ChIP-seq: Overlaps with genes and TEs were determined using BEDtools-2.28.0; 50% of the feature was required to be overlapped by a peak to be defined as an overlap.
RNA-seq: Adapters were trimmed using TrimGalore-0.4.2.
RNA-seq: For differential expression analysis, reads were mapped to TAIR10 with TopHat-2.0.10. Kallisto-0.43.0 was used to obtain TPM (Transcripts Per Million) values. Pairwise statistical analysis was undertaken with Sleuth-0.30.0 in R-3.6.0. Differentially expressed genes and TEs were identified by log2 fold change of ≥ 2 and q < 0.05.
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb, 100 kb, 50 kb, 10 kb, 1kb contact matrix (hic files).
Assembly: TAIR10
Supplementary files format and content: ChIP-seq: Bigwig files generated with bamCompare in deepTools-3.1.1. Scores at w1 or w50 resolution represent log2(IP/input).
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of genes or TEs marked by H2B.8 in sperm and seedling.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and h2b.8 sperm cell replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of drought treated and respective control WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes.
Supplementary files format and content: Hi-C: matrix and regions files of different resolution generated by Fan-C contain genomic contact and corresponding index information, respectively.

source_name: p35S::H2B.8-eGFP seedling

growth_protocol: Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.

extract_protocol:
Ten-day-old seedlings were harvested and fixed with 20 ml 2% formaldehyde solution for 15 min in vacuum conditions at room temperature and then quenched by adding 2.162 ml 2.5 M glycine. Fixed seedling tissue was rinsed with water three times and dried with tissue paper.   The nuclei were released by grinding in liquid nitrogen and then resuspended with 25 ml of extraction buffer I (0.4 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 13 μl protease inhibitor). Nuclei were filtered through miracloth (Calbiochem) and then centrifuged at 4000 rpm for 20 min at 4 °C. The supernatant was discarded whilst the pellet was resuspended with 1 ml of extraction buffer II (0.25 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 1% Triton X-100, 5mM β-mercaptoethanol, 0.1mM PMSF, 13 μl protease inhibitor). Then, the mixture was centrifuged at 14000 rpm for 10 min at 4 °C and the pellet was resuspended with 300 μl of extraction buffer III (1.7 M sucrose, 10 mM Tris HCl pH 8, 0.15% Triton X-100, 2 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 1 μl protease inhibitor), load the mixture onto the top of an equal amount of clean extraction buffer III, then centrifuge at 14000 rpm for 10 min.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.

value: ten-day-old seedlings


title: PIF7_21FR_1

value: 2 hours 21°C white light + Far-red


title: WT_seedling_Hi-C_rep2

source_name: WT seedling

value: WT


title: PIF7_21FR_2

source_name: Whole seedlings


title: PIF7_30WL_2

value: 2 hours 30°C white light


title: JIA PBMCs child7

description: miRNA

value: mononuclear cells from peripheral blood

value: 13-17 years old

value: children


title: JIA PBMCs child9

description: miRNA


title: PIF7_30WL_1


title: WT_seedling_Hi-C

data_processing:
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb, 100 kb, 50 kb, 10 kb, 1kb contact matrix (hic files).
Genome_build: TAIR10
Supplementary_files_format_and_content: Hi-C: matrix and regions files of different resolution generated by Fan-C contain genomic contact and corresponding index information, respectively.

extract_protocol:
Ten-day-old seedlings were harvested and fixed with 20 ml 2% formaldehyde solution for 15 min in vacuum conditions at room temperature and then quenched by adding 2.162 ml 2.5 M glycine. Fixed seedling tissue was rinsed with water three times and dried with tissue paper.   The nuclei were released by grinding in liquid nitrogen and then resuspended with 25 ml of extraction buffer I (0.4 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 13 μl protease inhibitor). Nuclei were filtered through miracloth (Calbiochem) and then centrifuged at 4000 rpm for 20 min at 4 °C. The supernatant was discarded whilst the pellet was resuspended with 1 ml of extraction buffer II (0.25 M sucrose, 10 mM Tris HCl pH 8, 10 mM MgCl2, 1% Triton X-100, 5mM β-mercaptoethanol, 0.1mM PMSF, 13 μl protease inhibitor). Then, the mixture was centrifuged at 14000 rpm for 10 min at 4 °C and the pellet was resuspended with 300 μl of extraction buffer III (1.7 M sucrose, 10 mM Tris HCl pH 8, 0.15% Triton X-100, 2 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 1 μl protease inhibitor), load the mixture onto the top of an equal amount of clean extraction buffer III, then centrifuge at 14000 rpm for 10 min.
The Hi-C library construction and sequencing were conducted by Annoroad Gene Technology Co., Ltd (Beijing, China). Briefly, The pelleted nuclei were washed twice with 1x ice cold CutSmart buffer and finally resuspended in 0.5 ml volume. SDS was applied to permeabilize nuclei at 65 °C for 10 min, Triton X-100 was added to quench SDS. Thereafter, chromatin was digested with 400 units MboI overnight at 37 °C with gentle rocking. MboI was then denatured to cease activity. Digested chromatin underwent DNA end repair with biotin-14-dCTP insertion followed by blunt-end ligation. After decrosslinking with proteinase K at 65 °C, DNA was purified by phenol chloroform extraction method. Biotin-14-dCTP was removed from non-ligated DNA fragment ends using T4 DNA polymerase. DNA was sheared to a range of 200 to 600 bp by sonication. Next, the fragments underwent end repair and were pulled down by streptavidin C1 magnetic beads to enrich for fragments containing contact information. Fragment ends were then A-tailed, sequencing adapters were ligated, and libraries were amplified by PCR for 12-14 cycles. Following purification, libraries were sequenced using the Illumina HiSeq platform with 2×150 bp length.

tag: library strategy

value: Hi-C


title: H2B8_seedling_Hi-C

source_name: 35Sp::H2B.8-eGFP seedling


title: JIA PBMCs child4

description: miRNA

value: 18 years old


title: PIF7_21WL_2

value: 2 hours 21°C white light


title: JIA PBMCs child3

description: miRNA

value: 5 years old


title: SAH_2(SAH+PBS_2)

city: Nanchong

first: Hui

last: Tang

state: Sichuan

address: No.97, South Renmin Road, Shunqing District

institute: Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly Rnor6 (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz)  using Hisat2(v2.1.0) with default parameters.
StringTie v1.3.3b was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ensembl.org/pub/release-89/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.89.gtf.gz.
Differential expression analysis of two conditions was performed using the limma R package (v3.32.10). Pvalue < 0.05 and absolute log2 (fold change) > 1 were set as the threshold for significantly differential expression.
Assembly: Rnor6
Supplementary files format and content: Files include Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: rat brain tissue

growth_protocol: A SAH rat model was established by injecting femoral artery blood into the cisterna magna.

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 6-gingerol or vehicle was injected intraperitoneally one hour post-SAH induction.

tag: agent

value: PBS

value: brain

tag: disease

value: SAH


title: SAH_1(SAH+PBS_1)


title: Control_2(SAH+6-gingerol_2)


title: PIF7_21WL_1

value: Whole seedlings

value: anti-MYC (9B11 , Cell siganling)

value: PIF7:PIF7-4xMYC (pif457)


title: Control_30FR

description: Double side size selection during library preparation,used as a control for #2 samples

value: 2 hours 30°C white light + Far-red


title: Control_3(SAH+6-gingerol_3)


title: Control_1(SAH+6-gingerol_1)


title: Control_21FR

description: One side size selection during library preparation, used as a control for #1 samples

value: 2 hours 21°C white light + Far-red


title: JIA PBMCs child2

description: miRNA

tag: disease state

value: Juvenile idiopathic arthritis

tag: age

value: 13 years old


title: SAH_3(SAH+PBS_3)


title: JIA PBMCs child1

description: miRNA

value: mononuclear cells from peripheral blood

value: 9 years old

tag: developmental stage


title: RNA-seq MM6 5LO-KI2 - diff - LPS- rep 2

status: Public on Jul 25 2022

city: Frankfurt am Main

first: Marius

last: Kreiss

address: Max-von-Laue-Str. 9

department: Pharmaceutical Chemistry

institute: Goethe-University

description: KI2vsKO2_diff+LPS.results.normalized_data_matrix

data_processing:
Base calling was automatically performed by RTA 2.4.11 on NextSeq500 or BCL Convert 1.2.1 on NextSeq2000
FASTQ generation was automatically performed by FASTQ generator v 1.0.0 via BaseSpace (Illumina)
Sequenced reads were trimmed (adapter & UMI) and filtered for low-quality and then annotated against GRCh38 release 92 using STAR 2.6.0c using RSEM 1.3.0
Differential expression analysis (WT vs. KO and KO vs. KI) was performed using EBSeq included in RSEM with an FDR of  ≤ 0.05 and an fold change ≥ 2
Differentially expressed genes were merged with the corresponding cell clone and finally checked for opposite regulation in KI
Assembly: hg38
Supplementary files format and content: Normalized data matrices containing normalized abundance data and summarizing table containing log2FC from 5-LO reglated genes identified in this study

source_name: MonoMac 6

growth_protocol: MM6 cells were grown in glutamine containing RPMI 1640 medium (supplemented with 10% (v/v) heat inactivated FCS, 10 µg/mL insulin, 1 x MEM non-essential amino acids, 1 mM sodium pyruvate, 1 mM oxaloacetate, 100 U/mL penicillin, and 100 µg/mL streptomycin) at 37°C and 5% CO2. The seeding density for experiments is about 0.25 x 10^6 cells /mL

extract_protocol:
Total RNA was extracted with TriZol (Invitrogen).
1 µg total RNA was used for the total RNA Library Prep Kit (Lexogen) according to the manufacturer's protocoll.

treatment_protocol: All samples were differentiated with 1 ng/mL TGF-β1 (Peprotech) and 50 nM Calcitriol (Cayman) for 72 h at 6% CO2. Inflammatory stimulation was obtained for the half of the samples using 1 µg/mL LPS (Sigma) for 6 h.

value: 5-LO knockin clone 2

tag: treatment 1

tag: treatment 2

value: LPS for 6 h


title: RNA-seq MM6 5LO-KI2 - diff - rep 1

description: KI2vsKO2_diff.results.normalized_data_matrix

value: untreated


title: BMP9 treated, PA-1 cell line, biological rep1

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: PA-1 cell line in Anoikis condition that was treated with BMP9 during 24 hours

hyb_protocol: Amplified/labeled samples were hybridized to Affymetrix HuGene-2_0-st Arrays for 16 h at 45°C using a GeneChip Hybridization Oven 645 and the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific). Hybridized arrays were washed and stained using the kit just mentioned and a GeneChip Fluidics Stations 450 (Thermo Fisher Scientific).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G system using Affymetrix GeneChip Command Console Scan Control 4.0 software.

data_processing:
The resulting probe cell intensity (CEL) files were quality controlled and processed at the gene-level using the Robust Multichip Analysis (RMA) algorithm to generate CHP files using GeneChip Expression Console 1.4.1.46 software. CHP files were imported into Transcriptome Analysis Console using HuGene-2_0-st-v1.na35.hg19.transcript.csv annotation file for differential gene expression analysis.
HuGene-2_0-st-v1.na35.hg19.transcript.csv (meta-probeset file)

source_name: PA-1 cell line, Anoikis, BMP9 treated, 24 h

label_protocol: Total RNA samples were amplified and biotinylated using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific), according to the manufacturer's recommendations.

growth_protocol: PA1 cells obatained from ATCC were grown in RPMI complete media with 10% FBS and plated in poly-hema coated ultra low attachment plates in individual biological replicates.

extract_protocol: Trizol extraction was used to isolate total RNA. RNA quality was assessed with a NanoDrop 2000 (Thermo Scientific) and an Agilent 2100 Bioanalizer.

treatment_protocol: At the time of plating in poly-hema coated plates cells were treated with 10ng/ml BMP9 or vehicle.

tag: Sex

value: female

tag: condition

value: anoikis


title: Vehicle treated, PA-1 cell line, biological rep3

description: PA-1 cell line in Anoikis condition that was vehicle treated during 24 hours

source_name: PA-1 cell line, Anoikis, Vehicle treated, 24 h

value: Vehicle


title: BMP9 treated, PA-1 cell line, biological rep3


title: RNA-seq MM6 5LO-KI2 - diff - rep 3


title: Vehicle treated, PA-1 cell line, biological rep1


title: Vehicle treated, PA-1 cell line, biological rep2


title: BMP9 treated, PA-1 cell line, biological rep2


title: RNA-seq MM6 5LO-KI2 - diff - LPS- rep 1


title: RNA-seq MM6 5LO-KI2 - diff - rep 2


title: RNA-seq MM6 5LO-KI2 - LPS - rep 3

description: KI2vsKO2_LPS.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KI1 - diff - rep 3

description: KI1vsKO1_diff.results.normalized_data_matrix

value: 5-LO knockin clone 1


title: RNA-seq MM6 5LO-KI1 - diff - LPS- rep 1

description: KI1vsKO1_diff+LPS.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KI1 - diff - rep 2


title: RNA-seq MM6 5LO-KI2 - LPS - rep 1


title: RNA-seq MM6 5LO-KI2 - rep 2

description: KI2vsKO2_wo.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KI2 - rep 1


title: RNA-seq MM6 5LO-KI1 - LPS - rep 2

description: KI1vsKO1_LPS.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KI1 - LPS - rep 1


title: RNA-seq MM6 5LO-KI2 - LPS - rep 2


title: RNA-seq MM6 5LO-KI1 - diff - LPS- rep 3


title: RNA-seq MM6 5LO-KI2 - diff - LPS- rep 3


title: RNA-seq MM6 5LO-KI1 - rep 1

description: KI1vsKO1_wo.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KI1 - diff - rep 1


title: RNA-seq MM6 5LO-KI1 - LPS - rep 3


title: RNA-seq MM6 5LO-KI2 - rep 3


title: RNA-seq MM6 5LO-KI1 - rep 3


title: RNA-seq MM6 5LO-KI1 - rep 2


title: RNA-seq MM6 5LO-KI1 - diff - LPS- rep 2


title: ChIP-seq MM6 WT - diff - LPS - input - rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ generation was automatically performed by FASTQ generator v 1.0.0
Sequenced reads were trimmed and masked for low-quality, annotiation against GRCh38 release 92 using Bowtie2
BAM files were filtered for mapping quality (>=20) and peak calling was performed using MACS2  with a minimum FDR (q-value) cutoff of 0.1
Assembly: hg38
Supplementary files format and content: BigWig files were created with BedGraph-to-bigWig converter using Galaxy v. 1.1.1 and peaks represent normalized alignment depth by MACS2
Supplementary files format and content: Peak files by MACS2 callpeak presented in .bed format

source_name: Mono Mac 6

growth_protocol: MM6 cells were grown in glutamine containing RPMI 1640 medium (supplemented with 10% (v/v) FCS, 10 µg/mL insulin, 1 x MEM non-essential amino acids, 1 mM sodium pyruvate, 1 mM oxaloacetate, 100 U/mL penicillin, and 100 µg/mL streptomycin) at 37°C and 5% CO2. The seeding density for experiments is about 0.25 x 10^6 cells/mL

extract_protocol:
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIP was performed
ChIP DNA was sent to EMBL and the library was prepared there according to their protocol

treatment_protocol: All samples were differentiated with 1 ng/mL TGF-β1 (Peprotech) and 50 nM Calcitriol (Cayman) for 72 h at 6% CO2. Inflammatory stimulation was obtained for the half of the samples using 1 µg/mL LPS (Sigma) for 2 h.

value: wild type

tag: chip antibody


title: ChIP-seq MM6 WT - diff - LPS - input - rep1


title: ChIP-seq MM6 WT - diff - LPS - input - rep2


title: ChIP-seq MM6 WT - diff - input - rep 1


title: ChIP-seq MM6 WT - diff - LPS - rep3

description:
bigwig_LPS_treatment.bigwig
MACS2_callpeak_LPS.bed

value: Anti-5-LO (abcam ab169755)


title: ChIP-seq MM6 WT - diff - LPS - rep2


title: ChIP-seq MM6 WT - diff - LPS - rep1


title: ChIP-seq MM6 WT - diff - rep 3

description:
bigWig_PBS_treatment.bigwig
MACS2_callpeak_PBS.bed


title: ChIP-seq MM6 WT - diff - rep 2


title: ChIP-seq MM6 WT - diff - rep 1


title: MCF-7 Mouse IgG ChIP-Seq

city: Macau

first: Edwin

middle: Chong Wing

last: CHEUNG

state: Macau

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

institute: University of Macau

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie v0.12.9 with default parameters
SAM to BAM conversion and sorting was performed using samtools v1.9.0
The duplicated reads were marked using Picard MarkDuplicates v2.20.0 utility
Peak calling was performed using MACS1.4 with pvalue < 1e-4
The alignment coverage was calculated and converted into bigwig format using deeptools v3.4.3 bamCoverage utility and visualized into IGV v2.7.2 (Genome Build: hg19)
Genome_build: hg19
Supplementary_files_format_and_content: .bed files representing the peaks in text formate
Supplementary_files_format_and_content: .bw files store alignment coverage in binary foramte

source_name: breast cancer cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and interested protein-DNA complexes were isolated with antibody.
library preparations were constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: breast cancer cell line

value: Mouse IgG (Santa Cruz, sc2025)


title: MCF-7 AP2C siTRIM37 ChIP-Seq

tag: genotype/variation

value: AP-2γ (Santa Cruz, sc12762x)


title: ChIP-seq MM6 WT - diff - input - rep 3

tag: genotype


title: Triticum aestivum treated with 0.1mM CN rep2

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

institute: CENIT SUPPORT SYSTEMS

description: Gene expression data from Triticum aestivum grown with 0.1 mM CN as Nitrogen source.

hyb_protocol: cDNAs were synthesized from 100 ng of purified RNAs and used for production of labeled probes, which were used to hybridize the Affymetrix GeneChip Wheat Genome Array (Affymetrix, Santa Clara, CA, USA) employing the GeneChip Fluidics Station 450

scan_protocol: Fluorescent signals emitted were scanned in a calibrated Affymetrix GeneChip Scanner 3000, and images analyzed in an Affymetrix GeneChip Operating Software (GCOS 1.2)

data_processing: For calculating the mean signal and for normalizing with the on-chip control genes the Model Based Expression (dChip) Index (Li and Wong, 2001) was used.

organism: Triticum aestivum

source_name: Roots from 10 wheat seedlings

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

growth_protocol: Wheat seeds were placed inside Phytatray II boxes (Sigma Aldrich, Madrid, Spain) containing Murashige & Skoog medium (MS, Duchefa Biochemie BV, Haarlem, The Netherlands) as previously described in Rubio et al. (2012), and boxes were kept at 25ºC under gentle stirring for 72 h. Spores of T34 were used to inoculate flasks containing 100 mL of potato dextrose broth medium (PDB, Difco Laboratories) at a concentration of 106 spores/mL. T34 cultures were then maintained at 25ºC and 180 rpm for 16 h. Then, fungal germlings were harvested by centrifugation at 4000 x g for 10 min, washed, resuspended in sterile distilled water and used to inoculate, at a concentration of 105 germlings/mL, Phytatray II boxes that contained 72-h-old wheat seedlings.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Phytatray II boxes containing wheat seedlings without inoculation of fungus were grown in parellel as control. After 24 h incubation at 25ºC and gentle shaking, the lids were removed in sterile conditions and the MS medium was replaced with a minimal medium (Lullien et al., 1987) containing 0, 0.1, 0.5 or 1 mM CN as N source. The eight culture conditions assayed were coded as follow: T0N0 (without T34 strain and 0 mM CN), T0N0.1 (without T34 strain and 0.1 mM CN), T0N0.5 (without T34 strain and 0.5 mM CN), T0N1 (without T34 strain and 1 mM CN), T1N0 (T34 strain and without CN), T1N0.1 (T34 strain and 0.1 mM CN), T1N0.5 (T34 strain and 0.5 mM CN) and T1N1 (T34 strain and 1 mM CN).

tag: tissue

value: Root

value: 0.1 mM CN


title: ChIP-seq MM6 WT - diff - input - rep 2


title: Triticum aestivum treated with 0.5mM CN rep2

description: Gene expression data from Triticum aestivum grown with 0.5 mM CN as Nitrogen source.

tag: treatment

value: 0.5 mM CN


title: Triticum aestivum with Trichoderma harzianum T34 treated with 0.5mM CN rep2

description: Gene expression data from Triticum aestivum in the presence of Trichoderma harzianum T34 grown with 0.5 mM CN as Nitrogen source.

value: inoculated with Trichoderma harzianum T34 and treated with 0.5 mM CN


title: Triticum aestivum treated with 0.5mM CN rep1


title: Triticum aestivum with Trichoderma harzianum T34 treated with 1mM CN rep2

description: Gene expression data from Triticum aestivum in the presence of Trichoderma harzianum T34 grown with 1 mM CN as Nitrogen source.

value: inoculated with Trichoderma harzianum T34 and treated with 1 mM CN


title: Triticum aestivum treated with 1mM CN rep1

description: Gene expression data from Triticum aestivum grown with 1 mM CN as Nitrogen source.

value: 1 mM CN


title: Triticum aestivum with Trichoderma harzianum T34rep2

description: Gene expression data from Triticum aestivum in the presence of Trichoderma harzianum T34.

value: inoculated with Trichoderma harzianum T34


title: Triticum aestivum treated with 0.1mM CN rep1


title: Triticum aestivum control rep1

description: Gene expression data from Triticum aestivum as control condition.


title: Triticum aestivum treated with 1mM CN rep2


title: Triticum aestivum with Trichoderma harzianum T34 treated with 1mM CN rep1


title: Triticum aestivum with Trichoderma harzianum T34 treated with 0.1mM CN rep2

description: Gene expression data from Triticum aestivum in the presence of Trichoderma harzianum T34 grown with 0.1 mM CN as Nitrogen source.

value: inoculated with Trichoderma harzianum T34 and treated with 0.1 mM CN


title: Triticum aestivum control rep2


title: Triticum aestivum with Trichoderma harzianum T34 treated with 0.5mM CN rep1


title: MCF-7 AP2C Negative Control ChIP-Seq


title: Triticum aestivum with Trichoderma harzianum T34rep1


title: MCF-7 siAP2C

data_processing:
Basecalls performed using CASAVA-1.8.2
The raw reads of every sample were first trimmed to 75bp and then mapped as paired-end sequencing reads against UCSC hg19 and the gene annotation reference GRCh37 using HISAT2.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by HISAT2 and SAMtools using the StringTie package.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

extract_protocol:
The total RNA of each sample was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
library preparations were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to the manufacturer’s protocol.


title: MCF-7 Rabbit IgG ChIP-Seq

value: Rabbit IgG (Santa Cruz, sc2027)


title: MCF-7 TRIM37 ChIP-Seq

value: TRIM37 (Bethyl Laboratories, A301-174A))


title: MCF-7 siTRIM37


title: PDAC_13

city: Beijing

first: Bo

last: Gao

address: No.11 Xizhimen South Street, Beijing, China

department: Department of General Surgery

institute: Peking university people's hospital

description:
in situ RNA probe hybridization
TMA2_012

data_processing:
The raw reads (raw sequencing FASTQ files) are compiled with the configuration file, which specifies the processing parameters.
The raw reads are processed by computationally removing the adapter sequences (resulting in trimmed reads), and merging paired-end reads (resulting in stitched reads).
The stitched reads are aligned to the RTS-ID barcodes in the reference assay, creating aligned reads and assigning counts to biological target names.
PCR duplicates are removed by sorting based on the Unique Molecular Identifier (UMI) in each read, resulting in deduplicated reads.Then the digital count conversion data was uploaded into the DSP Control Center for study creation in the DSP Data Analysis Suite.
Assembly: Sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Library strategy: GeoMx Seq

source_name: PDAC

extract_protocol:
Prepared slides and hybridize biological targets with UV-cleavable biological probes.Labelled cell types of interest with fluorescent morphology markers, then go into the next phase, Process Slide on GeoMx DSP. Loaded the prepared slides onto the GeoMx DSP instrument, enter identifying information for them, scan them to create fluorescent images, select regions of interest (ROIs), and then collect UV-cleaved oligos from these ROIs into the wells of a collection plate.Transfered the contents of the DSP collection to a PCR plate for Library prep and Sequencing. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Following collection on the GeoMx DSP instrument, the 96- well collection plate contains aspirates from the experimental regions of interest and primer sequences specifically labeled for each well.The aspirates are photocleaved oligos, each containing a readout tag sequence identifier (RTS ID) that identifies the biological target. Each oligo also includes a unique molecular identifier (UMI) sequence, enabling removal of duplicated PCR products in the subsequent data processing pipeline. Finally, SPR1 (sequencing primer read 1) and SPR2 (sequencing primer read 2) sequences allow hybridization to GeoMx Seq Code primers in PCR amplification. During PCR amplification, the GeoMx Seq Code primers add i5 and i7 indexing sequences (unique dual indexes) for multiplexing many GeoMx DSP aspirate sequences into a single sequencing run, as well as P5 and P7 sequences for binding to Illumina flow cells. Following a pooling, purification, and quality control process, the final NGS library is ready for sequencing on an Illumina NGS platform.

value: PDAC

tag: patient age

tag: patient sex

value: F

tag: tumor grade

tag: tumor stage


title: PDAC_14

description:
in situ RNA probe hybridization
TMA2_013


title: PDAC_16

description:
in situ RNA probe hybridization
TMA2_022

value: M


title: PDAC_15

description:
in situ RNA probe hybridization
TMA2_014


title: PDAC_10

description:
in situ RNA probe hybridization
TMA2_003


title: PDAC_12

description:
in situ RNA probe hybridization
TMA2_006


title: Triticum aestivum with Trichoderma harzianum T34 treated with 0.1mM CN rep1


title: PDA C_9

description:
in situ RNA probe hybridization
TMA1_025


title: PDAC_8

description:
in situ RNA probe hybridization
TMA1_024


title: PDAC_7

description:
in situ RNA probe hybridization
TMA1_021


title: PDAC_5

description:
in situ RNA probe hybridization
TMA1_016


title: PDAC_4

description:
in situ RNA probe hybridization
TMA1_012


title: PDAC_3

description:
in situ RNA probe hybridization
TMA1_011


title: PDAC_6

description:
in situ RNA probe hybridization
TMA1_020


title: PDAC_1

description:
in situ RNA probe hybridization
TMA1_005


title: ADM_16

description:
in situ RNA probe hybridization
TMA2_021

source_name: ADM

value: ADM


title: PDAC_11

description:
in situ RNA probe hybridization
TMA2_004


title: ADM_15

description:
in situ RNA probe hybridization
TMA2_020


title: PDAC_2

description:
in situ RNA probe hybridization
TMA1_006


title: ADM_10

description:
in situ RNA probe hybridization
TMA2_015


title: ADM_11

description:
in situ RNA probe hybridization
TMA2_016


title: ADM_13

description:
in situ RNA probe hybridization
TMA2_018


title: ADM_9

description:
in situ RNA probe hybridization
TMA2_011


title: ADM_12

description:
in situ RNA probe hybridization
TMA2_017


title: ADM_8

description:
in situ RNA probe hybridization
TMA2_010


title: ADM_7

description:
in situ RNA probe hybridization
TMA2_007


title: ADM_5

description:
in situ RNA probe hybridization
TMA 2_001


title: ADM_6

description:
in situ RNA probe hybridization
TMA2_005


title: ADM_1

description:
in situ RNA probe hybridization
TMA1_003


title: ADM_2

description:
in situ RNA probe hybridization
TMA1_004


title: Adjacent normal_14

description:
in situ RNA probe hybridization
TMA 2_008

source_name: adjacent normal

value: adjacent normal


title: Adjacent normal_15

description:
in situ RNA probe hybridization
TMA 2_009


title: Adjacent normal_13

description:
in situ RNA probe hybridization
TMA 2_002


title: ADM_4

description:
in situ RNA probe hybridization
TMA 1_019


title: ADM_3

description:
in situ RNA probe hybridization
TMA1_015


title: Adjacent normal_12

description:
in situ RNA probe hybridization
TMA 1_023


title: ADM_14

description:
in situ RNA probe hybridization
TMA2_019


title: Adjacent normal_9

description:
in situ RNA probe hybridization
TMA 1_017


title: Adjacent normal_6

description:
in situ RNA probe hybridization
TMA 1_010


title: Adjacent normal_8

description:
in situ RNA probe hybridization
TMA 1_014


title: Adjacent normal_5

description:
in situ RNA probe hybridization
TMA 1_009


title: Adjacent normal_4

description:
in situ RNA probe hybridization
TMA 1_008


title: Adjacent normal_3

description:
in situ RNA probe hybridization
TMA 1_007


title: MCF-7_siNC

value: breast cancer cell line

value: NC


title: Adjacent normal_2

description:
in situ RNA probe hybridization
TMA 1_002


title: Adjacent normal_1

description:
in situ RNA probe hybridization
TMA 1_001


title: RNA-seq MM6 5LO-KO2 - diff - LPS- rep 1

description: KO2vsWT_diff+LPS.results.normalized_data_matrix

value: 5-LO knockout clone 2

value: LPS for 6 h


title: Adjacent normal_16

description:
in situ RNA probe hybridization
TMA 2_023


title: RNA-seq MM6 5LO-KO2 - diff - LPS- rep 3


title: RNA-seq MM6 5LO-KO2 - diff - rep 3

description: KO2vsWT_diff.results.normalized_data_matrix

value: untreated


title: RNA-seq MM6 5LO-KO2 - diff - rep 2


title: RNA-seq MM6 5LO-KO2 - diff - rep 1


title: RNA-seq MM6 5LO-KO2 - LPS - rep 3

description: KO2vsWT_LPS.results.normalized_data_matrix


title: Adjacent normal_7

description:
in situ RNA probe hybridization
TMA 1_013


title: RNA-seq MM6 5LO-KO2 - diff - LPS- rep 2


title: RNA-seq MM6 5LO-KO2 - rep 1

description: KO2vsWT_wo.results.normalized_data_matrix


title: Adjacent normal_10

description:
in situ RNA probe hybridization
TMA 1_018


title: RNA-seq MM6 5LO-KO1 - diff - rep 3

description: KO1vsWT_diff.results.normalized_data_matrix

value: 5-LO knockout clone 1


title: RNA-seq MM6 5LO-KO1 - diff - LPS- rep 3

description: KO1vsWT_diff+LPS.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KO1 - diff - LPS- rep 1


title: RNA-seq MM6 5LO-KO2 - LPS - rep 1


title: RNA-seq MM6 5LO-KO1 - LPS - rep 1

description: KO1vsWT_LPS.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KO1 - LPS - rep 2


title: RNA-seq MM6 5LO-KO2 - rep 2


title: RNA-seq MM6 5LO-KO1 - diff - rep 2


title: RNA-seq MM6 5LO-KO1 - diff - LPS- rep 2


title: RNA-seq MM6 5LO-KO1 - rep 3

description: KO1vsWT_wo.results.normalized_data_matrix


title: RNA-seq MM6 5LO-KO2 - rep 3


title: RNA-seq MM6 WT - diff - rep 3

description:
KO1vsWT_diff.results.normalized_data_matrix
KO2vsWT_diff.results.normalized_data_matrix

value: wild type


title: RNA-seq MM6 5LO-KO1 - rep 2


title: RNA-seq MM6 5LO-KO1 - diff - rep 1


title: RNA-seq MM6 WT - diff - rep 1


title: RNA-seq MM6 5LO-KO1 - LPS - rep 3


title: RNA-seq MM6 WT - rep 2

description:
KO1vsWT_wo.results.normalized_data_matrix
KO2vsWT_wo.results.normalized_data_matrix


title: RNA-seq MM6 WT - rep 1


title: RNA-seq MM6 5LO-KO1 - rep 1


title: RNA-seq MM6 5LO-KO2 - LPS - rep 2


title: RNA-seq MM6 WT - diff - LPS - rep1

description:
KO1vsWT_diff+LPS.results.normalized_data_matrix
KO2vsWT_diff+LPS.results.normalized_data_matrix


title: RNA-seq MM6 WT - LPS - rep3

description:
KO1vsWT_LPS.results.normalized_data_matrix
KO2vsWT_LPS.results.normalized_data_matrix


title: FAIRE-seq MM6 5LO-KO - diff - input - rep 1

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ generation was automatically performed by FASTQ generator v 1.0.0
Sequenced reads were trimmed and masked for low-quality, annotiation against GRCh38 release 92 using Bowtie2
BAM files were filtered for mapping quality (>=20) and peak calling was performed using MACS2  with a minimum FDR (q-value) cutoff of 0.1
Assembly: hg38
Supplementary files format and content: tdf files were created with IGV-tools v. 2.11.2 and peaks represent normalized alignment depth by MACS2
Supplementary files format and content: Peak files by MACS2 callpeak presented in .bed format
Library strategy: FAIRE-seq

value: 5-LO knockout


title: RNA-seq MM6 WT - diff - rep 2


title: Adjacent normal_11

description:
in situ RNA probe hybridization
TMA 1_022


title: RNA-seq MM6 WT - LPS - rep2


title: RNA-seq MM6 WT - rep 3


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - input - rep2


title: FAIRE-seq MM6 WT - diff - LPS - input - rep1


title: FAIRE-seq MM6 WT - diff - input - rep 2


title: RNA-seq MM6 WT - diff - LPS - rep2


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - input - rep1


title: FAIRE-seq MM6 5LO-KO - diff - input - rep 2


title: RNA-seq MM6 WT - LPS - rep1


title: FAIRE-seq MM6 5LO-KO - diff - rep 3

description:
KO_PBS_FAIRE.tdf
MACS2 callpeak on KO PBS.bed

value: FAIRE


title: FAIRE-seq MM6 WT - diff - input - rep 1


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - input - rep3


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - rep1

description:
KO_LPS_FAIRE.tdf
MACS2 callpeak on KO LPS.bed


title: FAIRE-seq MM6 WT - diff - LPS - input - rep2


title: FAIRE-seq MM6 WT - diff - LPS - rep3

description:
WT_LPS_FAIRE.tdf
MACS2 callpeak on WT LPS.bed


title: RNA-seq MM6 WT - diff - LPS - rep3


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - rep2


title: FAIRE-seq MM6 5LO-KO - diff - input - rep 3


title: FAIRE-seq MM6 5-LO-KO - diff - LPS - rep3


title: FAIRE-seq MM6 WT - diff - LPS - input - rep3


title: FAIRE-seq MM6 WT - diff - rep 2

description:
WT_PBS_FAIRE.tdf
MACS2 callpeak on WT PBS.bed


title: FAIRE-seq MM6 WT - diff - LPS - rep1


title: FAIRE-seq MM6 WT - diff - input - rep 3


title: FAIRE-seq MM6 WT - diff - rep 3


title: K562 cells expressing BASP1-G2A - ATAC-seq - rep1

city: Bristol

first: Alexander

last: Moorhouse

address: Biomedical Sciences Building, University Walk,

department: Cell and Molecular Medicine

institute: University of Bristol

description:
GK1_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)

data_processing:
Filtered and cleaned FASTQ data were aligned to the reference genome.
Gene expression was determined using Subread. Peaks were called with MACS2.
DESeq2 was used for differential analysis of gene expression and merged peak regions.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.csv: Differential gene expression results are provided for RNA-seq, peaks are provided for ATAC-seq.

source_name: K562 cells

extract_protocol: not provided

value: Expressing BASP1-G2A


title: K562 cells expressing wild type BASP1 - ATAC-seq - rep2

description:
BK2_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)

value: Expressing WT BASP1


title: FAIRE-seq MM6 5LO-KO - diff - rep 1


title: K562 cells - ATAC-seq - rep3

description:
VK3_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)

value: Control


title: FAIRE-seq MM6 5LO-KO - diff - rep 2


title: K562 cells expressing BASP1-G2A - ATAC-seq - rep2

description:
GK2_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing wild type BASP1 - ATAC-seq - rep3

description:
BK3_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing BASP1-G2A - ATAC-seq - rep3

description:
GK3_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing BASP1-G2A - RNA-seq - rep3

description:
GK3_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: FAIRE-seq MM6 WT - diff - LPS - rep2


title: K562 cells expressing BASP1-G2A - RNA-seq - rep1

description:
GK1_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing wild type BASP1 - RNA-seq - rep3

description:
BK3_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing wild type BASP1 - RNA-seq - rep2

description:
BK2_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing wild type BASP1 - ATAC-seq - rep1

description:
BK1_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells - RNA-seq - rep2

description:
VK2_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells - ATAC-seq - rep1

description:
VK1_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells - ATAC-seq - rep2

description:
VK2_ATAC-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells - RNA-seq - rep3

description:
VK3_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: K562 cells expressing BASP1-G2A - RNA-seq - rep2

description:
GK2_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: FAIRE-seq MM6 WT - diff - rep 1

description:
WT_PBS_FAIRE.tdf
MACS2 callpeak on WT PBS.bed


title: KDM5A and KDM5B shRNA

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Single cell RNA-seq was performed using Drop-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

growth_protocol: Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone), antibiotic-free media in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for not more than 5 passages before collection for scRNA analysis. Cells were seeded in a 6-well plate 2 days before transduction, so they will appear 80% confluent at the time of transduction. Cells in each well were transduced with the 100 µL 10x viral stock in growth medium containing 7.5 µg mL-1 polybrene overnight. For transduction with two viruses, cells were treated with 100 µl of each 10x viral stock. Next morning, cells were washed twice with 2 mL PBS to remove viral particles and the medium was changed to 2 mL fresh antibiotic-free RPMI, containing 10% FBS. Cells were allowed 8 hours for recovery and then split from each well into a p100 plate for corresponding treatment. Upon completing the treatment, cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

extract_protocol:
Drop-seq on the single cell suspension
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)

treatment_protocol: Cells were treated with the 6.25 µM KDM5A inhibitor CPI-455 for 4 days. In particular, 1x 106 cells were seeded on a p100 plate in media containing 2.5 µL of 25 mM CPI-455 (prepared in DMSO). Next day, 10 μL of 2 mM erlotinib (prepared in DMSO) was added to obtain the final concentration of 2 µM. Knockdown of KDM5A was achieved by transducing cells with pLVTHM-shKDM5A-GFP. Media was changed on 2 µM erlotinib on the fourth day after transduction. Similarly, the knockdown of KDM5A and KDM5B was achieved by transducing cells with pLVTHM-shKDM5A-GFP and pLVTHM-shKDM5B-GFP viruses. Media was changed on 2 µM erlotinib on the fifth day after transduction. Overexpression of KDM5A was achieved by transducing cells with pLenti-CMV-Hygro-3xFLAG-HA-KDM5A viruses. Media was changed on 2 µM erlotinib on the sixth day after transduction. All cells mentioned above were treated with erlotinib for 1 day. The scrambled shRNA, pLVTHM-shsc-GFP, was used to transduce control cells. These cells were not treated with erlotinib. Another control was cells that were neither transduced with lentiviruses nor treated with erlotinib.

value: treated with 2 µM erlotinib and lentiviruses encoding KDM5A and KDM5B shRNA


title: K562 cells expressing wild type BASP1 - RNA-seq - rep1

description:
BK1_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: untreated D0


title: KDM5A overexpression

value: treated with 2 µM erlotinib and lentiviruses encoding KDM5A cDNA


title: scrambled shRNA

value: treated with control lentiviruses


title: KO3_9

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description: Library of 92 cells

library_source: transcriptomic single cell

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Assembly: mm10
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary files format and content: cellbarcodes_cellid.csv is a supplemetary file contains cellds and one of the 192  unique cellbarcode associated with the cell id.

source_name: dermal mast cells

growth_protocol: Mast cells were isolated from ear skin of C57BL/6J  wt and Tln knockout mice.

extract_protocol:
Mast cells were isolated from ear skin of C57BL/6J Mcpt5-Cre wt and Tln knockout mice .
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.

treatment_protocol: no treatment

tag: strain

value: C57BL/6J Mcpt5-Cre Tln1fl/fl R26LSLYFP

value: Ear skin

tag: reporter/marker

value: Mcpt5 Cre+/-


title: K562 cells - RNA-seq - rep1

description:
VK1_RNA-seq
biosample encode accession: ENCBS748AAA (SAMN06044655)


title: KDM5A shRNA

value: treated with 2 µM erlotinib and KDM5A shRNA lentiviruses


title: KO3_10

description: Library of 92 cells


title: CPI-455

value: treated with 2 µM erlotinib and 6.25 µM CPI-455


title: KO3_6

description: Library of 92 cells


title: KO3_2

description: Library of 92 cells


title: Arabidopsis thaliana JAR1-OE D5

city: Bonn

first: Ute

middle: C.

last: Vothknecht

address: Kirschallee 1

department: IZMB

institute: University of Bonn

description: Replication 2

data_processing:
CLC Genomics Workbench (v.12.03, https://www.qiagenbioinformatics.com/) was used to process the raw sequencing data.
Quality control and trimming were performed on FASTQ files of the samples.
Quality trimming was performed based on a quality score limit of 0.05 and a maximum number of two ambiguities.
To map the additional JAR1 reads from the JAR1-OE lines, an additional chromosome comprising the YFP sequence was added to the Araport 11 (Cheng et al., 2017) genome and the annotation file.
The FASTQ samples were then mapped to the modified Araport 11 genome, while only classifying reads as mapped which uniquely matched with ≥ 80% of their length and shared ≥ 90% identity with the reference genome. For the mapping to the gene models reads had to match with ≥ 90% of their length and share ≥ 90% similarity with a maximum of one hit allowed. Subsequently, counts for YFP and JAR1 were combined.
Genome_build: Araport 11 genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Rosette leaf

growth_protocol: Plants were grown in climatized growth chambers equipped with Philips TLD 18W of alternating 830/840 light color temperature) at 22°C under long-day conditions (16 h light/8 h dark) with 100 µmol photons m-2 s-1.

extract_protocol:
Total RNA was extracted from the whole rosette leaves of 32 day-old plants using the Quick-RNA Miniprep Kit (Zymo-Research, USA).
Approximately 200 ng of RNA was used for library construction. Sequencing libraries were prepared using the Lexogen‘s QuantSeq 3‘-mRNA-Seq Kit and sequenced on an Illumina HiSeq 2500 V4 platform with a read length of 1x50 bases. For each of the samples, three biological replicates were sequenced with an average sequencing depth of 10 million reads.

treatment_protocol: Plants were grown for 18 days with regular watering using identical volumes of tap water. Afterward, plants were either watered normally (control) or were exposed to drought stress conditions (drought) by withholding watering for up to 14 days (called as day 32).

tag: conditions

value: Drought

value: Leaf

tag: age

value: day 32

value: Overexpression line of JAR1.1


title: KO3_3

description: Library of 92 cells


title: KO2_10

description: Library of 92 cells


title: KO3_5

description: Library of 92 cells


title: KO2_9

description: Library of 92 cells


title: KO2_11

description: Library of 92 cells


title: KO1_3

description: Library of 92 cells


title: Arabidopsis thaliana JAR1-OE C1

description: Replication 1


title: Arabidopsis thaliana JAR1-OE C3

description: Replication 3


title: KO3_7

description: Library of 92 cells


title: KO3_8

description: Library of 92 cells


title: KO1_1

description: Library of 92 cells


title: Arabidopsis thaliana jar1-11 C3

description: Replication 3

value: knockdown line of JAR1 (SALK_034543)


title: Arabidopsis thaliana JAR1-OE D6

description: Replication 3


title: KO3_1

description: Library of 92 cells


title: Arabidopsis thaliana JAR1-OE D4

description: Replication 1


title: KO2_12

description: Library of 92 cells


title: KO3_4

description: Library of 92 cells


title: Arabidopsis thaliana jar1-11 D4

description: Replication 1


title: wt3_3

description: Library of 92 cells

value: C57BL/6J Mcpt5 Cre R26LSLYFP


title: KO1_4

description: Library of 92 cells


title: Arabidopsis thaliana WT Col-0 D5

description: Replication 2

value: wild-type Col-0


title: KO1_2

description: Library of 92 cells


title: Arabidopsis thaliana jar1-11 D5

description: Replication 2


title: wt2_2

description: Library of 92 cells


title: Arabidopsis thaliana jar1-11 D6

description: Replication 3


title: wt1_16

description: Library of 92 cells


title: Arabidopsis thaliana WT Col-0 C1

description: Replication 1


title: wt3_4

description: Library of 92 cells


title: wt3_2

description: Library of 92 cells


title: wt1_13

description: Library of 92 cells


title: Arabidopsis thaliana jar1-11 C2

description: Replication 2


title: wt1_14

description: Library of 92 cells


title: Arabidopsis thaliana JAR1-OE C2

description: Replication 2


title: YAP.Mp rep 4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq 2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 (Patro et al. 2017). Gene level summaries were prepared using tximport version 1.20.0 (Soneson, Love, and Robinson 2015) running under R version 4.1.0 (R Core Team 2021).
Genome_build: zv11 with an ensembl version 104 annotation
Supplementary_files_format_and_content: gphelps_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary_files_format_and_content: gphelps_l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset

organism: Danio rerio

source_name: cells isolated from 5 dpf larvae that express a mitfa:GFP reporter

extract_protocol:
RNeasy Micro Kit (Qiagen)
Samples were analyzed for RNA integrity using a Femto Analyzer, and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT (Illumina) and sequenced on a HiSeq2000 (Illumina) using 40nt single end reads.

treatment_protocol: Zebrafish 5 dpf larvae (100-1,000 per sample) were anesthetized in 0.1% tricaine.

tag: genetic background

value: AB/Tubingen (TAB5/14)

tag: transgene

value: wild-type mitfa; half tp53_M214K/+, half tp53_+/+


title: SUS-NEG-31

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using HTSeq-count software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files

source_name: Blood

extract_protocol:
Blood RNA from 6–7 individual mice per group was used in this study. Male mice submandibular blood was collected using 20-G hypodermic needles into EDTA-coated tubes. The tubes were centrifuged at 1000xg for 20 min at 4°C, and 100 μl of the blood cell fractions were put in RNAprotect animal blood tubes (Qiagen,) and stored at -80°C. Total RNA, including miRNAs, was extracted using RNeasy Protect animal blood kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies) and RNA integrity was checked using 4200 TapeStation.
rRNA depletion along with globin depletion was performed using QIAGEN FastSelect rRNA HMR/Globin Kit. RNA-seq library preparation used NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs were fragmented for 15 min at 94°C. The first and second cDNA strands were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends, and a universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using Agilent Tapestation 4200 and quantified using Qubit 2.0 Fluorometer. Sequencing libraries were multiplexed and clustered on the Illumina HiSeq instrument according to the manufacturer’s instructions. The samples were sequenced using a 150 paired end configuration.

value: Blood

tag: Sex

value: male

value: stress susceptible (SUS)

value: NEG (scrambled control oligonucleotide)


title: SUS-NEG-52


title: Arabidopsis thaliana jar1-11 C1

description: Replication 1

value: Control


title: SUS-NEG-28


title: wt3_1

description: Library of 92 cells

value: Ear skin

value: Mcpt5 Cre+/-


title: Arabidopsis thaliana WT Col-0 C2

description: Replication 2


title: SUS-NEG-16


title: wt2_4

description: Library of 92 cells


title: Arabidopsis thaliana WT Col-0 D4

description: Replication 1


title: wt2_3

description: Library of 92 cells


title: Arabidopsis thaliana WT Col-0 C3

description: Replication 3


title: wt2_1

description: Library of 92 cells


title: SUS-LNA-55

value: LNA (antisense oligonucleotide of microRNA 144-3p)


title: YAP.Mp rep 1


title: SUS-NEG-76


title: YAP.Mm rep 1

value: mitfa null (w2/w2); half tp53_M214K/+, half tp53_+/+


title: Arabidopsis thaliana WT Col-0 D6

description: Replication 3

value: Drought

value: Leaf