title: 3_29 RNA-seq

source_name: fusiform gyrus


title: 3_28 RNA-seq

status: Public on Dec 30 2019

type: SRA

city: Chengdu

first: keying

last: Lu

state: Sichuan

address: Wuhou

department: State Key Laboratory of Biotherapy

country: China

institute: Sichuan university

library_source: transcriptomic

data_processing:
RNA-seq: The fastq files generated by the Illumina workflow underwent read-level quality control before mapping, using FastQC (v0.11.4). For sample with poor read quality, quality trimming was performed using Trim Galore (v0.4.4, Quality Phred score cut-off: 30).The HISAT2 (v2.0.5, default parameters) was utilized for mapping the reads with the Mmul 8.0.1 reference genome and the Mmul 8.0.1.91 transcriptomic annotation GTF. Read counts of genes were generated using HTSeq (v0.6.1).
ATAC-seq: paired-end reads were aligned to the rhesus macaque genome (Mmul 8.0.1, downloaded from ENSEMBL), using bwa mem (v0.7.12) with -M parameter. First, PCR duplicates were removed using Picard (v1.119). Reads mapped to mitochondrial DNA were then excluded. Only uniquely mapped and properly paired reads with insert size less than 2kb and mapping quality over 30 were kept for downstream analysis. UCSC bedGraphToBigWig was used to generate bigWig files. Peak calling was performed with MACS2 (v2.1.0.20151222) using parameters ?--nomodel --nolambda --shift 100 --extsize 200 -B --SPMR?.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample; bigwig

molecule: total RNA

organism: Macaca mulatta

source_name: entorhinal cortex & perirhinal cortex

extract_protocol:
RNA-seq:RNA degradation and contamination was detected by 1% agarose gels; Then, RNA purity was checked using the kaiao K5500® Spectrophotometer (Kaiao, Beijing, China). The RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). ATAC-seq:A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
RNA-seq:A total amount of 3 ?g RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Epicentre Ribo-Zero? Gold Kits(Human/Mouse/Rat) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra? Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) . ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 ?L. Libraries were amplified for a total of 10?15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).

tag: macaque id

value: Rhesus 3

tag: tissue

value: brain

tag: gender

value: male

tag: age

value: 10 years


title: 3_26 RNA-seq

source_name: superior temporal gyrus


title: NS1_RNAseq

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

data_processing:
Quality control was done with an in-house R script
Adapter trimmng was done with reaper (EMBL-EBI)
Clean reads were mapped to Arabidopsis TAIR10 genome using bismark. To increase the coverage, mates from the paired-end were mapped as independent single end reads: R1 as directional and R2 and non-directional
Mapping sam files were deduplicated using samtools rmdup
bismark_methylation_extractor was used to do the methylation calling of cytosines covered by 3 or more reads
Methylation status of a cytosines was calculated as #C/(#C+#NC) where #C is the absolute number of reads in which C was converted to T by bisulfite treatment and NC is the absolute number of reads in which C was unafected by bisulphite treatment
For transcriptomic analysis, the raw RNA-seq libraries were mapped to the TAIR10 genome using STAR. In the analysis of differentially expressed genes, raw RNA-seq reads were mapped using bowtie2. Expression counts were generated using summarizeOverlaps using the AtRTD2 transcriptome or the TAIR10 TE annotation as references. Differential expression was detected using DESeq2 with absolute log2FoldChange >= 1 and FDR <= 0.05 as expression thresholds.
Subsequent analysis were performed in R. The gene and transposable element models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph of converted and non converted cytosines per methylation context, filtered by coverage < 3 after merging the biological replicates. Those files were used as input for the detection of DMRs
Supplementary_files_format_and_content: Text files of the matrix of normalized counts per gene transcript and TEs

organism: Arabidopsis thaliana

source_name: Mature leaf

growth_protocol: The Arabidopsis thaliana (L.) Heynh wild-type accession Columbia (Col) was used in all experiments. Seeds were sown on 0.5× basal salts Murashige and Skoog (MS) medium (Duchefa, Haarlem, The Netherlands), stratified at 4°C for one day and then transferred to growth chambers for germination at 20°C under short day (SD, 8 h light) photoperiods for ten days before being transferred to soil. Plants were grown for 42 days under short day (SD, 8 h light) photoperiods.

extract_protocol:
For the RNA-seq, RNA extraction and reverse transcription were performed as described previously (Alexandre et al., 2009) with minor modifications. DNA-free RNA was reverse-transcribed using a RevertAid First Strand cDNA Synthesis Kit (Fermentas, Helsingborg, Sweden).
The Ultraovation kit from NUGEN was used to perform the bisulphite conversion. RNA-seq libraries were constructed using the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: On the 42nd day, leaves number 5-6th from the rosette were individually covered with a black cloth mitten. Tissue was collected on the 48th day at 10:00. Non-senescent tissue corresponds to a mix of the uncovered leaves from the same plants.

tag: ecotype

value: Columbia

tag: genotype

value: WT

value: uncovered leaves

value: 48 days old

tag: biological replicate


title: S2_BSeq

library_source: genomic

molecule: genomic DNA

value: leaves no. 5-6th darkened for 5 days


title: 3_25 RNA-seq

source_name: inferior temporal gyrus


title: GF rep3

city: Gainesville

first: Christian

last: Jobin

state: Florida

department: Medicine

country: USA

institute: University of Florida

data_processing:
Reads were quality filtered at Q20 and trimmed to remove remaining adaptors using Trimmomatic version 0.36
Aligned to Illumina iGenome Mus musculus GRCm38 reference genome using Tophat version 2.1.1 utilizing Bowtie2 version 2.3.0 following the approach of Gilad and Mizrahi-Man (Reanalysis of mouse ENCODE comparative gene expression data. F1000Res 4, 121 (2015))
cuffquant was used to perform transcript quantification and exported the raw counts (un-normalized counts) to text files. The Raw counts were then imported to edgeR version 3.16.5 for detecting differentially expressed genes.
Genome_build: Illumina iGenome Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited text files of EdgeR normalized expression

organism: Mus musculus

source_name: colon

extract_protocol:
mirVana miRNA isolation kit, with phenol (AM1560, ThermoFisher Scientific) according to the manufacturer’s instructions, with the addition of a ~ 1:1 mix of 1mm acid-washed glass beads and 0.1mm zirconia beads and a Precellys24 (Bertin Instruments) bead beater for tissue disruption and lysis. Extracted RNA was treated with the Turbo DNA-free Kit (AM1907, Ambion) to remove DNA.
ScriptSeq v2 RNASeq Library Preparation Kit (SSV21124, Illumina)

treatment_protocol: biofilm-negative , biofilm-positive, no treatment

tag: strain

tag: treatment

value: no treatment


title: 4_38 RNA-seq

source_name: pons

value: Rhesus 4

value: female

value: 3.2 years


title: BF-T rep5

value: pooled tissue-derived microbes from biofilm-positive tumor tissue collected from CRC patients


title: 3_38 RNA-seq


title: S1_BSeq


title: BF-bx rep5

value: pooled tissue-derived microbes from biofilm-negative tissue collected from healthy patients via colonoscopy biopsy


title: GF rep2


title: 3_33 RNA-seq

source_name: anterior cingular gyrus


title: 3_23 RNA-seq

source_name: inferior occipital gyrus


title: 3_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 3_32 RNA-seq

source_name: posterior cingular gyrus


title: BF-T rep4


title: NS1_BSeq


title: BF-T rep3


title: 3_21 RNA-seq

source_name: anterior superior occipital gyrus


title: BF-bx rep3


title: 3_20 RNA-seq

source_name: cuneus gyrus


title: BF-bx rep4


title: BF-T rep2


title: 3_19 RNA-seq

source_name: annectant gyri, in macaque


title: 3_24 RNA-seq

source_name: occipito-temporal gyrus


title: BF-bx rep1


title: BF-bx rep2


title: NS2_BSeq


title: 3_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 3_16 RNA-seq

source_name: Intraparietal sulcus


title: 3_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 6_46 ATAC-Seq

data_processing:
ATAC-seq: paired-end reads were aligned to the rhesus macaque genome (Mmul 8.0.1, downloaded from ENSEMBL), using bwa mem (v0.7.12) with -M parameter. First, PCR duplicates were removed using Picard (v1.119). Reads mapped to mitochondrial DNA were then excluded. Only uniquely mapped and properly paired reads with insert size less than 2kb and mapping quality over 30 were kept for downstream analysis.  ATAC-seq peak calling was performed with Genrich (v0.6, available at https://github.com/jsh58/Genrich, parameters: -r -m 30 -q 0.05 -a 200 -j -y -e MT,Y -b) for each region. The BED files recording ATAC-seq signals were converted to BedGraph using “bedtools genomecov” and scaled by a factor of 1,000,000/LibrarySize. Then the scaled BedGraph files were converted to BigWig files using bedGraphToBigWig for genome visualization.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: bigwig

extract_protocol:
A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).
ATAC-seq:A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).

value: Rhesus 6

tag: age(years)


title: 4_46 ATAC-Seq


title: 7_46 ATAC-Seq

value: Rhesus 7


title: 10_46 ATAC-Seq

value: Rhesus 10


title: 8_46 ATAC-Seq

value: Rhesus 8

value: brain


title: siL2 12h rapa 2

type: RNA

city: Heidelberg

first: Marcel

last: Tiebe

state: Germany

address: Humboldtstr., 18

country: Germany

institute: DKFZ Heidelberg

hyb_protocol: Standard Illumina Hybridisation Protocol   /  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)  /  1,5 ug of cRNA were hybridized for 17 hr at 58°C on Illumina Mouse (WG-6_V2)-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

source_name: p53-/- TSC2-/- mouse embryonic fibroblast cell lines

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 500ng total RNA / Label: Biotin, Cy3-Streptavidin

growth_protocol: Cells are grown in DMEM (4.5g/L Glucose, L-Glutamine, #41965-039 GIBCO) with 10% FBS and Pen-Strep

extract_protocol: RNA was isolated with TRIZOL standard protocol.

treatment_protocol: 3 days of siRNA knockdown, then 12 hours of 20nM Rapamycin treatment or 12 hours of EtOH treatment as control

tag: rapamycin

value: 12 hours 20nM rapamycin

tag: sirna

value: Crebl2 siRNA

value: TSC2 null mouse embryonic fibroblast cell line


title: siL2 12h rapa 1


title: GF rep1


title: 3_14 RNA-seq

source_name: superior parietal lobule

value: Rhesus 3

value: male

value: 10 years


title: 2_46 ATAC-Seq

value: Rhesus 2


title: 11_32 ATAC-seq

value: Rhesus 11

value: 9.8 years


title: siL2 12h rapa 3


title: siL2 ctrl 3

value: Ethanol


title: BF-T rep1

value: pooled tissue-derived microbes from biofilm-positive tumor tissue collected from CRC patients


title: 3_18 RNA-seq

source_name: AG, angular gyrus


title: 11_25 ATAC-seq

source_name: inferior temporal gyrus

value: female


title: 3_13 RNA-seq

source_name: inferior postcentral gyrus


title: 11_46 ATAC-Seq


title: 11_14 ATAC-seq


title: siL2 ctrl 1


title: Luc 12h rapa 3

value: Luciferase siRNA


title: 10_25 ATAC-seq

value: 5 years


title: 10_32 ATAC-seq

value: Rhesus 10


title: 3_12 RNA-seq

source_name: superior postcentral gyrus


title: 3_11 RNA-seq

source_name: inferior precentral gyrus


title: 3_10 RNA-seq

source_name: superior precentral gyrus


title: 8_32 ATAC-seq

value: Rhesus 8

value: 3.8 years


title: 10_14 ATAC-seq

value: brain


title: Luc 12h rapa 2

value: 12 hours 20nM rapamycin


title: 8_22 ATAC-seq

source_name: posterior superior occipital gyrus


title: 8_25 ATAC-seq


title: 8_2 ATAC-seq

source_name: middle frontal gyrus


title: 3_9 RNA-seq

source_name: insula


title: Luc 12h rapa 1

value: TSC2 null mouse embryonic fibroblast cell line


title: Luc ctrl 2


title: 7_25 ATAC-seq

value: Rhesus 7

value: 4 years


title: CRISPR_mut_enhancer_rep1

city: Ciudad de Mexico

first: Felix

last: Recillas-Targa

address: Circuito Exterior s/n Ciudad Universitaria

department: Genetica Molecular

country: Mexico

institute: Instituto de Fisiologia Celular, UNAM

description: CRISPR mutant clone. Deletion of  intronic enhancer of Notch

data_processing:
Library strategy: Hi-C
Individual in silico mutant genomes were built for all CRISPR mutants to allow for precise mapping of reads without gaps. The sequence of breakpoints generated at deletion sites for each CRISPR mutant (as determined by Sanger Sequencing) were used to replace the wild-type sequence for the resulting mutant sequence in the chromosome X using R. A specific index for each mutant genome was build using Bowtie2. Also, mutant genomes were used to generate mutant specific MboI digestion files for subsequent analysis using HiC-Pro digest_genome.py
Mapping, filtering, correction and generation of Hi-C matrices were done using HiC-Pro. Briefly, read pairs were mapped independently to the wild-type or mutant genomes generated in silico using Bowtie2 with HiC-Pro default parameters. Replicates for each condition were merged. After filtering, valid-pairs were used to generate raw and ICE normalized matrices at 1 kb, 5 kb, 20 kb and 100 kb bin resolution. To correct for differences in sequencing depth matrices were normalized by the smallest number of valid-read pairs.
Genome_build: Drosophila melanogaster 6 (dm6)
Supplementary_files_format_and_content: Sparse normalized hi-c matrices for merged samples of each genotype at 1kb, 5kb and 20kb resolution are provided as proccessed data files

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: Drosophila S2R+ cells were cultured at 25°C in Schneider’s Drosophila Medium (Thermofisher) supplemented with 10% FBS (Biowest) and penicillin/streptomycin (Invitrogen)

extract_protocol: in nucleus Hi-C libraries were generated for S2R+ wild-type cells and CRISPR mutants at least in duplicates using an in nucleus Hi-C protocol with minor modifications for S2R+ cells (Rubín et al 2017). Briefly, 40x106 S2R+ cells were fixed with formaldehyde at a final concentration of 2% for 10 minutes at room temperature and fixing reaction was stopped by adding 1M Glycine for 5 minutes rocking. Cells were washed with cold-PBS and flash frozen for short-term storage at -70°C or used immediately for subsequent experiments. The genomes were digested with MboI (NEB) and 5’ overhangs were filled with Biotin-14-dATP (Invitrogen). Hi-C libraries were sequenced at the Babraham Institute sequencing facility.

tag: cell type

value: late embryonic stage derived cells


title: 7_32 ATAC-seq

source_name: posterior cingular gyrus

value: male


title: 3_8 RNA-seq

source_name: medial orbital gyrus

value: Rhesus 3

value: 10 years


title: 7_22 ATAC-seq


title: 3_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 7_14 ATAC-seq


title: CRISPR_5pN_755_rep1

description: CRISPR mutant clone. Deletion of 755 base pairs 5’ of Notch


title: 6_32 ATAC-seq

value: Rhesus 6


title: 6_22 ATAC-seq


title: CRISPR_mut_enhancer_rep2


title: 6_25 ATAC-seq


title: Luc ctrl 1

value: Ethanol


title: CRISPR_5pN_343_rep2

description: CRISPR mutant clone. Deletion of 343 base pairs 5’ of Notch


title: 3_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 3_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: siL2 ctrl 2

source_name: p53-/- TSC2-/- mouse embryonic fibroblast cell lines

value: Crebl2 siRNA


title: 6_14 ATAC-seq

source_name: superior parietal lobule

value: female


title: CRISPR_5pN_755_rep2


title: CRISPR_5pN_343_rep1


title: 4_32 ATAC-seq

value: Rhesus 4

value: 3.2 years


title: CRISPR_5pN_183_rep2

description: CRISPR mutant clone. Deletion of 183 base pairs 5’ of Notch


title: 4_14 ATAC-seq


title: 3_3 RNA-seq

source_name: inferior frontal gyrus


title: 7_2 ATAC-seq


title: CRISPR_5pN_183_rep1


title: 3_22 ATAC-seq


title: 3_32 ATAC-seq


title: 3_4 RNA-seq

source_name: posterior superior frontal gyrus


title: CRISPR_5pN_102_rep2

description: CRISPR mutant clone. Deletion of 102 base pairs 5’ of Notch


title: 3_2 ATAC-seq


title: 3_1 RNA-seq

source_name: Olfactory bulb


title: 3_14 ATAC-seq


title: CRISPR_5pN_102_rep1


title: Cloned_array_oligo_library_forward

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

description:
Amplication from cloned library
ForwardReverse_sequences_coordinates.tsv

data_processing:
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software. Multiplexed paired end (PE) Illumina sequencing data was split based on sample index allowing up to zero substitutions in the barcode sequence. In some cases, technical replicates were concatenated to achieve sufficient read counts.
The MPRAflow pipeline (Gordon et al, 2019), freely available on Github, was used to process the MPRA data. A brief overview of this pipeline is described here:
For oligo validation, consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). For RNA/DNA counts, sequences were matched against the designed barcode sequences.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
To determine the RNA/DNA ratios per insert, we summed up the counts of all barcodes contributing and determined the ratio of the average normalized counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: *elements.fa (FASTA) and *sequences_coordinates.tsv (tab-separated value) files contain all designed oligo sequences for barcode association mapping, along with chromosomal coordinates of each element, and element type (positive control, negative control, or other). *assignments.tsv.gz files contain the mappings between barcodes and their associated element, along with barcode counts supporting the association. *ActivityRatios*.tsv files contain RNA/DNA ratios for individual replicates or with replicates averaged.

molecule: other

organism: Homo sapiens

source_name: oligo array synthesis

growth_protocol: Array-synthesized 230bp oligos (Agilent Technologies) were synthesized either containing the complete construct to be cloned or as overlapping fragments for Multiplex Pairwise Assembly or Hierarchical Multiplex Pairwise Assembly.

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
For each RNA replicate, 3x500ng was reverse transcribed with Superscript IV (Invitrogen) using a primer downstream of the barcode, which contained a UMI. The resulting cDNA was pooled and split into 8 reactions, amplified with Kapa Robust polymerase for 3 cycles using an indexed P5 primer and P7. PCR products are then cleaned up with AMPure XP beads (Beckman Coulter) to remove the primers and concentrate the products. These products underwent a second round of amplification in 6 reactions per replicate and followed in real time with Sybr Green. All reactions were pooled at this point, cleaned up with AMPure CP beads, run on an agarose gel, and submitted for sequencing.

treatment_protocol: 2.4million cells were seeded in 10cm dishes. For plasmid-based MPRAs, the cells were transfected with 10 ug of plasmid libraries (HSS, ORI, and pGL4) using X-tremeGENE HP (Roche) with an Xtreme-GENE:DNA ratio of 2:1. For the lentiMPRAs, cels were infected with lentiviral libraries (5’/5’ WT/MT, 5’/3’ WT/MT, and 3’/3’ WT/MT) along with 8ug/ml polybrene, with the estimated MOI of 50 for wild-type and 100 for mutant libraries. Cells were incubated for 3 days. All experiments for nine libraries were carried out simultaneously to minimize batch effect. Three independent replicate cultures were transfected on different days.

tag: cell line

value: cloned oligonucleotide library

value: 10-beta electrocompetent E. coli (C3020)


title: WT_rep2

description: Wild-type cells

value: Wild-type


title: WT_rep3

description: Wild-type cells


title: 6_2 ATAC-seq

value: brain


title: 2_50 RNA-seq

source_name: putamen

value: Rhesus 2


title: enh_rep2_RNAseq

data_processing:
RNA-seq data was analyzed using Salmon and DESeq2. To estimate transcript-level abundance for each dataset Salmon (v0.10.2) was used  with a specific index for the Drosophila melanogaster transcriptome (dm6) and options –validateMappings and --gcBias. Quantification data from Salmon was then imported into R and we created an input table with gene level quantification data as input for DESeq2. We tested for differential expression (DE) between wild-type and the CRISPR enhancer mutant using DESeq2. We called DE at the gene level with a fold-change of at least 0.5 and a corrected p-value of <0.05.  To create signal tracks from RNA-seq data, sequencing reads were mapped against the Drosophila melanogaster genome (dm6) using Bowtie2 with default parameters. SAM files were converted into BAM files using samtools view. BAM files were sorted (samtools sort) and indexed (samtools index). deepTools v3.3.0 was used to calculate Pearson Correlation and PCA for all datasets. BAM files from replicates were merged due to high correlation (Pearson Correlation >0.9) and BAM files from merged experiments were used to create signal tracks with bamCoverage –normalizeUsing BPM
Genome_build: Drosophila melanogaster 6 (dm6)
Supplementary_files_format_and_content: singal tracks for wild-type and enhancer mutant in bigwig format

extract_protocol: Total RNA was extracted from wild-type and enhancer mutants in duplicate using TRIzol reagent following manufacturer’s instructions. Total RNA libraries for all samples were generated and sequenced by Novogene. Two independent libraries per condition were sequenced in a HiSeq 4000 platform paired-end 150 bp.

value: CRISPR-mutant-enhancer


title: 3_2 RNA-seq


title: WT_rep1

description: Wild-type cells


title: 2_49 RNA-seq

source_name: caudate nucleus


title: 2_48 RNA-seq

source_name: accumbens nucleus


title: WT_rep2_RNAseq


title: Healthy Donor # 30a  (mRNA)

city: Setia Alam

first: Ezalia

last: Esa

address: NIH

department: Haematology unit

country: Malaysia

institute: Institute for Medical Research

description: 30a ctrl

hyb_protocol: Standard Nanostring protocol

scan_protocol: After hybridization of probe, the miRNA counts were measured using Nanostring digital analyser.

data_processing: Data generated by the digital analyser is interpreted by Nanostring in-house software, the nSolver. Raw data was normalised by in-house housekeeping genes provided by Nanostring.

label: Biotin

source_name: donor

label_protocol: Quantification of mRNA profiles was done using the nCounter PanCancer pathways panel kit (Nanostring Technologies, Seattle, WA, USA), following the manufacturer’s protocols. The product utilizes the direct ligation of oligonucleotide tags onto total RNA, thus allowing miRNA and mRNA to be directly measured with great specificity and sensitivity while eliminating the use of reverse transcriptase or amplification.

extract_protocol: Buffy coat was separated from the peripheral blood using Ficoll-Paque density gradient media. Buffy coat is lysed using Qiazol lysis reagent (Qiagen, Hilden, Germany) followed by total RNA extraction using miRNeasy kit (Qiagen, Hilden, Germany).

tag: individual

value: Donor # 30a

tag: disease state

value: Healthy

value: Blood

value: Female

tag: ethnicity

value: Malay


title: Healthy Donor # 25a  (mRNA)

description: 25a ctrl

value: Donor # 25a


title: X11_WT_YS_MAC1

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description:
pMAC_Ys
RUN214_RUN218.A-11_WT_YS_MAC1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (Version25.06.2015) whole genome using STAR aligner.
differential expression analyses of read counts was perforemed using EdgeR
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method proposed by Robinson and Oshlack (Robinson & Oshlack, 2010).
Supplementary_files_format_and_content: comma-separated values (csv) text file, the processed data file includes Gene Identifier, gene name, description, normalized count (between-sample-normalization, TMM)

source_name: primitive macrophage fetal yolk sack

extract_protocol:
Tissues were removed, cell were FACS sorted and 20,000-100,000cells were collected into TRIzol and frozen at -80°C till RNA extraction. TPhase separation was achieved with the addition of chloroform (Sigma), and total RNA was precipitated from the aqueous layer with isopropanol (Sigma) using glycogen (Roche) as a carrier
The TruSeq RNA Stranded sample kit (Illumina) was used to construct the sequencing libraries

tag: developmental stage

value: embryo

value: Yolk sack

value: primitive macrophage


title: WT_rep1_RNAseq

source_name: S2R+ cells

value: late embryonic stage derived cells


title: X10_WT_FL_MON_AM2

description:
mAM_fLiMo_2
20150904.A-10_WT_FL_MON_AM2

source_name: fetal liver Monocyte transferred to lung

value: adult

tag: tissue

value: lung


title: enh_rep1_RNAseq


title: 2_52 RNA-seq

source_name: pituitarium

tag: macaque id

tag: gender

value: male

value: 10 years


title: Donor 3 HS8

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: 8A Biomedical Grove

department: Glycotherapeutics Group

country: Singapore

institute: Institute of Medical Biology

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation after backgorund subtraction with GenomeStudio (Illumina)

label: biotin

source_name: human bone marrow-mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA amplification kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: agent

value: heparan sulfate

tag: ethinicty

value: Chinese

tag: age

value: bone marrow-mesenchymal stem cells


title: Donor 2 Control

description: replicate 1

value: control


title: Donor 1 HS8

description: replicate 1


title: 2_45 RNA-seq

source_name: dentate gyrus

value: Rhesus 2

value: brain


title: 2_51 RNA-seq

source_name: globus pallidus


title: 2_46 RNA-seq


title: X9_WT_FL_MON_AM1

description:
mAM_fLiMo_1
RUN214_RUN218.A-9_WT_FL_MON_AM1

tag: strain

value: fetal liver Monocyte transferred to lung


title: X8_WT_FL_MAC_AM2

description:
mAM_fLiMa_2
RUN214_RUN218.A-8_WT_FL_MAC_AM2

source_name: fetal liver Macrophage transferred to lung


title: Donor 1 Control

description: replicate 1


title: 2_44 RNA-seq

source_name: amygdala


title: Donor 3 Control

description: replicate 1


title: X13_WT_YS_MAC_AM1

description:
mAM_Ys
RUN214_RUN218.A-13_WT_YS_MAC_AM1

source_name: fetal yolk sack macrophage transferred to lung


title: 2_43 RNA-seq

description: Sample was excluded from downstream expression analysis and therefore not included in Rhesus_RNA_gene_count.txt

source_name: midbrain


title: 2_47 RNA-seq


title: X6_WT_FL_MON2

description:
pMON_fLi_2
RUN214_RUN218.A-6_WT_FL_MON2

source_name: primitive monocyte fetal liver

value: liver

value: primitive monocyte


title: Donor 2 HS8

description: replicate 1


title: X5_WT_FL_MON1

description:
pMON_fLi_1
RUN214_RUN218.A-5_WT_FL_MON1

value: embryo


title: 2_42 RNA-seq

source_name: Substantia Nigra


title: X4_WT_FL_MAC2

description:
pMAC_fLi_2
RUN214_RUN218.A-4_WT_FL_MAC2

source_name: primitive macrophage fetal liver


title: 2_41 RNA-seq

source_name: Ventral tegmental area


title: X3_WT_FL_MAC1

description:
pMAC_fLi_1
20150904.A-3_WT_FL_MAC1


title: Healthy Donor # 56b  (mRNA)

description: 56b ctrl

value: Donor # 56b

value: Healthy

value: Blood

value: Male

value: Malay


title: Healthy Donor # 53b  (mRNA)

description: 53b ctrl

value: Donor # 53b


title: 2_40 RNA-seq

source_name: cerebellum vermis

value: male

value: 10 years


title: Healthy Donor # 46b  (mRNA)

description: 46b ctrl

source_name: donor

value: Donor # 46b

value: Chinese


title: Healthy Donor # 41b  (mRNA)

description: 41b ctrl

value: Donor # 41b


title: 2_39 RNA-seq

source_name: cerebellar cortex

value: Rhesus 2


title: Healthy Donor # 15b  (mRNA)

description: 15b ctrl

value: Donor # 15b

value: Female


title: Healthy Donor # 28b  (mRNA)

description: 28b ctrl

value: Donor # 28b


title: Healthy Donor # 14b  (mRNA)

description: 14b ctrl

value: Donor # 14b


title: 2_38 RNA-seq

source_name: pons

value: brain


title: X1_WT_AM1

description:
AM_1
20150904.A-1_WT_AM1

source_name: Macrophage adult lung

value: adult

value: lung

value: Macrophage


title: Healthy Donor # 12b  (mRNA)

description: 12b ctrl

value: Donor # 12b

value: Healthy

value: Blood

value: Male


title: B_Csf2_HZ_MO

description:
pMON_fLu
20141128.A-B_Csf2_HZ_MO

source_name: primitive monocyte fetal lung

value: embryo

value: primitive monocyte


title: A_Csf2_HZ_MP

description:
pMAC_fLu
20141128.A-A_Csf2_HZ_MP

source_name: primitive macrophage fetal lung

value: primitive macrophage


title: 2_37 RNA-seq

source_name: medulla oblongata

value: male

value: 10 years


title: Healthy Donor # 9b  (mRNA)

description: 9b ctrl

value: Donor # 9b

value: Malay


title: 2_36 RNA-seq

source_name: hypothalamus

value: Rhesus 2


title: 2_35 RNA-seq

source_name: thalamus


title: 2_34 RNA-seq

source_name: corpus callosum


title: Hepa1-6 Crebl2  2

data_processing:
Base call and quality scoring was done using RTA (1.18.64)
Quality filter and read trimming was done with "Trim Galore!" on the usegalaxy.org website on default settings, automatic detection of adapters (Galaxy Version 0.4.3.1)
Filtered reads were aligned using "TopHat" on the usegalaxy.org website (Galaxy Version 2.1.1) with default settings and using built-in genome
Resulting BAM-files were counted using "htseq-count" on the usegalaxy.org website  (Galaxy Version 0.9.1), Mode "Union, Stranded "Yes", Minimum alignment quality "10", Feature type "exon", otherwise default settings
Genome_build: mm9
Supplementary_files_format_and_content: TAB delimited text file with the raw readcounts given out from "htseq-count" for each biological sample, counted with "mouse_genes_GENCODEVM11_GRCm38_basic_GTF"

source_name: Hepa1-6 hepatoma cell line

extract_protocol:
RNA extraction with RNAeasy Kit (Qiagen, #74104) and treated with RNA-free DNAse (Qiagen)
Library preparation was done using the TruSeq® Stranded Total RNA Library Prep Kit (#20020597) according to the manufacturer's instructions.

treatment_protocol: 3 days of siRNA knockdown, using Lipofectamine RNAiMAX from Invitrogen (#13778)

value: hepatoma cell line


title: Healthy Donor # 6b  (mRNA)

description: 6b ctrl

value: Donor # 6b

value: Female

value: Chinese


title: Healthy Donor # 8b  (mRNA)

description: 8b ctrl

value: Donor # 8b


title: Healthy Donor # 3b  (mRNA)

description: 3b ctrl

value: Donor # 3b


title: X2_WT_AM2

description:
AM_2
RUN214_RUN218.A-2_WT_AM2

value: adult

value: lung

value: Macrophage


title: 2_32 RNA-seq

source_name: posterior cingular gyrus

value: brain


title: Hepa1-6 Luc 3

value: Renilla Luciferase


title: Healthy Donor # 1b  (mRNA)

description: 1b ctrl

value: Donor # 1b

value: Healthy

value: Blood


title: Healthy Donor # 30  (mRNA)

description: 30 ctrl

value: Donor # 30


title: 2_33 RNA-seq

source_name: anterior cingular gyrus

value: male

value: 10 years


title: Hepa1-6 Crebl2  1

value: hepatoma cell line


title: 2_31 RNA-seq

source_name: lingual gyrus

value: Rhesus 2


title: Hepa1-6 Luc 2


title: Healthy Donor # 25  (mRNA)

description: 25 ctrl

value: Donor # 25

value: Female

value: Malay


title: Healthy Donor # 28  (mRNA)

description: 28 ctrl

value: Donor # 28


title: Hepa1-6 Luc 1


title: 2_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 2_29 RNA-seq

source_name: fusiform gyrus


title: C2C12 Crebl2 Rapa 3

source_name: C2C12 myoblast cell line

value: Crebl2 siRNA 1

value: Rapamycin 20nM

value: myoblast cell line


title: C2C12 Crebl2 Rapa 2


title: Hepa1-6 Crebl2  3


title: Healthy Donor # 15  (mRNA)

description: 15 ctrl

source_name: donor

value: Donor # 15

value: Male


title: 2_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex

value: brain


title: C2C12 Crebl2 Rapa 1


title: Healthy Donor # 11  (mRNA)

description: 11 ctrl

value: Donor # 11

value: Healthy


title: 2_26 RNA-seq

source_name: superior temporal gyrus


title: 2_27 RNA-seq

source_name: temporal polar gyrus


title: Healthy Donor # 9 (mRNA)

description: 9 ctrl

value: Donor # 9

value: Blood

value: Chinese


title: Healthy Donor # 7 (mRNA)

description: 7 ctrl

value: Donor # 7


title: Healthy Donor # 16  (mRNA)

description: 16 ctrl

value: Donor # 16

value: Indian


title: 2_23 RNA-seq

source_name: inferior occipital gyrus

value: Rhesus 2

value: male

value: 10 years


title: Healthy Donor # 8  (mRNA)

description: 8 ctrl

value: Donor # 8


title: 2_25 RNA-seq

source_name: inferior temporal gyrus


title: Tac

city: Guangzhou

first: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

data_processing:
Cell Ranger 3.0 were used process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Compress files of bacodes, geatures and matrix.

source_name: CD45+ cells from heart

extract_protocol:
Heart tissue were digested, filtered and incubatied by CD45 fluorescent antibody. CD45+ cells were sorted by flow cytometry, then samples were processed through multiple GEM wells to generate  libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 10 weeks

tag: genotype

value: wild type

tag: condition

value: transverse aortic constriction (TAC)

value: heart

value: CD45+ cells


title: Sham

value: sham


title: C2C12 Luc Rapa 3

value: Renilla Luciferase

tag: rapamycin

value: Rapamycin 20nM

value: myoblast cell line


title: 2_22 RNA-seq

source_name: posterior superior occipital gyrus

value: brain


title: C2C12 Crebl2 EtOH 3

tag: sirna

value: Crebl2 siRNA 1

value: Ethanol


title: 2_24 RNA-seq

source_name: occipito-temporal gyrus


title: C2C12 Crebl2 EtOH 2


title: C2C12 Crebl2 EtOH 1


title: 2_21 RNA-seq

source_name: anterior superior occipital gyrus


title: C2C12 Luc Rapa 2


title: C2C12 Luc Rapa 1


title: 2_20 RNA-seq

source_name: cuneus gyrus


title: C2C12 Luc EtOH 3


title: dsGFP_F1_B2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description: Embryos injected with dsRNA targeting GFP at zygote, collected at 8-cell stage

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads with adaptors, low-complexity or low-quality were trimmed by trim_galore to generate clean reads.
Clean reads were mapped to mouse genome (mm10) using STAR.
FPKM (Fragments Per Kilobase per Million mapped reads) of Refseq genes were calculated by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files of gene names and tpm values for each sample.

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/9J)

growth_protocol: KSOM medium

extract_protocol:
8 cell embryos were first treated with acidic Tyrode solution to remove the zona pellucida and then transferred into M2 medium. After washed in PBS without Ca2+ and Mg2+, 10 embryos were manually picked into cell lysis buffer with a mouse pipette.
Embryo poly-A mRNA were reverse transcribed by SuperScript II and pre-amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by library generation using TruePrep DNA Library Prep Kit V2 for illumina Kit (Vazyme, TD501-503).

treatment_protocol: Embryos injected with dsRNA targeting GFP (control),Tfap2c, Tead4, or Tfap2c and Tead4.

tag: conditions

value: 8-cell embryos


title: Tead4KD_F1_B2

description: Embryos injected with dsRNA targeting Tead4 at zygote, collected at 8-cell stage

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/7J)


title: dsGFP_F1_B1

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/8J)

value: Embryos injected with dsRNA targeting GFP at zygote, collected at 8-cell stage


title: Newly diagnosed CN-AML Patient # 95  (mRNA)

description: 95 case

source_name: primary leukemia

value: Patient # 95

value: Newly diagnosed with CN-AML

value: Blood

value: Male

value: Chinese


title: Newly diagnosed CN-AML Patient # 97  (mRNA)

description: 97 case

value: Patient # 97

value: Female


title: C2C12 Luc EtOH 2

tag: cell line


title: 2_19 RNA-seq

source_name: annectant gyri, in macaque

value: Rhesus 2

value: male

value: 10 years


title: Newly diagnosed CN-AML Patient # 105  (mRNA)

description: 105 case

tag: individual

value: Patient # 105

value: Malay


title: Newly diagnosed CN-AML Patient # 106  (mRNA)

description: 106 case

value: Patient # 106

tag: disease state


title: Newly diagnosed CN-AML Patient # 103  (mRNA)

description: 103 case

value: Patient # 103

tag: ethnicity


title: Tead4KD_F1_B1

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/6J)

value: Embryos injected with dsRNA targeting Tead4 at zygote, collected at 8-cell stage


title: 2_18 RNA-seq

source_name: AG, angular gyrus

value: brain


title: Newly diagnosed CN-AML Patient # 91 (mRNA)

description: 91 case

value: Patient # 91


title: C2C12 Luc EtOH 1

source_name: C2C12 myoblast cell line

value: Renilla Luciferase

value: Ethanol

value: myoblast cell line


title: Tfap2cKD_F1_B2

description: Embryos injected with dsRNA targeting Tfap2c at zygote, collected at 8-cell stage

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/5J)

value: 8-cell embryos


title: Newly diagnosed CN-AML Patient # 88  (mRNA)

description: 88 case

value: Patient # 88

value: Newly diagnosed with CN-AML

value: Blood

value: Male


title: Newly diagnosed CN-AML Patient # 86  (mRNA)

description: 86 case

value: Patient # 86


title: T-bet-KO iTreg input

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Basecalls performed using CASAVA
Reads were filtered to remove adapters using fastq-mcf and for quality using seqkt
Reads were then aligned to the mouse genome (mm9) with Bowtie2 (default settings)
Regions of significant enrichment (10^-7) were identified using MACS version 1.4 (Zhang et al., 2008) using input as background, with the setting –keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks derived from analyses

source_name: iTreg

growth_protocol: CD4+ T cells from spleens and lymph nodes of 4- to 10-wk-old mice were purified by CD4 positive selection (Miltenyi Biotec) followed by sorting of naive CD4+CD25-CD62LhighCD44low cells using a FACSAria II (BD Biosciences). Cells were activated by plate-bound anti-CD3 and anti-CD28 (both 10 ug/ml; clones 145-2C11 and 37.51, respectively; Bio X Cell)

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent.  Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 10 µl of purified anti-T-bet serum (9856; Jenner et al., PNAS 2009). Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNAseA, proteinase K and phenol:chloroform extraction followed by ethanol precipitation
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 35 or 50 bp single-end read sequencing with an Illumina GAIIx or HiSeq 2000 sequencer

treatment_protocol: iTreg cells were generated by culturing in recombinant human TGF-β1 (33 ng/ml) and IL-2 (20 ng/ml; R & D Systems) for 7 days

tag: cell type

value: iTreg

value: Balb/c

tag: chip antibody

value: Custom rabbit anti-T-bet serum (9856)


title: 2_17 RNA-seq

source_name: anterior/posterior marginal gyrus

tag: macaque id

value: Rhesus 2

tag: tissue

value: male

value: 10 years


title: Tfap2cKD_F1_B1

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/4J)

value: Embryos injected with dsRNA targeting Tfap2c at zygote, collected at 8-cell stage


title: WT iTreg input replicate 2


title: Newly diagnosed CN-AML Patient # 85  (mRNA)

description: 85 case

value: Patient # 85

tag: gender

value: Female

value: Chinese


title: T-bet-KO iTreg T-bet ChIP


title: 2_15 RNA-seq

source_name: posterior superior parietal gyrus

value: brain


title: 2_16 RNA-seq

source_name: Intraparietal sulcus


title: DoubleKD_F1_B2

description: Embryos injected with dsRNA targeting Tfap2c+Tead4 at zygote, collected at 8-cell stage

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/3J)

value: 8-cell embryos


title: Newly diagnosed CN-AML Patient # 82  (mRNA)

description: 82 case

value: Patient # 82


title: DoubleKD_F1_B1

source_name: Mouse embryo (F1 :♀C57BL/6J×DBA/2J ♂C57BL/6J×DBA/2J)

value: Embryos injected with dsRNA targeting Tfap2c+Tead4 at zygote, collected at 8-cell stage


title: Newly diagnosed CN-AML Patient # 80 (mRNA)

description: 80 case

value: Patient # 80

value: Newly diagnosed with CN-AML

value: Blood

value: Malay


title: WT iTreg T-bet ChIP replicate 2

value: iTreg

value: Balb/c


title: dsGFP_F1_A2

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/10J)

value: Embryos injected with dsRNA targeting GFP at zygote, collected at 8-cell stage


title: 2_13 RNA-seq

source_name: inferior postcentral gyrus

value: Rhesus 2

value: male


title: dsGFP_F1_A1

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/9J)


title: 2_12 RNA-seq

source_name: superior postcentral gyrus

value: 10 years


title: Screening 1 LLL-Y2H

city: Wuhan

first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: Yeast two hybrid screening

data_processing:
Data filtering: The raw sequencing reads without complete attL site “TAGCGTGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGGCGTTGAC” and flanking MmeI recognition sites “TCCGAC” were excluded.  Reads with adapters sequences was also excluded. Custom perl script was used.
Trimming: The remaining reads was trimmed to be two side subreads by removing the middle attL site and MmeI recognition sites.
Aligning: The two subreads libraries were aligned to bait library and prey library respectively using BLAST+. The parameter "task option" was set as "blastn-short". Only unambiguously aligned reads without mismatch were retained.
Counting: Interaction frequency of a protein pair was calculated by counting the sequencing pairs that could be aligned to them.
Revising: Proteins with too many interactors were removed from the interaction network (cutoff was set as 45 here). Interactions with too little supporting reads were also removed (cutoff was set as 5 here).
Supplementary_files_format_and_content: tab-delimited text files include interactions between tb protein name and host protein name.

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: Lung, brain and Whole bacteria

growth_protocol: Clontech Yeast Protocols Handbook

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

treatment_protocol: Yeast plasmids were extracted using the Yeast Plasmid Kit

tag: mouse tissue

value: lung and brain

tag: bacteria tissue

value: whole bacteria

tag: mouse age

value: post natal day 45

tag: mouse strain

value: BALB/c

tag: bacteria strain


title: full library LLL-Y2H

description: Yeast two hybrid screening


title: Tead4KD_F1_A2

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/8J)

value: Embryos injected with dsRNA targeting Tead4 at zygote, collected at 8-cell stage

value: 8-cell embryos


title: 2_11 RNA-seq

source_name: inferior precentral gyrus

value: brain

tag: age


title: Tead4KD_F1_A1

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/7J)


title: Newly diagnosed CN-AML Patient # 76 (mRNA)

description: 76 case

source_name: primary leukemia

value: Patient # 76

value: Female


title: Newly diagnosed CN-AML Patient # 78 (mRNA)

description: 78 case

value: Patient # 78

value: Newly diagnosed with CN-AML

value: Blood


title: 2_10 RNA-seq

source_name: superior precentral gyrus


title: Tfap2cKD_F1_A2

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/6J)

value: Embryos injected with dsRNA targeting Tfap2c at zygote, collected at 8-cell stage


title: Newly diagnosed CN-AML Patient # 67 (mRNA)

description: 67 case

value: Patient # 67

value: Malay


title: 2_14 RNA-seq

source_name: superior parietal lobule

value: Rhesus 2

value: male


title: 2_9 RNA-seq

source_name: insula

value: 10 years


title: Newly diagnosed CN-AML Patient # 66 (mRNA)

description: 66 case

value: Patient # 66


title: DoubleKD_F1_A2

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/3J)

value: Embryos injected with dsRNA targeting Tfap2c+Tead4 at zygote, collected at 8-cell stage


title: Newly diagnosed CN-AML Patient # 63 (mRNA)

description: 63 case

value: Patient # 63


title: Screening 2 LLL-Y2H

description: Yeast two hybrid screening

value: lung and brain

value: whole bacteria

value: post natal day 45

value: BALB/c


title: DoubleKD_F1_A1

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/2J)

value: 8-cell embryos


title: 2_7 RNA-seq

source_name: ventromedial prefrontal cortex

value: brain


title: Newly diagnosed CN-AML Patient # 45 (mRNA)

description: 45 case

value: Patient # 45

value: Newly diagnosed with CN-AML

value: Female

value: Chinese


title: Newly diagnosed CN-AML Patient # 46 (mRNA)

description: 46 case

value: Patient # 46

value: Blood

value: Malay


title: Newly diagnosed CN-AML Patient # 43 (mRNA)

description: 43 case

value: Patient # 43

value: Male


title: 2_4 RNA-seq

source_name: posterior superior frontal gyrus

value: Rhesus 2

value: male

value: 10 years


title: 2_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: RNA Seq_Irx5 KO_rep3

city: Shanghai

first: Li

last: Jinsong

address: Yueyang Road

institute: SIBCB, CAS

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: day 4 differentiating BMSCs during osteoblastogenesis

growth_protocol: Bone marrow stromal cells from WT and Irx5 knockout mice were collected and passaged twice.  6 × 10^5 cells were seeded into a well of 6-well-plate and cultured in the osteoblast differentiation medium (a-MEM containing 10% FBS, 5 mM β-glycerophosphate (Sigma, G9422), 50 ug/ml L-ascorbic acid (Sigma, A5960) and 1% penicillin/streptomycin) for 4 days.

extract_protocol:
Cells were collected and 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.
Libraries were prepared according to Illumina's instructions

value: BMSCs from tibiae and femurs of 4-week-old Irx5 knockout mice

tag: strain


title: oligohydramnios_pregnant_women_rep4

first: hongchang

last: huang

state: Guangdong

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: oligohydramnios pregnant women

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol (Invitrogen, CA, USA) was used to extract total RNA from tissues following the standard protocol of manufacture’s protocol. Concentration and qualification of the isolated total RNA was assessed by Nanodrop 2001 spectrophotometer (Thermo Fisher Scientific, MA, USA).

treatment_protocol: The fetal membrane of a woman who had just given birth was quickly placed in liquid nitrogen in 30 minutes. Approximate 1cm3 of tissue block were ressected for grinding. Samples were grinded in a motor-driven homogenizer.

value: female

tag: tag

tag: sample type

value: oligohydramnios pregnant women


title: Tfap2cKD_F1_A1

source_name: Mouse embryo (F1 ♀C57BL/6J×CBA/J; ♂C57BL/6J×DBA/5J)

tag: conditions

value: Embryos injected with dsRNA targeting Tfap2c at zygote, collected at 8-cell stage

value: 8-cell embryos


title: oligohydramnios_pregnant_women_rep2


title: 2_5 RNA-seq

data_processing:
RNA-seq: The fastq files generated by the Illumina workflow underwent read-level quality control before mapping, using FastQC (v0.11.4). For sample with poor read quality, quality trimming was performed using Trim Galore (v0.4.4, Quality Phred score cut-off: 30).The HISAT2 (v2.0.5, default parameters) was utilized for mapping the reads with the Mmul 8.0.1 reference genome and the Mmul 8.0.1.91 transcriptomic annotation GTF. Read counts of genes were generated using HTSeq (v0.6.1).
ATAC-seq: paired-end reads were aligned to the rhesus macaque genome (Mmul 8.0.1, downloaded from ENSEMBL), using bwa mem (v0.7.12) with -M parameter. First, PCR duplicates were removed using Picard (v1.119). Reads mapped to mitochondrial DNA were then excluded. Only uniquely mapped and properly paired reads with insert size less than 2kb and mapping quality over 30 were kept for downstream analysis. UCSC bedGraphToBigWig was used to generate bigWig files. Peak calling was performed with MACS2 (v2.1.0.20151222) using parameters ?--nomodel --nolambda --shift 100 --extsize 200 -B --SPMR?.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample; bigwig

source_name: anterior superior frontal gyrus

extract_protocol:
RNA-seq:RNA degradation and contamination was detected by 1% agarose gels; Then, RNA purity was checked using the kaiao K5500® Spectrophotometer (Kaiao, Beijing, China). The RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). ATAC-seq:A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
RNA-seq:A total amount of 3 ?g RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Epicentre Ribo-Zero? Gold Kits(Human/Mouse/Rat) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra? Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) . ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 ?L. Libraries were amplified for a total of 10?15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).

value: brain


title: RNA Seq_Irx5 KO_rep1


title: Newly diagnosed CN-AML Patient # 35 (mRNA)

description: 35 case

tag: individual

value: Patient # 35

tag: disease state

value: Newly diagnosed with CN-AML


title: oligohydramnios_pregnant_women_rep5


title: Newly diagnosed CN-AML Patient # 34 (mRNA)

description: 34 case

value: Patient # 34

tag: ethnicity

value: Indian


title: Newly diagnosed CN-AML Patient # 29 (mRNA)

description: 29 case

value: Patient # 29

value: Blood


title: 2_8 RNA-seq

source_name: medial orbital gyrus


title: oligohydramnios_pregnant_women_rep3


title: normal_amniotic_fluid_control_rep5

source_name: normal amniotic fluid control

value: normal amniotic fluid control


title: 2_3 RNA-seq

source_name: inferior frontal gyrus


title: RNA Seq_WT_rep3

tag: cell type

value: BMSCs from tibiae and femurs of 4-week-old Wild-type mice


title: RNA Seq_WT_rep2

tag: passages


title: 2_2 RNA-seq

source_name: middle frontal gyrus

tag: macaque id

value: Rhesus 2

tag: tissue


title: 2_1 RNA-seq

source_name: Olfactory bulb

tag: gender

value: male


title: Newly diagnosed CN-AML Patient # 28 (mRNA)

description: 28 case

source_name: primary leukemia

value: Patient # 28

value: Male

value: Chinese


title: Newly diagnosed CN-AML Patient # 27 (mRNA)

description: 27 case

value: Patient # 27


title: DIA_19nt_2w_repA

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

institute: University of Washington

description: small RNA

data_processing:
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker-1 clipped and aligned to mouse hairpins from mirBase release 15 using bowtie (version 0.12.7) with 2 mismatches and command -- best
Genome_build: mm9, mirBase release 15
Supplementary_files_format_and_content: File of reads per million (RPM) mapped microRNA hits for mouse small RNA sequencing samples in tab delimited text format

source_name: Diaphragm

extract_protocol:
Liver samples were snap frozen in liquid nitrogen and ground into powder.  Samples were homogenized and RNA was extracted by Trizol
3ug of RNA for liver samples and 1ug of alll other samples were ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to 4nt barcoded adapters. Dual-ligated RNA was reverse transcribed, PCR amplified and size selected on 4% NuSieve (Lonza) agarose.  Small RNA sequencing was performed on the Illumina miSeq platform.

value: Diaphragm

tag: time after aav6-shrna

tag: stem


title: RNA Seq_WT_rep1


title: normal_amniotic_fluid_control_rep3

value: female


title: X7_WT_FL_MAC_AM1

description:
mAM_fLiMa_1
20150904.A-7_WT_FL_MAC_AM1

source_name: fetal liver Macrophage transferred to lung

tag: developmental stage

value: adult

value: lung


title: oligohydramnios_pregnant_women_rep1

value: oligohydramnios pregnant women


title: normal_amniotic_fluid_control_rep4


title: normal_amniotic_fluid_control_rep2


title: GLE_treated_rep3

status: Public on Dec 29 2019

first: Qilong

last: Chen

address: 1200, Cailun Road

institute: TCM center

description: GLE treated Hepa1-6-bearing C57 BL/6 mouse

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent, Santa Clara, CA, USA).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.

source_name: GLE treated mouse tumor, replicate 3

label_protocol: total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP

growth_protocol: Hepa1-6 cell was cultured in DMEM medium, supplemented with 10% fetal bovine serum, 100 U/ml penicillin-streptomycin mixed antibiotics at 37 °C in a humidified 5% CO2 incubator. The mice of were inoculated in the right flank, which with 0.1 ml of logarithmic phase Hepa1-6 cells.

extract_protocol: The total RNA were extracted using TRIzol reagent (Invitrogen, Grand Island, NY, USA) and quality evaluations were performed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: According to the conversion of the human clinical dosage and the mouse body surface area, the drug dose of mouse was calculated. The conversion coefficient of human and mouse was 9.1 (the human body weight was defined as 60 kg), and the total GLE dose of a 10 g mouse for one day was 0.023 g . The model group mice were treated with 0.9% NaCl, 0.2 ml per mouse, and once a day for 28 consecutive days.

value: tumor

tag: model

value: Hepa1-6-bearing C57BL/6

tag: treatment

value: GLE


title: GLE_treated_rep1

source_name: GLE treated mouse tumor, replicate 1

tag: age


title: GLE_treated_rep2

source_name: GLE treated mouse tumor, replicate 2


title: Model_rep1

description: Hepa1-6-bearing C57 BL/6 mouse model

source_name: Untreated mouse tumor, replicate 1


title: Re-Sub day 7 culutre, replicate 3, experiment set 3

city: Cleveland

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic, Lerner Research Institute

description:
Exp3_all.genes_counts_final.txt
ReSub_7d_3_exp3

data_processing:
Sequence reads are aligned to the reference genome using STAR
gene counts are derived from uniquely aligned reads using Subread:featureCount
Supplementary_files_format_and_content: genes_counts

source_name: colonic epithelial monolayer

growth_protocol: Colonic spheroids were passaged in L-WRN media for up to 30 generations. Spheroids were dissociated and plated onto Transwells pre-coated with 10% Matrigel to form an epithelial monolayer. In the first 7 days, L-WRN media was present in both the top and bottom compartment of Transwell. L-WRN media was then removed to create air-liquid interface (ALI). Monolayers were cultured under ALI conditions for up to 28 days. In some experimental settings, ALId21 monolayers were re-submerged with L-WRN media in the top compartment for various amount of time.

extract_protocol:
Rneasy micro kit (Qiagen) was used to extract total RNA from the monolayer cultures
rRNA was depleted using Ribo-Zero kit. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: colonic spheroid-derived monolayer

tag: experiment

value: experimental set 3

tag: time point

value: day 7 after re-submersion

tag: replication

value: replication 3


title: Input_Prol_rep2_RIP-seq

city: New York

first: Elena

last: Grossi

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Nuclear RNA; Ribo-depletion, DNAse-treatment, single-end sequencing

data_processing:
Fastq were trimmed using Trimmomatic
Data were aligned to the genome assembly hg19 using STAR with default parameters
BAM files were further analysed by RIPseeker package (version 1.18.0)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for each processed data sample

source_name: Input_proliferating human fibroblasts

extract_protocol:
Cells were collected and nuclei were isolated and icubated with specific antibody. Total input RNA or RNA bound to SMARCB1 was retrieved and DNAse-treated.
rRNA was depleted using Ribo-Zero Kit and polyA+ and - RNA was used for library preparation performed with Illumina's TruSeq Stranded Library Prep Kit. Library prep and sequencing was performed at EMBL Genomics Core Facilities

value: BJ hTERT ER:Ras human fibroblasts

tag: genotype/variation

value: Stably expressing hTERT gene; inducible expression of ER:Ras

tag: passage

value: less than 20 passages


title: Input_Prol_rep3_RIP-seq

tag: cell type


title: SMARCB1_IP_Prol_rep1_RIP-seq

tag: rip antibody

value: SNF5 - ChIP Grade (ab12167)


title: Input_Sen_rep3_RIP-seq

source_name: Input_senescent human fibroblasts

value: 6 Days of 4OHT administration


title: SMARCB1_IP_Sen_rep1_RIP-seq

source_name: SMARCB1_IP_senescent human fibroblasts


title: SMARCB1_IP_Sen_rep3_RIP-seq


title: SMARCB1_IP_Sen_rep2_RIP-seq


title: SMARCB1_IP_Prol_rep3_RIP-seq


title: Input_Prol_rep1_RIP-seq


title: SMARCB1_IP_Prol_rep2_RIP-seq


title: Input_Sen_rep1_RIP-seq


title: Input_Sen_rep2_RIP-seq


title: Model_rep2

description: Hepa1-6-bearing C57 BL/6 mouse model

source_name: Untreated mouse tumor ,replicate 2


title: whole brain single cell RNA-seq of nr1d1:VNP fish

first: Haifang

last: Wang

address: NO 320, Yue Yang Road

institute: Institute of Neuroscience

data_processing:
Raw sequencing data was converted to matrices of expression counts using the cellranger software provided by 10X Chromium system. Reads were aligned to a zebrafish reference transcriptome (ENSEMBL Zv11, release 95).
The gene expression matrix were then loaded into Seurat package in R for clustering. Cells with less than 500 genes or percentage of mitochondiral genes>0.02 were excluded.
Genome_build: Zv11
Supplementary_files_format_and_content: processed data is a matrix, each row represent one gene, while each column represent one cell.

organism: Danio rerio

source_name: Zebrafish brain

growth_protocol: Embryos were produced by natural spawning in the morning and raised in egg-water containing methylene blue (0.3 ppm) in a light-controlled incubator under 12h/12h LD cycles at 28 oC. ZT0 is defined as the time when the lights are turned on (9 A.M.).

extract_protocol:
6.5 dpf larval heads were dissected on dissection medium (DMEF/F12 with 2% 100X penicillin-streptomycin ) and pineal region were enriched by pipetting the pineal into the tube. Dissociation of the brain cells following the protocol from Miguel A. Lopez-Ramirez et al. (www.jove.com, 2016). Briefly, Add 300ul papain solution to the dissected tissue, digest the tissue at 37 in water heater for 15 minute, pipetting during digest. Then stop the digestion by adding 1.2ml of washing solution. Washing the cells twice using washing solution. In the end, sterilize the cells using 40um pore size filter. Stain cells using trypan blue and count the living cells using a hemocytometer.
The library were constructed following the instruction of 10X Chromium system.

treatment_protocol: The fish were untreated.

tag: genotype

value: brain

tag: brain region

value: pineal


title: normal_amniotic_fluid_control_rep1

source_name: normal amniotic fluid control

value: female

tag: tag

tag: sample type

value: normal amniotic fluid control


title: Model_rep3

description: Hepa1-6-bearing C57 BL/6 mouse model

source_name: Untreated mouse tumor, replicate 3

tag: tissue


title: Re-Sub day 7 culutre, replicate 2, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_7d_2_exp3

value: replication 2


title: wild-type #3

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

country: Japan

institute: Tokai University

description: gene expression, alternative splicing in adult brain

hyb_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v13.0, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

source_name: wild-type #3 (sv129/B6 BG)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: SV129/C57B6 mix background

value: brain (midbrain)

value: wild-type


title: wild-type #2

source_name: wild-type #2 (sv129/B6 BG)


title: Re-Sub hour 24 culutre, replicate 3, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_24h_3_exp3

value: colonic spheroid-derived monolayer

value: 24 hours after re-submersion


title: Re-Sub day 7 culutre, replicate 1, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_7d_1_exp3

value: experimental set 3

value: day 7 after re-submersion

value: replication 1


title: Re-Sub hour 8 culutre, replicate 2, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_8h_2_exp3

value: 8 hours after re-submersion


title: Re-Sub hour 8 culutre, replicate 1, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_8h_1_exp3


title: Re-Sub hour 8 culutre, replicate 3, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_8h_3_exp3

value: replication 3


title: Re-Sub hour 24 culutre, replicate 1, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_24h_1_exp3


title: ALI day 1 culutre, replicate 1, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d1_1_exp2

value: experimental set 2

value: day 1 after ALI switch


title: ALI day 0 culutre, replicate 3, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d0_3_exp2

value: day 0 after ALI switch


title: Re-Sub hour 0 culutre, replicate 1, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_0h_1_exp3

value: 0 hour after re-submersion


title: Re-Sub hour 0 culutre, replicate 3, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_0h_3_exp3


title: Re-Sub hour 0 culutre, replicate 2, experiment set 3

description:
Exp3_all.genes_counts_final.txt
ReSub_0h_2_exp3


title: ALI day 0 culutre, replicate 1, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d0_1_exp2


title: ALI day 21 culutre, replicate 1, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d21_1_exp1

value: experimental set 1

value: day 21 after ALI switch


title: ALI day 0 culutre, replicate 2, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d0_2_exp2

value: replication 2


title: ALI day 1 culutre, replicate 2, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d1_2_exp2


title: ALI day 2 culutre, replicate 3, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d2_3_exp2

value: day 2 after ALI switch


title: ALI day 2 culutre, replicate 2, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d2_2_exp2


title: ALI day 1 culutre, replicate 3, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d1_3_exp2


title: ALI day 2 culutre, replicate 1, experiment set 2

description:
Exp2_all.genes_counts_final.txt
ALI_d2_1_exp2


title: wild-type #1

description: gene expression, alternative splicing in adult brain

source_name: wild-type #1 (sv129/B6 BG)

value: SV129/C57B6 mix background

value: brain (midbrain)


title: ALI day 14 culutre, replicate 2, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d14_2_exp1

value: colonic spheroid-derived monolayer

value: day 14 after ALI switch


title: ALI day 21 culutre, replicate 2, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d21_2_exp1


title: Slm1 KO #2

source_name: Slm1 KO #2 (sv129/B6 BG)

value: homozygous (khdrbs2)


title: ALI day 14 culutre, replicate 1, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d14_1_exp1


title: Sam68/Slm1 double KO #1

source_name: Sam68/Slm1 double KO #1 (sv129/B6 BG)

value: homozygous (khdrbs1, khdrbs2)


title: ALI day 0 culutre, replicate 2, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d0_2_exp1


title: ALI day 7 culutre, replicate 2, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d7_2_exp1

value: day 7 after ALI switch


title: Slm1 KO #3

source_name: Slm1 KO #3 (sv129/B6 BG)


title: ALI day 4 culutre, replicate 2, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d4_2_exp1

value: day 4 after ALI switch


title: ALI day 4 culutre, replicate 1, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d4_1_exp1

value: replication 1


title: ALI day 7 culutre, replicate 1, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d7_1_exp1


title: ALI day 0 culutre, replicate 1, experiment set 1

description:
Exp1_all.genes_counts_final.txt
ALI_d0_1_exp1


title: A172 DMOG - R3

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

description: Biological replicate 2

hyb_protocol: According to Affymetrix WT PLUS Reagent Kit user manual,  5.5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Human Gene 2.0 ST Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing:
The Affymetrix microarray chips “human gene 2.0 ST” were analyzed using the oligo package and annotated using NetAffx4 OtCEL files were imported from disk or ded by RMA normalization and summary.
Processed data are presented as log2 normalized RMA values. The Hypoxia_Normoxia_5days and DMOG experiments were analyzed separately and included in tabs in the file Hypoxia_DMOG_normalized.xlsx.

label_protocol: The Affymetrix WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: Human GBM cell line A172 was obtained from ATCC. Cells were cultivated in complete DMEM medium. At 80-90% confluency cells were harvested and seeded for experiments. 24 hours after seeding, a medium change was effected and treatments were carried out.

extract_protocol: Total RNA was harvested from cultured cells using the RNeasy Mini Kit (Qiagen, 80204)

treatment_protocol: For Hypoxia_Normoxia_5days experiment cells were either placed under hypoxia (1% oxygen) or normoxia (18.6% oxygen) for 5 days. For DMOG experiment, cells were treated either with carrier control (EtOH) or with 3mM dimethyloxalylglycine (DMOG) for 24 hours.

tag: cell line

value: DMOG

tag: condition


title: A172 Control R1

description: Biological replicate 1

value: EtOH Control


title: A172 Control R4

description: Biological replicate 3


title: A172 Control R3

description: Biological replicate 2


title: Sam68/Slm1 double KO #2

source_name: Sam68/Slm1 double KO #2  (sv129/B6 BG)


title: A172 DMOG - R4

description: Biological replicate 3


title: A172 01 HD5

description: Biological replicate 1

value: Hypoxia


title: A172 04 ND5

description: Biological replicate 4

value: Normoxia


title: A172 05 HD5

description: Biological replicate 5


title: A172 01 ND5

description: Biological replicate 1


title: A172 05 ND5

description: Biological replicate 5


title: A172 02 ND5

description: Biological replicate 2


title: A172 DMOG - R1

description: Biological replicate 1


title: A172 03 ND5

description: Biological replicate 3


title: A172 03 HD5

description: Biological replicate 3


title: Aph_Rep2_S5

city: Paris

first: Chunlong

address: 26 rue d’Ulm

country: France

institute: Institut Curie

description: Enrichement of BrdU labelled DNA (Replicate 2)

data_processing:
Library strategy: Repli-seq
The sequencing data were demultiplexed using the distribution of CASAVA software (CASAVA-1.8.2 bcl2fastq2 v2.18.12)
Illumina adapters were removed using Cutadapt-1.15, keeping only reads with a minimal length of 10 nucleotides.
The reads were mapped on the human genome (Hg19), the chicken genome (galGal4, BrdU label DNA as positive control) and the salmon genome (GCF_000233375.1_ICSASG_v2, unlabelled DNA as negative control) using bwa-0.6.2-r126.
The PCR duplicates were removed by Picard tools (http://broadinstitute.github.io/picard).
The sequence reads located within the regions likely resulted from the sequencing hotspots (defined as the 0,5% windows with the highest amount of reads within 200bp windows) were also removed.
The read density was them computed for each 50 kb nonoverlapping windows (w) for each sample Si corresponding to different S phase fractions (i = 1–6).
The background levels were them estimated and the density profiles were normalized as described in previous study (Chen Genome Res 2010).
A Replication Index (RI), measuring the difference between the Aph and NT signals summed over the six periods, was defined as the Z-score computed on the delta(Aph – NT) by using all 50 kb window along the human genome.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files on sample records are for individual replicates, bigwig files on the series records are replicate means, scores represent the Replicaton Index (RI) or the normalized Repli-Seq signal

source_name: human lymphoblastoid cells

growth_protocol: Epstein–Barr-virus-immortalized human B lymphocytes (JEFF cells) were grown in RPMI-1640 plus GlutaMAX-I medium (GIBCO) with 10% fetal calf serum (PAN-Biotech GmbH), 100 µg/ml of penicillin and streptomycin (GIBCO).

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h and Aph treated cells (600 nM, for a total of 16 h) were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M).

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

tag: treatment

tag: s phase


title: Aph_Rep2_S4


title: Aph_Rep2_S6/G2/M


title: Aph_Rep2_S3


title: Slm1 KO #1

source_name: Slm1 KO #1 (sv129/B6 BG)

tag: strain


title: A172 04 HD5

description: Biological replicate 4

tag: experiment


title: A172 02 HD5

description: Biological replicate 2


title: Aph_Rep1_S3

description: Enrichement of BrdU labelled DNA (Replicate 1)


title: Aph_Rep2_G1/S1


title: Aph_Rep1_S6/G2/M


title: Aph_Rep1_S4


title: Aph_Rep2_S2


title: Aph_Rep1_S5


title: NT_Rep3_S5

description: Enrichement of BrdU labelled DNA (Replicate 3)

value: Non-Treated


title: NT_Rep3_G1/S1


title: Aph_Rep1_S2


title: NT_Rep2_S3


title: NT_Rep3_S2


title: Aph_Rep1_G1/S1


title: NT_Rep2_S5


title: NT_Rep3_S3


title: NT_Rep2_G1/S1


title: NT_Rep2_S2


title: NT_Rep3_S4


title: NT_Rep1_S5


title: NT_Rep2_S4


title: NT_Rep1_S6/G2/M


title: NT_Rep1_S4


title: Gbm2_Mebendazole_0.5uM

city: La Jolla

first: Chen

last: Farhy

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

description: PolyA RNA

data_processing:
Read data, processed in BaseSpace (basespace.illumina.com).
Aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Genome_build: Homo sapiens genome hg19 (GRCh37)
Supplementary_files_format_and_content: All processed data files are .genes.fpkm_tracking - as outputted by BaseSpace.

source_name: Glioblastoma tumor propagating cells

growth_protocol: Normal Neural progenitors media containing EGF and FGF.

extract_protocol:
Total RNA was isolated from GBM2 cells using the RNeasy Kit (Qiagen), 0.25 ug total RNA was used to isolate mRNAs and for library preparation. PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).
Libraries were pooled and single-end sequenced (1X75) on the Illumina NextSeq 500 using the High-Output V2 kit (Illumina).

value: Glioblastoma tumor propagating cells

value: Passage 14

tag: treatment time

value: 3 days


title: Gbm2_SAHA_3uM

description: PolyA RNA

value: 1 days


title: Gbm2_DMSO_0.1%

description: PolyA RNA


title: Gbm2_Bmp4_3

description: PolyA RNA

value: Bmp4 (100ng/ml)


title: Gbm2_Etoposide_0.3uM

description: PolyA RNA


title: Gbm2_Trifluridine_3uM

description: PolyA RNA


title: Gbm2_TSA_1uM

description: PolyA RNA


title: Gbm2_Valproic_Acid_15uM

description: PolyA RNA


title: Gbm2_Digoxin_0.3uM

description: PolyA RNA


title: Gbm2_Digitoxigenin_0.3uM

description: PolyA RNA


title: Gbm2_Serum_3

description: PolyA RNA

value: Serum (FBS 10%)


title: NT_Rep1_S2


title: NT_Rep1_S3


title: NT_Rep1_G1/S1


title: Gbm2_Bmp4_1

description: PolyA RNA


title: Gbm2_Control_3

description: PolyA RNA

value: Untreated Control


title: Gbm2_Serum_1

description: PolyA RNA


title: RNA Seq_Irx5 KO_rep2

source_name: day 4 differentiating BMSCs during osteoblastogenesis

value: BMSCs from tibiae and femurs of 4-week-old Irx5 knockout mice


title: Gbm2_Irinotecan_0.5uM

description: PolyA RNA


title: Gbm2_Fenbendazole_0.5uM

description: PolyA RNA


title: Gbm2_Control_2

description: PolyA RNA


title: Gbm2_Bmp4_2

description: PolyA RNA


title: Gbm2_Cytarabine_0.3uM

description: PolyA RNA


title: Gbm2_Serum_2

description: PolyA RNA


title: H3K27ac_ASO_LINC_repl2_ChIP-seq

description: paired-end sequencing

data_processing:
Fastq were trimmed using Trimmomatic
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with the --very sensitivity parameter
Data were filtered and duplicates were eliminated using PICARD and samtools.
peaks were called using MACS2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from bedGraphs using bedGraphsToBigWig

source_name: BJ hTERT ER:Ras cells

extract_protocol:
Cells were double-crosslinked and nuclei were isolated. Lysates were clarified from sonicated nuclei and incubated with the corresponded antibody
Antibody-DNA complexes were decrosslinked and DNA was isolated by SPRI beads. Libraries were prepared as previously described (Blecher-Gonen et al., 2013). Libraries were sequenced on the an Illumina Nextseq500 platform following the manufacturer's protocols.

value: proliferating human fibroblasts

tag: constructs

value: Stably expressing hTERT gene; inducible expression of ER:Ras

value: less than 20 passages

value: ASO_LINC#3 transient transfection - cells collected after 36 hours

tag: antibody

value: Anti-Histone H3 (acetyl K27) - ChIP Grade (ab4729)


title: H3K27ac_ASO_LINC_repl1_ChIP-seq

description: paired-end sequencing

tag: passage


title: H3K27ac_ASO_CTRL_repl2_ChIP-seq

description: paired-end sequencing

value: ASO_CTRL transient transfection - cells collected after 36 hours


title: ASO_LINC_rep3_RNA-seq

description: antisense oligonucleotide transfection

data_processing:
Sequenced reads were trimmed for adaptor sequence
Data were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters.
Differential expression analysis was carried out by using edgeR (Robinson et al.,2010)
Genome_build: hg19
Supplementary_files_format_and_content: one tab-delimited text matrix including raw counts values of each gene in each sample

source_name: H226 squamous lung carcinoma cells

extract_protocol:
Total RNA was extracted using Maxwell Simply RNA kit (Promega) following manufacturer instructions
1µg of quality-verified RNA was used for library preparation. First strand cDNA synthesis has been carried out using dT oligos

tag: cell type

value: squamous lung carcinoma cells

tag: transfected with

value: ASO_LINC#3 transient transfection - cells collected after 48 hours


title: H3K27ac_ASO_CTRL_repl1_ChIP-seq

description: paired-end sequencing


title: SMARCB1_ASO_CTRL_repl2_ChIP-seq

description: paired-end sequencing

value: SNF5 - ChIP Grade (ab12167)


title: H3K4me2_ChIP-seq

description: paired-end sequencing

value: Anti-Histone H3 (di methyl K4) [Y47] - ChIP Grade (ab32356)


title: SMARCB1_ChIP-seq

description: paired-end sequencing

value: SNF5 - ChIP Grade ab12167


title: SMARCB1_ASO_LINC_repl1_ChIP-seq

description: paired-end sequencing


title: SMARCB1_ASO_LINC_repl2_ChIP-seq

description: paired-end sequencing


title: ASO_LINC_rep1_RNA-seq

description: antisense oligonucleotide transfection


title: D60

first: Pengyan

last: Xia

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

data_processing:
Raw sequencing data was checked by FastQC software.
fastq sequences were trimmed by FASTX-Toolkit.
Gene counts were obtained by aligning reads to the mouse mm10 genome by using CellRanger software (version 2.0.1) to generate the single cell information.
Raw cell counts were filtered in Seurat CreateSeuratObject function with the following criteria: one gene was expressed in at least 3 cells and at least 200 genes were detected in one cell. Mitochondrial genes inside one cell was also calculated with a percentage under 20%. Cells were further filtered with the following requirements: gene numbers inside on cell were no more than 8000 and no less than 200. "FindVariableGenes" function of Seurat was used to get the variable genes with the following parameters: x.low.cutoff 0.05, x.high.cutoff 8 and y.cutoff 0.5.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Colon tumor infiltrating ILCs

growth_protocol: Mice were maintained in SPF conditions with normal conditions of diet otherwise indicated.

extract_protocol:
Colon tumor infiltrating ILCs (Lin-CD45+CD127+) (Lin=CD3e,CD8a,CD19,CD11b,CD11c,Gr1,F4/80,Ter119) from tumors at day 60 (D60) or day 120 (D120) were isolated by flow cytometry and subjected to 3’ droplet-based scRNA sequencing. Purity of ILC cells was over 95% for each sample that was determined by post sorting analysis of flow cytometry.
Tumor infiltrating ILCs (Lin-CD45+CD127+) (Lin=CD3e,CD8a,CD19,CD11b,CD11c,Gr1,F4/80,Ter119) were isolated and cell suspensions (300-500 living cells per microliter) were loaded on a Chromium Single Cell Controller (10xGenomics) to generate single-cell Gel Bead-In-Emulsions (GEM) by using Single Cell 3’ Library and Gel Bead Kit V2 (10xGenomics, 120237). mRNAs of captured cells were barcoded through reverse transcription. Barcoded cDNAs were pooled and cleaned up by using DynaBeads® MyOne Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq cDNA libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10xGenomics, 120237) according to the manufacture’s protocol followed by sequencing on an Illumina HiSeq X Ten with pair end 150bp (PE150).
10x genomics scRNA-seq

treatment_protocol: WT mice were i.p. injected with azoxymethane (AOM, 10 mg/kg body weight), and treated with 1.5% DSS in drinking water for three cycles.

value: Colon tumor infiltrating ILCs

tag: age

value: D60 post AOM induction


title: heat stress Pituitary biological replicate 6

city: Hangzhou

first: Jialiang

last: Han

address: yuhantang street 866

institute: zhejiang university

data_processing:
Clean reads were generated by removing reads containing adapter, reads containing ploy-N and low quality (Phred score Q ≤20) reads from raw data.
the clean reads were mapped to the latest mouse reference genome (ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/) using Hisat2 v2.0.5.
The expression values (FPKM) of each gene were calculated based on the length of the gene and the read count mapped to this gene by featureCounts v1.5.0-p3.
Differential expression analysis between two groups (three biological replicates per group) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

source_name: pituitary

extract_protocol:
The hypothalamus, pituitary and left inguinal (#4) mammary gland of all dams were collected, cleaned in ice-cold phosphate-buffered saline (PBS), and snap frozen in liquid nitrogen before storage at –80 °C.RNA was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sequencing library preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: animals：timed-pregnancy ICR mice, control group (25 °C, 55% ±5% RH) and heat stress group (36 °C, 55% ±5% RH). Temperature: controlled by an artificial climate incubator to expose the cages housing the mice to the experimental temperature (36 °C) and relative humidity (RH: 55% ±5%). Animals were sacrificed immediately after treatment on day 13 for the purpose to study the peak lactation responses to heat stress. The hypothalamus, pituitary and left inguinal (#4) mammary gland of all dams were collected.

value: ICR

value: 10 weeks, lactating 13 days

tag: stress

value: heat stress

value: pituitary


title: SMARCB1_ASO_CTRL_repl1_ChIP-seq

description: paired-end sequencing

value: proliferating human fibroblasts


title: ASO_LINC_rep2_RNA-seq

description: antisense oligonucleotide transfection


title: H3K4me3_ChIP-seq

description: paired-end sequencing

value: Stably expressing hTERT gene; inducible expression of ER:Ras

value: Anti-trimethyl-Histone H3 (Lys4) (07-473 Millipore)


title: heat stress Mammary gland biological replicate 8

source_name: mammary gland

value: mammary gland


title: Sam68/Slm1 double KO #3

source_name: Sam68/Slm1 double KO #3  (sv129/B6 BG)

value: SV129/C57B6 mix background

value: brain (midbrain)

tag: genotype

value: homozygous (khdrbs1, khdrbs2)


title: heat stress Mammary gland biological replicate 7


title: ASO_CTRL_rep3_RNA-seq

description: antisense oligonucleotide transfection

value: squamous lung carcinoma cells

value: ASO_CTRL transient transfection - cells collected after 48 hours


title: Gbm2_Control_1

description: PolyA RNA

value: Glioblastoma tumor propagating cells

value: Passage 14

value: Untreated Control

value: 3 days


title: ASO_CTRL_rep2_RNA-seq

description: antisense oligonucleotide transfection


title: heat stress Mammary gland biological replicate 6

value: ICR


title: heat stress Mammary gland biological replicate 4

value: 10 weeks, lactating 13 days


title: ASO_CTRL_rep1_RNA-seq

description: antisense oligonucleotide transfection


title: H3K27ac_ChIP-seq

description: paired-end sequencing

value: less than 20 passages

value: Anti-Histone H3 (acetyl K27) - ChIP Grade (ab4729)


title: heat stress Mammary gland biological replicate 5

value: heat stress


title: Qseq_S6

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description:
QuantSeq library ~ 30 M reads per sample
Qseq_counts.txt, QseqSal_counts.txt

data_processing:
RNA-Seq and QuantSeq reads (fastq files) were mapped to the Ensembl Homo sapiens genome (GRCh38). Mapping was performed with Tophat2 (v 2.0.12)  (Langmead and Salzberg 2012) calling Bowtie2 (v 2.2.3) (Kim et al. 2013)
The featureCounts function of Subread (v 1.4.6-p5) (Liao et al. 2014) was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 gtf file.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
The abundance quantification method Salmon (Patro et al. 2017) to calculate transcript abundance based on the transcript fasta files downloaded from ensemble-release87, (Homo_sapiens.GRCh38.cdna.all.fa and Homo_sapiens.GRCh38.ncrna.all.fa)
The Bioconductor package tximport (Soneson et al. 2015) was used to convert transcripts to gene counts which could be used in downstream differential expression analysis.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
Genome_build: Ensembl Homo sapiens genome (GRCh38).
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: PBMC treated with Poly (I:C)

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) followed by purification on an RNeasy column (Qiagen)
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used  .The six RNA-Seq libraries  were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.
QuantSeq libraries were prepare using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina, according to the manufacturer’s instructions.
QuantSeq libraries were sequenced using the Illumina NextSeq 500 to produce 75 bp single-end reads for each sample

treatment_protocol: Cryobanked peripheral blood mononuclear cells (PBMC) were thawed and cultured in AIM-V medium (Gibco) with 50 μg/ml polyI:C extract (Invivogen), or medium alone (control) in triplicate. After 24 h, cells were harvested and total RNA was extracted.

value: Treated


title: D120

value: Colon tumor infiltrating ILCs

value: D120 post AOM induction


title: Qseq_S5

source_name: peripheral blood mononuclear cells (PBMC)

value: Control


title: heat stress Mammary gland biological replicate 3

value: mammary gland


title: Qseq_S4


title: Qseq_S2


title: heat stress Mammary gland biological replicate 1


title: control Mammary gland biological replicate 7

value: control


title: Rseq_S6

description:
RNA-Seq library ~ 92 M reads per sample
Rseq_counts.txt, RseqSal_counts.txt


title: Qseq_S1


title: Rseq_S4


title: heat stress Mammary gland biological replicate 2


title: control Mammary gland biological replicate 4


title: Rseq_S5


title: control Mammary gland biological replicate 3


title: control Mammary gland biological replicate 2


title: control Mammary gland biological replicate 5


title: control Mammary gland biological replicate 1


title: Rseq_S1


title: Rseq_S2


title: heat stress Hypothalamus biological replicate 8

source_name: hypothalamus

value: hypothalamus


title: R6/1 poor rep3

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description:
41
processed data file: Processed.txt

data_processing:
Base calling using Illumina CASAVA software.
Filtering of ribosomal and mitochondrial sequences and 5’end trimming of 2 bases (bowtie in TopHat Alignment v1.0.1).
Assignment to genomic features (GenomicAlignment -R version 3.5.3).
Genome_build: UCSC mm20
Supplementary_files_format_and_content: Processed.txt: Tab-delimited text file with Ensembl ID and read counts for all the samples.

source_name: Striatum

growth_protocol: Standard animal housing conditions.

extract_protocol:
Freshly dissected striata were submerged in RNAlater until processing using TRIzol reagent and further clean-up with RNeasy Mini columns, following manufacturers’ recommendations.
Libraries were prepared using Illumina standard protocols (TruSeq Strander mRNA kit) from 150 ng of starting material.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: 14 weeks

tag: gender

value: Male

value: Striatum

tag: performance

value: Poor


title: heat stress Hypothalamus biological replicate 7

tag: tissue


title: R6/1 poor rep2

description:
37
processed data file: Processed.txt


title: R6/1 poor rep4

description:
44
processed data file: Processed.txt


title: Qseq_S3

tag: condition


title: heat stress Hypothalamus biological replicate 5

tag: strain


title: R6/1 poor rep1

description:
4
processed data file: Processed.txt


title: control Mammary gland biological replicate 8