title: NES (Cytosol) Target 1

description:
NES-T1
processed data files:
Nes_targets_fwd.norm_avg.bw
Nes_targets_rev.norm_avg.bw
Nes_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: ES_KO_D0_1_Gata4_4C

status: Public on Jun 20 2019

type: SRA

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: CRG

library_source: genomic

data_processing:
Library strategy: UMI-4C seq
(RNAseq) RNAseq was aligned with STAR and genome annotation Gencode M17.
(RNAseq) Annotation was done using STAR --genecounts option.
(UMI-4C) Split fastq files at restriction enzyme (RE) sites, producing the corresponding fragments
(UMI-4C) Alignment using bwa mem and default options
(UMI-4C) Remove supplementary and low mapping quality (< 20) alignments
(UMI-4C) Annotate pair reads as specific if there is a RE site in the first read
(UMI-4C) Annotate pair reads as mapped if at least one fragment (besides the first one) is properly aligned
(UMI-4C) Keep only read pairs that are specific, mapped and not duplicated (same alignment positions for all its fragments)
Genome_build: mm10
Supplementary_files_format_and_content: (RNAseq) bigwig files were generated with deeptools, (UMI-4C) txt processed files

molecule: genomic DNA

organism: Mus musculus

source_name: ESCs

growth_protocol: Mouse ESCs were cultured on plastic dishes pre-coated with 0.1% (W/V) EmbryoMax® gelatine (EMD Millipore) with either DMEM/F12 medium and Neurobasal® medium mixed at 1:1 ratio, supplemented with MEM non-essential amino acids solution (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL), beta-mercaptoethanol (ME, 50μM), N2 and B27 supplements, the small-molecule inhibitors PD0325901 (1μM, Selleck Chemicals) and CHIR99021 (3 μM, Selleck Chemicals), and ESGRO® Leukaemia Inhibitory Factor (LIF) (1000 U/mL, EMD Millipore), or with KnockoutTM DMEM medium supplemented with 15% (V/V) ES cell qualified foetal bovine serum (ES FBS), MEM non-essential amino acids (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL) and 50μM ME.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. UMI-4C libraries were purified with AmpureXP beads.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library Preparation Kit. UMI-4C libraries were prepared according stardard NEBNext DNA libaray preparation instructions.

treatment_protocol: ESCs was induced to form EBs with “EB differentiation medium” (KnockoutTM DMEM medium supplemented with 10% FBS, MEM non-essential amino acids (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL) and 50μM ME and plated as hanging drops (400 cells in 20μL) on the lid of a 100 mm Petri dish. The cultures were harvested 3 days later and transferred into bacterial dishes for further culture in suspension.

tag: genotype

tag: cell type

value: ESCs

tag: passages

value: Day 0

tag: group

value: Gata4 4C tag


title: EB_WT_D6_2_Foxa2_4C

value: wild type

value: embryoid bodies

value: Day 6

value: Foxa2 4C tag


title: myo_KO_13

city: Stockholm

first: Pauliina

last: Damdimopoulou

address: Karolinska University Hospital OBGY K57

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
The libraries were sequenced by two lanes of Illumina HiSeq2000 instrument. The sequenced raw STRT reads were processed by STRTprep [PMID: 26874359]; v3dev branch, d7efcde commit (https://github.com/shka/STRTprep/tree/v3dev) to demultiplex according to the barcode, and to exclude redundant reads according to the UMI; sequence of the template switching oligo (UMI, barcode and tri-G) were trimmed.
A gft file comprising annotations retrieved from UCSC and the ERCC annotations, was used to estimate the reads in all annotated genes using htseq-count.
Genome_build: Mm9
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts of annotated genes and ERCC controls

molecule: total RNA

source_name: Uterus

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen, Hilden, Germany) and quality measured with the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Ten nanograms of high-quality RNA (RIN>8) was used for RNA-seq.
One 46-plex STRT RNA-seq library was made using 10 ng RNA as described previously (Krjutskov et al. 2016 Hum Reprod 31:844) with the following modifications: barcoded 10 µM template-switching oligonucleotides were added prior to reverse transcriptase, ERCC spike-in Mix A was diluted 15,300-fold with clean water, and 1 µl was taken per library reverse transcriptase master mix. Twenty cycles of PCR were used for the first round of amplification and ten additional cycles for the second round to introduce Illumina-compatible universal sequences.

treatment_protocol: Sexually mature Plag1KO and WT females were superovulated by i.p. injections of 5 IU pregnant mare serum (Folligon; Intervet, Dublin, Ireland), followed two days later by 5 IU human chorionic gonadotropin (hCG) (Chorulon; Intervet, Dublin, Ireland). The following day the animals were killed and uteri removed.

tag: tissue

value: myometrium

tag: mouse id


title: NucPore (Nuclear Pore) Control 2

city: Stanford

first: Furqan

middle: M

last: Fazal

state: California

address: 269 Campus Drive, CCSR 2130

department: Genetics

country: USA

institute: Stanford University

description:
NUCP-C2
processed data files:
NucPore_controls_fwd.norm_avg.bw
NucPore_controls_rev.norm_avg.bw
NucPore_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

data_processing:
Library strategy: APEX-seq
The RNA-seq reads were initially subject to barcode removal and primer trimming using a published script (Flynn et al., Nature Protocols 2016) based on Trimmomatic: (https://github.com/qczhang/icSHAPE/blob/master/scripts/trimming.pl): perl trimming.pl -1 $fastq-file1 -2 $fastq-file2 -p $trimmed-file1 -q $trimmed-file2 -l 0 -t 0 -c phred33 -a adapter.fa -m 36
The reads were then mapped using STAR (Dobin et al., Bioinformatics 2013) to the GRCh38 Ensembl genome, with Homo_sapiens.GRCh38.84.gtf annotations (http://uswest.ensembl.org/index.html), using the following command: STAR --genomeDir ~/genome/human/star --runThreadN 8 --readFilesIn $trimmed-file1 $trimmed-file2 --outFileNamePrefix $output-samfile
The mapped reads were then counted using HTSEQ (Anders et al., Bioinformatics 2015) : python -m HTSeq.scripts.count -m intersection-nonempty -s reverse -i gene_id $output-samfile ~/genome/human/Homo_sapiens.GRCh38.84.gtf > $txt
The mapped data was visualized using the UCSC browser track. To generate genome tracks we used samtools to generate stranded BAM files for each library from the SAM file. The BAM file was then used to generate a bedgraph following the command: genomeCoverageBed -bg -split -ibam $bam -g ~/genome/human/star/chrNameLength.txt > $bed_file
Genome_build: hg38
Supplementary_files_format_and_content: Tab-deliminted text files include either DESEQ2 log2foldchanges and Padjusted values; or count data from STAR and HTSEQ. Differentially-expressed genes were determined using DESeq2 (Love et al., Genome Biology 2014), using FDR < 0.05 and 18 controls. All P-values from DESeq2 are FDR adjusted for multiple-hypothesis testing. For the OMM perturbation experiments, we used the same 18-control strategy, but replacing the unperturbed OMM APEX-seq and NES APEX-seq values with the corresponding drug-perturbed values. There were two exceptions to the 18-control approach in all our analysis. For the LMA gene in nuclear lamina, and the SENP2 gene in the nuclear pore construct, the unlabeled control had high counts for these genes in the RNA-seq data, as these genes were used to target APEX to the corresponding location. Therefore, to compensate, we replaced the LMA 18-control DESeq2 log2fold change with the 2-control log2fold change (using LMA controls) in the LMA data; we did the same for SENP2 in the nuclear pore dataset. Otherwise, all other data was as is.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HEK 293T cells from the ATCC (passages < 25) were cultured in a 1:1 DMEM/MEM mixture (Cellgro) supplemented with 10% fetal bovine serum, 50 units/mL penicillin, and 50 mg/mL streptomycin at 37oC under 5% CO2

extract_protocol:
To labeled and unlabeled (controls) HEK 293T cells in 10-cm plates, we added ~1 ml DPBS containing 5 mM Trolox and 10 mM sodium ascorbate, as well as ~4 ul Ribolock RNAse inhibitor (Thermo Fischer Scientific). The cells were then scrapped off 10-cm plates using cell lifters (Corning), transferred to 2-ml Eppendorf tubes, and spun at 500G for 4 minutes to pellet cells. The supernatant was removed, and the cells were processed using the RNeasy plus mini kit (Qiagen) following the manufacture protocol, including adding beta-mercaptoethanol to the lysis buffer. The cells were sent through the genomic DNA (gDNA) eliminator column supplied with the kit. One modification to the protocol was replacing the RW1 buffer with RWT buffer (Qiagen) for washing. The extracted RNA was eluted into RNAse-free water, and RNA integrity was checked using the Agilent bioanalyzer 2100 using the “high-sensitivity” setting. Only RNA with a RIN (RNA integrity number) > 8.5 was used for subsequent experiments. RNAs shorter than 100 nt were not efficiently recovered.
RNA Seq libraries were prepared from enriched RNA (corresponding to ~30-50 µg of pre-enriched RNA) using the Illumina TruSeq Stranded mRNA Protocol, which included polyA+ selection. The prepared libraries were stranded and were quality-controlled by sequencing on the Illumina Miseq. Good libraries (> 80% unique reads) were sequenced on the Illumina Hiseq400 at ~35 million paired (2 x 75) reads per library. The correlation between biological replicates was high (between 0.96 and 1). For the MITO APEX Seq we also generated total RNA samples (by omitting the polyA+ selection step in the TruSeq protocol), as well as a polyA+ selected technical replicate for 1 of the labeled samples.

treatment_protocol: 18-24 hrs after plating HEK 293T cells stably expressing the corresponding APEX2 fusion construct, APEX labeling was initiated by changing the medium to fresh medium containing 500 mM biotin-phenol (Iris Biotech GMBH). This was incubated at 37oC under 5% CO2 for 30 min. H2O2 (Sigma Aldrich) was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min (Rhee et al., Science 2013). The reaction was quenched by replacing the medium with an equal volume of 5 mM Trolox, 10 mM sodium ascorbate and 10 mM sodium azide in Dulbecco's phosphate-buffered saline (DPBS). Cells were washed with DPBS containing 5 mM Trolox and 10 mM sodium ascorbate three times before proceeding to imaging, RT-qPCR or RNA-seq experiments. The unlabeled controls were processed identically, except that the H2O2 addition step was omitted.

tag: protocol

value: APEX-seq

tag: cell line

tag: cell compartment

value: Nuclear Pore


title: myo_WT_12 [E4]

value: WT


title: EB_WT_D6_1_T_4C

value: T 4C tag


title: NucPore (Nuclear Pore) Control 1

description:
NUCP-C1
processed data files:
NucPore_controls_fwd.norm_avg.bw
NucPore_controls_rev.norm_avg.bw
NucPore_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: WT_PL_Dark_rep2

type: RNA

city: Taipei

first: Geng-Jen

last: Jang

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16.5 hr at 45°C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip Operating System 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The value of polysome-bound RNAs is normalized to PL% (the ratio of polysome-bound RNAs in total RNA).

label: biotin

organism: Arabidopsis thaliana

source_name: 4-d-old Col-0, Dark

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 300 ng total RNA (MessageAmp Premier RNA Amplification Kit Manual, 4386269 Rev. G, Life Technologies Corporation).Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seeds were surface-sterilized and germinated on half-strength Murashige and Skoog

extract_protocol: Total RNA and polysome-bound RNA were extracted as described previously [(Liu et al, Mol Syst Biol 8, 566 (2012)]

treatment_protocol: 4-d-old etiolated seedlings treated with or without 4-h white light

value: seedlings (aerial parts)

tag: ecotype

value: control

tag: treatment

value: dark

tag: rna fraction

value: polysome-bound RNA


title: myo_KO_11


title: NucPore (Nuclear Pore) Target 2

description:
NUCP-T2
processed data files:
NucPore_targets_fwd.norm_avg.bw
NucPore_targets_rev.norm_avg.bw
NucPore_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: myo_WT_10


title: EB_WT_D6_1_Gata6_4C

value: Gata6 4C tag


title: myo_KO_9


title: EB_WT_D6_1_Foxa2_4C


title: EB_WT_D6_1_Gata4_4C


title: LMA (Nuclear Lamina) Control 2

description:
LMA-C2
processed data files:
Lma_controls_fwd.norm_avg.bw
Lma_controls_rev.norm_avg.bw
Lma_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Nuclear Lamina


title: endo_KO_13 [D8]

value: endometrium


title: dcp5_PL_L4h_rep1

source_name: 4-d-old dcp5-1, L4h

value: white light


title: NucPore (Nuclear Pore) Target 1

description:
NUCP-T1
processed data files:
NucPore_targets_fwd.norm_avg.bw
NucPore_targets_rev.norm_avg.bw
NucPore_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: LMA (Nuclear Lamina) Target 2

description:
LMA-T2
processed data files:
Lma_targets_fwd.norm_avg.bw
Lma_targets_rev.norm_avg.bw
Lma_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: LMA (Nuclear Lamina) Control 1

description:
LMA-C1
processed data files:
Lma_controls_fwd.norm_avg.bw
Lma_controls_rev.norm_avg.bw
Lma_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: EB_KO_D6_2_T_4C


title: WT_SS_Dark_rep1

value: total RNA


title: WT_PL_Dark_rep1


title: ut_KO_14

value: uterus


title: ut_KO_13


title: WT_PL_L4h_rep1

source_name: 4-d-old Col-0, L4h


title: dcp5_PL_Dark_rep1

source_name: 4-d-old dcp5-1, Dark


title: EB_KO_D6_2_Gata6_4C

value: embryoid bodies

value: Day 6


title: EB_KO_D6_2_Gata4_4C

value: Gata4 4C tag


title: EB_KO_D6_2_Foxa2_4C

value: Foxa2 4C tag


title: NIK (Nucleolus) Control 2

description:
NIK-C2
processed data files:
Nik_controls_fwd.norm_avg.bw
Nik_controls_rev.norm_avg.bw
Nik_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: APEX-seq

value: Nucleolus


title: LMA (Nuclear Lamina) Target 1

description:
LMA-T1
processed data files:
Lma_targets_fwd.norm_avg.bw
Lma_targets_rev.norm_avg.bw
Lma_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: ut_WT_12

value: WT


title: ut_KO_11


title: EB_KO_D6_1_T_4C

value: T 4C tag


title: ut_WT_10


title: NIK (Nucleolus) Control 1

description:
NIK-C1
processed data files:
Nik_controls_fwd.norm_avg.bw
Nik_controls_rev.norm_avg.bw
Nik_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: NIK (Nucleolus) Target 2

description:
NIK-T2
processed data files:
Nik_targets_fwd.norm_avg.bw
Nik_targets_rev.norm_avg.bw
Nik_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: EB_KO_D6_1_Gata6_4C


title: EB_KO_D6_1_Gata4_4C


title: EB_KO_D6_1_Foxa2_4C


title: NIK (Nucleolus) Target 1

description:
NIK-T1
processed data files:
Nik_targets_fwd.norm_avg.bw
Nik_targets_rev.norm_avg.bw
Nik_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: Nucleus (NLS) Control 2

description:
NLS-C2
processed data files:
Nls_controls_fwd.norm_avg.bw
Nls_controls_rev.norm_avg.bw
Nls_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Nucleus


title: endo_WT_8


title: endo_WT_7


title: IL10 rep3

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
trim reads for quality with trm galore (-q 20)
quasi mapping with salmon (--numBootstraps 30)
DEG at gene level with R tximport and DESeq2 packages compare CD11b to CD103 samples
Genome_build: mm10
Supplementary_files_format_and_content: cDC1_vs_IL10_gene_res_exp_TPM_ann.xls contains TPM and counts for the samples and p-values and statistics comparing CD11b to CD103 samples

source_name: IL-10 treated cDC1 (live, CD11c+, CD11b-, CD8α+, MHC class II+)

extract_protocol:
RNeasy Micro kit (Qiagen)
RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq kit (Roche) according to manufacturer’s instruction. First, poly A RNA was isolated from 100ng total RNA using oligo-dT magnetic beads. Purified RNA was then fragmented at 85C for 6 min., targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25C for 10mins, 42C for 15mins and an inactivation step at 70C for 15mins. This was followed by second strand synthesis at 16C, 60mins. Double stranded cDNA fragments were purified using Ampure XP beads (Beckman). The dscDNA were then A-tailed, and ligated with illumina adaptors. Adaptor-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Sequencing was performed on Illumina NextSeq platform generating paired end reads of 76bp.

treatment_protocol: 8–12 week C57BL/6 mice were subcutaneously injected with 5 × 10^6 murine Flt3L-secreting B16 melanoma cells. Mice were sacrificed at day 14 post B16 melanoma cell injection. Spleens were collected from individual mice and digested in RPMI containing fatal bovine serum (2%; Sigma), collagenase IV (0.5mg/mL; Sigma), collagenase D (0.5mg/mL; Roche) and DNase I (100units/mL; Sigma) for 45 minutes at 37°C in a CO2 incubator. After digestion, EDTA (10mM final concentration) was added for another 5 minutes to disrupt DC:T cell conjugates. Undigested material was removed by filtering through a 70µm cell strainer. Then DCs were enriched using the EasySepTM dendritic cell enrichment Kit (Stemcell Technologies) according to the manufacturer’s instructions. The enriched DCs were stained with DAPI, CD11c, CD11b, CD8alpha and MHC class II monoclonal antibodies for 30 min on ice, washed and sorted on BD Aria cell sorter.  Purified CD8alpha+ DCs from each mouse were split in two equal parts and were in vitro cultured at 2 million cells/mL with or without recombinant murine IL-10 (200 ng/mL) for 4hrs.

tag: strain

value: Spleen

value: cDC


title: endo_WT_5


title: IL10 rep2


title: endo_KO_4


title: endo_KO_6


title: cDC rep3

source_name: cDC1 (live, CD11c+, CD11b-, CD8α+, MHC class II+)


title: 68KD Pol II

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v. 1.9.1 with the following parameters: --minimum-length 10 -e 0.05 --times 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 15,10
Alignment was done with Bowtie2 v. 2.2.5 to hg19.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.3.1
Mapped reads were de-duplicated with Picard
BigWig files were generated with deepTools2 v.2.2.4 with bamCoverage tool and the following parameters: -bs 10 --normalizeTo1x 2451960000 -e -p max
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: ChIP-seq

growth_protocol: 293 cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

tag: chip antibody

value: 293 Flp-In


title: endo_WT_3


title: Nucleus (NLS) Target 1

description:
NLS-T1
processed data files:
Nls_targets_fwd.norm_avg.bw
Nls_targets_rev.norm_avg.bw
Nls_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: Nucleus (NLS) Target 2

description:
NLS-T2
processed data files:
Nls_targets_fwd.norm_avg.bw
Nls_targets_rev.norm_avg.bw
Nls_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: 68KD Input


title: 293 Flp-In Pol II


title: cDC rep1


title: endo_KO_2


title: endo_WT_1


title: myo_WT_8

value: myometrium


title: ZH487 shControl_RNAseq

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

data_processing:
Reads were aligned to the human genome (hg19 build) with the Gencode reference transcriptome (v19) using STAR (v2.3.0e).
Read counts for each gene were quantified as the total number of reads mapping to exons using htseq-count (0.6.0).
bigWig coverage tracks were produced using deepTools2.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage tracks, and Expression Microarray results.

source_name: adherent glioblastoma-derived cell line

growth_protocol: The human glioblastoma cell line LN229 was obtained from ATCC (cat. CRL-2611). Cells were cultured in DMEM containing 1 g/L glucose (D5921, Sigma) supplemented with 10% tetracycline-free fetal bovine serum (Clontech), 1% penicillin and streptomycin (P/S) mix, and glutamine (0.5 mM).     The ZH487 glioblastoma spheroid primary cells were originally established at the University of Zurich Hospital.  ZH487 cells were cultured in Neurobasal medium (Cat. 12348017, NBM) supplemented with 2% B27 (cat. 12587010, retinoic acid-free, Invitrogen), EGF (20 ng/ml, AF-100-15, Peprotech), FGF (20 ng/ml, cat. 100-18B, Peprotech) and glutamine (0.5 mM).     DNA methylation array (Illumina EPIC) analysis classified the ZH487 primary tumour and derived cell line as part of the RTK I subtype.    All cell lines were cultured under 10% CO2 at 37℃ with humidity.    Cell identities were verified by the Multiplex human Cell line Authentication Test (MCA). Cells were also tested for mycoplasma contamination with the Multiplex cell test (Multiplexion GmbH, Friedrichshafen, Germany).

extract_protocol:
Total RNA was isolated using the RNeasy Microkit (Qiagen) according to the manufacturer's standard protocol.
Libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit v2 according to the manufacturer's instructions. Briefly, 1000ng of total RNA was used for the polyA-based selection and fragmented. The first-strand cDNA was synthesized with random hexamer and SuperScript II (Invitrogen) following with second-strand synthesis, then the double-stranded cDNA fragments were end-repaired, A-tailed on the 3′ end, ligated to indexed adapters and amplified with 6 cycles of PCR. The final libraries were validated using Qubit (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent Technologies). Subsequently, the libraries were diluted to 10nM and pooled in equimolar ratios. The pooled library was sequenced with the Illumina HiSeq2000 (50 bp single-end) system.

treatment_protocol: Inducible SOX10 knockdown LN229 cells were established by infecting cells with pLKO-Tet-On non-targeting (nt) shRNA and pLKO-Tet-On SOX10 shRNA (TRCN0000018988) lentiviral particles and puromycin selection (1 µg/ml) for 7 days. shRNA expression was induced by adding 0.1 µg/ml doxycycline to the medium for at least 7 days. ZH487 cells constitutively expressing SOX10-targeting shRNA were established by trasnfection with the pLKO1 plasmid bearing the SOX10 shRNA.

tag: subtype

value: RTK_I-like cell line

tag: gender

value: male


title: ut_KO_9


title: ZH487 shSOX10_RNAseq


title: CD7D_2: Normal diet (7 days), replicate 2

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

data_processing:
Removal of duplicate reads using ParDRe rel. 1.2.5, allowing one mismatch and using an 18 bp prefix
Removal of recognizable adapter using cudadapt v1.8.1
Removal of low quality read ends with Trimmomatic 0.22 in paired end mode (filters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20)
Alignment to reference transcriptome with kallisto 0.43, 200 bootstrap replicates
Analysis and postprocessing using sleuth
Genome_build: Flybase dmel 6.08 transcriptome, with EGFP and Gal4 transcripts added
Supplementary_files_format_and_content: abundance.tsv file – Raw quantitation output from kallisto including TPM estimates
Supplementary_files_format_and_content: genes.csv file – Model fits and significance calls from sleuth, pooled at the gene level
Supplementary_files_format_and_content: transcripts.csv file – Model fits and significance calls from sleuth, pooled at the transcript level

organism: Drosophila melanogaster

source_name: Labellum

growth_protocol: Flies were grown on standard cornmeal food (Bloomington Food B) at 25° C under a 12:12 hour light-dark cycle (lights on at 7AM).

extract_protocol:
For Gr5a-GAL4/UAS-OGT-RNAi experiments, 20 proboscis per sample were dissected into Trizol (Ambion), and homogenized with plastic pestles. RNA was extracted by acid phenol chloroform (Ambion), and precipitated by isopropanol with Glycoblue Blue Coprecipitant (Invitrogen). RNA pellet was washed as needed with 75% ethanol. RNA was eluted in RNAse DNase free water and treated by DNAse I, following manufacturer’s instructions (Turbo DNA-free DNA removal kit, Ambion). For the SD7 and CD libraries, 200 proboscis were dissected in 1xPBS and homogenized in Trizol (Ambion). RNA was extracted by chloroform followed by RNA clean up using RNeasy MinElute Clean Up Kit (Qiagen), and on column DNA digestion by DNAse I (Qiagen). The concentration and integrity of RNA was validated using Agilent Bio-analyzer systems and Qubit RNA High Sensitivity Assay (Invitrogen).
Libraries were generated using the Ovation RNA-Seq System for Model Organisms (Nugen, 0350-32) for CD vs SD experiments, and Ovation SoLo RNA-Seq System for Drosophila (Nugen, 0502-96) for Gr5a-GAL4/UAS-OGT-RNAi SD experiments. All reactions included integrated HL-dsDNase treatment (ArcticZymes, Cat. #70800-201).

treatment_protocol: For dietary manipulations, age matched flies were either placed on standard cornmeal diet, or standard cornmeal diet supplemented with different sugars in groups of 30-35 flies

tag: diet

value: Normal diet

tag: genotype/variation

value: parental

value: Labellum


title: myo_WT_7

tag: genotype


title: 293 Flp-In Input


title: Nucleus (NLS) Control 1

description:
NLS-C1
processed data files:
Nls_controls_fwd.norm_avg.bw
Nls_controls_rev.norm_avg.bw
Nls_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: CD7D_1: Normal diet (7 days), replicate 1


title: myo_KO_6


title: ZH487_shSOX10_BRD4

data_processing:
ChIP-seq datasets were processed using a custom pipeline implemented in Snakemake. Briefly, reads were trimmed using the Trimgalore tool (https://github.com/FelixKrueger/TrimGalore) and aligned using Bowtie with standard parameters. Duplicates and multi-mapping reads were removed using the samtools package and the XS flag in the bam files. Input control and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite. Peaks were called using the callpeak mode in MACS2 (https://github.com/taoliu/MACS) for broad and narrow peaks. In addition, SICER was used to call peaks using the gap 600 and window 200 parameters. Various QC parameters (FRiP, PCR bottleneck coefficient, cross-strand correlation) were determined according to the ENCODE guidelines. In addition, visual QC was performed using the signal profile at TSS of annotated genes and the fingerprint method from the DeepTools2 suite.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig tracks of SES-normalised coverage; bed files of MACS2 narrowPeak calls

source_name: gliomasphere patient-derived cell line

extract_protocol:
Cells were cross-linked with 1% methanol-free formaldehyde for 15 min and quenched with 0.125M glycine. Chromatin was isolated by adding lysis buffer and Dounce homogenization. Collected chromatin was sheared via sonication to an average length of 300-500bp. Input genomic DNA was prepared from collected chromatin by treatment with RNase, proteinase K and de-crosslinking under heat, and then isolated by ethanol precipitation. Pellets were resuspended and DNA quantified on a NanoDrop spectrophotometer. Estimated total chromatin yield was calculated based on this amount. 30ug of chromatin was pre-cleared with protein A agrose beads (Invitrogen), and DNA precipitated using 4ug of antibody against SOX10 or BRD4. This DNA was isolated from the beads by washing followed by SDS buffer elution, RNase/proteinase K treatment and de-crosslinking under heat (65C overnight incubation). DNA was then purified using phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared from ChIPped and input DNA via standard protocols (enzymatic end-polishing, dA-addition and adaptor ligation) on an Apollo 342 automated system (Wafergen Biosystems/Takara).

value: RTK_I cell-like line

tag: chip antibody vendor

value: Bethyl Laboratories

tag: chip antibody cat.#


title: IL10 rep1

tag: tissue

tag: cell type


title: ZH487_shControl_BRD4


title: myo_WT_5

tag: mouse id


title: cDC rep2


title: SD7D_1: Sugar diet (7 days), replicate 1

value: High sugar diet


title: ZH487_shControl_SOX10

value: Abcam


title: myo_WT_3


title: myo_KO_2


title: LN229_shControl_BRD4


title: LN229_shControl_SOX10


title: Input

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

country: China

institute: Hangzhou Normal University

data_processing:
filtering, fastp
mapping, bowtie2
sam file processing, samtools
peak-calling, MACS2
peak annotation, ChIPseeker
Genome_build: hg19
Supplementary_files_format_and_content: bw, pileup of mapped reads
Supplementary_files_format_and_content: bed, binding region

source_name: Cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with antibody.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Complete Genomics following the manufacturer's protocols.

value: input


title: myo_WT_1

value: WT


title: FOXK2_ChIP


title: ZH487_shSOX10_ATACseq_rep2

data_processing:
ATAC-seq datasets were processed using a custom pipeline implemented in Snakemake. Briefly, reads were trimmed using the Trimgalore tool (https://github.com/FelixKrueger/TrimGalore) and aligned using Bowtie with standard parameters. Duplicates and multi-mapping reads were removed using the samtools package and the XS flag in the bam files.Peaks were called using the callpeak mode in MACS2 (https://github.com/taoliu/MACS) for broad and narrow peaks.Various QC parameters (FRiP, PCR bottleneck coefficient, cross-strand correlation) were determined according to the ENCODE guidelines.
A consensus peakset was defined from the two biological replicates by taking the merged peaks generated by the findOverlapsOfPeaks function from the R/Bioconductor package ChIPpeakAnno. ATAC signal was calculated for these peaks using bigWigAverageOverBed.
Differentially "bound" peaks were identified using the R/Bioconductor package DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig genome-wide coverage tracks; MACS narrowPeak calls

extract_protocol:
ATAC-seq was performed in biological duplicates, as described in http://msb.embopress.org/content/15/5/e8339 Briefly: viable frozen cells were incubated with Tn5 in 0.1% Igepal CA-630 (37C, 30'). Transposition was stopped with EDTA and DNA purifired using AMPure beads.
After DNA purification, barcodes were added using PCR and DNA re-purified again on AMPure beads. These prepared libraries were then sequenced (50 bp, single-end) on an Illumina HiSeq 2000 or 4000.

value: RTK_I-like glioblastoma cell line


title: ut_WT_8

value: uterus


title: sexual_stage5 rep3-1_WT

city: East Lansing

first: Wonyong

last: Kim

state: Michigan

address: 612 Wilson Road, Room 166

department: Plant Biology

institute: Michigan State University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 High Output flow cell (v4) using Illumina HiSeq SBS reagents (v4) in a 1x50bp paired end format. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
Poor quality reads were trimmed and/or filtered out, and adapters and homopolymers were trimmed from raw reads, using the ngsShoRT program v2.2, with parameters -lqs 12 -tera_avg 20 -5a_mp 98 -rmHP_ml 10
Filtered reads were mapped to the genome, using the HISAT2 program v2.0.4, with default parameters
Read counts for gene loci in the de novo annotations were calculated using the htseq-count program v0.6.1. Gene expression levels in RPKM values were computed after normalization by effective library size estimated by trimmed mean of M values, using the edgeR R package v3.14.0.
Genome_build: Fusarium neocosmosporiellum str. NRRL_22166 version spades_s14
Supplementary_files_format_and_content: tab-delimited text file include a matrix of RPKM values for all samples and the associated GFF3 file

organism: Fusarium neocosmosporiellum

source_name: carrot agar culture

extract_protocol:
Fungal hyphae were scraped out from carrot agar culture and frozen in liquid nitrogen, and total RNA was isolated using the standard Trizol extraction protocol with additional extraction steps.
The KAPA Stranded RNA-Seq Library Preparation Kit was used with 2 ug of total RNA for the construction of cDNA libraries.
Stranded RNA-seq with poly-A captured RNA samples

value: ascospores

value: wild-type


title: sexual_stage5 rep2-2_WT


title: ut_WT_7


title: ZH487_shControl_ATACseq_rep2


title: ZH487_shSOX10_ATACseq_rep1


title: sexual_stage5 rep2-1_WT


title: ut_KO_6


title: SD7D_2: Sugar diet (7 days), replicate 2


title: ZH487_shControl_ATACseq_rep1


title: ut_WT_5


title: sexual_stage4 rep3-2_WT

value: asci


title: sexual_stage5 rep1_WT


title: ut_KO_4


title: LN229_shSOX10_ATACseq_rep2


title: myo_KO_4

value: myometrium


title: LN229_shSOX10_BRD4


title: LN229_shControl_ATACseq_rep2


title: sexual_stage5 rep3-2_WT


title: ut_WT_3


title: sexual_stage4 rep3-1_WT


title: ut_KO_2


title: LN229_shSOX10_ATACseq_rep1


title: sexual_stage4 rep2-1_WT


title: ut_WT_1


title: sexual_stage4 rep1_WT


title: LN229_shControl_ATACseq_rep1


title: RNA-RepB-2

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
For start-seq: Adapters were removed with Cutadapt,Trimmed reads were aligned with Hisat. Only uniquely mapping reads were used to generate bigwigs. Bigwig files of 5prime end coverage and 3prime end coverage separated by strand were also generated, resulting in 4 bigwig files per start-seq sample.
For RNA-seq: reads were aligned to rn6 genome using STAR. Transcripts wer assembled with stringtie.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files contain coverage, TPM and FPKM values for each RNA-Seq sample. Bigwigs of start-seq files represent the coverage of 5prime end ("leading") or 3prime ("trailing") of reads on either forward or reverse strand

organism: Rattus norvegicus

source_name: cortical Neural progenitors

growth_protocol: embryonic day 14 (E14) Sprague Dawley rats were used to extract cortices. Cells from cortices were grown in Knockout DMEM/F-12 (Gibco) supplemented with 2% StemPro Neural Supplement (Gibco), 2mM GlutaMAX (Gibco), 20ng/ml bFGF (Gibco), and 20ng/ml EGF (Gibco) and collected after a second passage.

extract_protocol:
Total RNA was extracted using Trizol manufacturer's protocol. Small RNA preparation for start-seq was done by size-selection on 6% urea-TBE gel.
mRNA libraries were prepared using NEBNext Ultra II RNA-seq library preparation kit with polyA selection. Start-seq libraries were prepared using enzymatic treatments of gel-selected small RNA with RNA polyphosphatase (Lucigen), polynucleotide kinase (New England Biolabs, NEB), and 5'-terminator exonuclease (Lucigen) and Rpph enzyme (NEB) and ligation with adapters based on Illumina Tru-Seq small RNA kit. Material was PCR-amplified using Tru-Seq small RNA kit reagents as recommended by the manufacturer.

value: cortical neural progenitors

tag: developmental stage

value: Sprague Dawley


title: sexual_stage3 rep3-2_WT

value: paraphyses


title: A549 with siRUNX3 exposed to TGF-β for 48 hours 2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
A549 with siRUNX3 exposed to TGF-β for 48 hours, replicate 2.
VK.Rx3.TGFb_FPKM.txt

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to BGI gene reference using bowtie with default parameters settings
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM gene expression value

source_name: cell line

growth_protocol: RPMI plus 10% FBS

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

treatment_protocol: Control or RUNX3 siRNA transfected cells were exposed to TGF-β for 48 hours.

tag: cell line

tag: transfection

tag: exposure

value: TGF-β


title: sexual_stage4 rep2-2_WT


title: RNA-RepA-2


title: RNA-RepB-1


title: A549 with siRUNX3 1

description:
A549 with siRUNX3, replicate 1
VK.Rx3.TGFb_FPKM.txt

value: vehicle control


title: sexual_stage3 rep2-2_WT


title: A549 with control siRNA exposed to TGF-β for 48 hours 2

description:
A549 with control siRNA exposed to TGF-β for 48 hours, replicate 2
VK.Rx3.TGFb_FPKM.txt

value: control siRNA


title: RNA-RepA-1


title: sexual_stage3 rep3-1_WT


title: A549 with control siRNA exposed to TGF-β for 48 hours 1

description:
A549 with control siRNA exposed to TGF-β for 48 hours, replicate 1
VK.Rx3.TGFb_FPKM.txt


title: sexual_stage3 rep1_WT


title: A549 with control siRNA transfection 2

description:
A549 with control siRNA transfection, replicate 2
VK.Rx3.TGFb_FPKM.txt


title: startSeq-RepB

description:
Start-Seq
short, capped RNA from nucleus


title: sexual_stage2 rep3_WT

value: perithecial wall


title: startSeq-RepA


title: A549 with control siRNA transfection 1

description:
A549 with control siRNA transfection, replicate 1
VK.Rx3.TGFb_FPKM.txt


title: sexual_stage2 rep2_WT


title: sexual_stage5 rep3_WT [re-analyzed GSM2931604]

organism: Fusarium graminearum


title: sexual_stage2 rep1-2_WT


title: sexual_stage5 rep2_WT [re-analyzed GSM2931603]


title: A549 with siRUNX3 2

description:
A549 with siRUNX3, replicate 2
VK.Rx3.TGFb_FPKM.txt


title: sexual_stage5 rep1_WT [re-analyzed GSM2931602]


title: A549 with siRUNX3 exposed to TGF-β for 48 hours 1

description:
A549 with siRUNX3 exposed to TGF-β for 48 hours, replicate 1
VK.Rx3.TGFb_FPKM.txt


title: sexual_stage2 rep1-1_WT


title: sexual_stage4 rep3_WT [re-analyzed GSM2931601]


title: mCRC002 acquired resistance to Cetuximab_miRNA

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

description: small RNA

data_processing:
raw reads produced by Solexa sequencing machine
Remove adaptors and too small and polyA reads
The raw read counts for each miRNA were calculated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts of all mature miRNAs for each sample.

source_name: liver metastatic biopsy of colorectal carcinoma

extract_protocol:
Total RNA was isolated from fresh frozen tumor tissuse using Trizol reagent.
illumina SBS-sequencing by synthesis

value: colorectal carcinoma


title: AGS_con

city: Daejeon

first: Jong Hwan

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: control

growth_protocol: AGS cells were maintained in complete RPMI 1640 medium (WelGENE) at 37°C in a humidified 5% CO2 incubator. Complete media was supplemented with 10% fetal bovine serum (WelGENE), 1% antibiotic-antimycotic solution (gibco).

extract_protocol:
The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: control : AGS cells transfected with empty vector, HOXC10 overexpressed cells : AGS cells transfected with HOXC10 clone vector.

value: AGS


title: mCRC002 pre-treated_miRNA

description: small RNA


title: sexual_stage4 rep2_WT [re-analyzed GSM2931600]


title: sexual_stage1 rep2_WT

value: ascogonia


title: sexual_stage1 rep3_WT


title: sexual_stage3 rep2-1_WT


title: mCRC001 acquired resistance to Cetuximab_miRNA

description: small RNA


title: sexual_stage3 rep3_WT [re-analyzed GSM2931598]


title: mCRC001 pre-treated_miRNA

description: small RNA


title: sexual_stage4 rep1_WT [re-analyzed GSM2931599]


title: sexual_stage0 rep3_WT

value: vegetative hyphae


title: sexual_stage1 rep1_WT


title: sexual_stage0 rep2_WT


title: mCRC002 pre-treated

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat version 2.0.13 with default parameters.
The raw read counts for each gene were calculated using the HTSeq-count script by counting the number of reads overlapping with genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts of all genes for each sample.

extract_protocol:
Total RNA was isolated from fresh frozen tumor tissuse using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: sexual_stage3 rep1_WT [re-analyzed GSM2931596]


title: sexual_stage3 rep2_WT [re-analyzed GSM2931597]


title: AGS_HOXC10

description: AGS_HOXC10 over

source_name: HOXC10 overexpression


title: sexual_stage0 rep1_WT


title: mCRC002 acquired resistance to Cetuximab


title: mCRC001 acquired resistance to Cetuximab


title: sexual_stage2 rep3_WT [re-analyzed GSM2931595]


title: mCRC001 pre-treated


title: sexual_stage2 rep1_WT [re-analyzed GSM2931593]


title: PHS treatment-180min without 351vector

city: Kyoto

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

country: Japan

institute: Kyoto Univ. Sch. of Medicine

hyb_protocol: Competitive hybridization was performed on the DNA microarray (DNA CHIP RESEARCH INC, Yeast Chip Ver2). Supplier's condition was followed for hybridization and washing. In short, arrays were hybridized with 5xSSC-0.5% SDS at 65˚C for overnight and washed with 0.2xSSC-0.1% SDS at 55˚C.

scan_protocol: Data was obtained using an Affymetrix 428 array scanner.  Software version was 1.1.0.100. Scaning speed was of 0.5mm/sec.

data_processing:
Raw data from each channel was evaluated by signal strength and spots giving reliable strength at least in on channel were collected. Median of each channel was used to compensate the difference in Cy5. We used ImaGene version 4.0 (BioDiscovery) to quantify the signal strength of each spots. We used microsoft Excel 2004 for Mac for further calculation.
normalized log2 ratio (Cy5/Cy3) representing test/reference

organism: Saccharomyces cerevisiae

source_name: Mock treated WT (SEY6210a strain) without YEp351 vector

label_protocol: One microgram of polyA+ RNA from these cells were labeled using a CyScribe first-strand cDNA labeling kit (Amersham) where control and phytosphingosine-treated cells were labeled with Cy5 and Cy3, respectively.

growth_protocol: Overnight culture was diluted to OD=0.2 and cultured in SD medium with sodium acetate to adjust to nutral pH.

extract_protocol: Total RNA was purified with hot-phenol method and mRNA was enriched with mTRAP mRNA isolation kit(Activemotif). Quality of mRNA was confirmed with Bioanalyzer2100 thus mRNA quality of these two samples were reliable.

treatment_protocol: Culture was treated with 20 μM phytosphingosine at 30˚C for indicated times.

source_name: Phytosphingosine-treated WT (SEY1620 strain) with YEp351 vector

tag: agent

value: Log-phase cells were treated with phytosphingosine in SD medium with sodium acetate (at neutral pH) for indicated time.

tag: time point

value: 180 min


title: PHS treatment-180min

source_name: Mock treated WT (SEY6210a strain) with YEp351 vector

tag: strain


title: sexual_stage1 rep3_WT [re-analyzed GSM2931592]


title: PHS treatment-120min

value: 120 min


title: sexual_stage1 rep2_WT [re-analyzed GSM2931591]

value: wild-type


title: PHS treatment-60min

value: 60 min


title: PHS treatment-30min

value: 30 min


title: sexual_stage0 rep3_WT [re-analyzed GSM2931589]


title: sexual_stage0 rep1_WT [re-analyzed GSM2931587]


title: Gal_4: Gal/+ (7 days high sugar diet), replicate 4

value: High sugar diet

value: Gr5a-GAL4 / +

value: Labellum


title: Gal_3: Gal/+ (7 days high sugar diet), replicate 3


title: sexual_stage2 rep2_WT [re-analyzed GSM2931594]


title: Gal_1: Gal/+ (7 days high sugar diet), replicate 1


title: Gal_2: Gal/+ (7 days high sugar diet), replicate 2


title: sexual_stage1 rep1_WT [re-analyzed GSM2931590]


title: RNAi_3: OGT RNAi (7 days high sugar diet), replicate 3

value: Gr5a-GAL4 / UAS-OGT RNAi


title: sexual_stage0 rep2_WT [re-analyzed GSM2931588]


title: 13047_WT_RNA-seq

city: Richardson

first: Joseph

middle: Michael

last: Boll

state: TX

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

data_processing:
Reads were imported into CLC Genomics Workbench
Reads were aligned to annotated genome with mismatch, insertion, and deletion cost of 3. Length and Similartiy fraction were set to 0.95. The alignment files were ATCC13047 (ASM2556v1)
Expression was reported as RPKM value
ΔphoPQ and ΔpmrAB RPKM expression values were compared to WT RPKM expression values to indicate fold change in transcripts
Supplementary_files_format_and_content: Excel files were generated by exporting the gene name fold change relative to wild type. Scores represent the fold change of the trancript.

organism: Enterobacter cloacae subsp. cloacae ATCC 13047

source_name: OD600 0.7 mid log phase LB broth

growth_protocol: E. cloacae strains were grown to OD600 = 0.7 n in 5 ml of LB broth at 37 degrees with shaking.

extract_protocol:
Trizol extraction and zymo RNA isolation
NEBNext Ultra RNA library prep kit for Illumina

value: Wild type


title: 13047_ΔphoPQ_RNA-seq

value: pmrAB KO


title: RNAi_2: OGT RNAi (7 days high sugar diet), replicate 2


title: RNAi_1: OGT RNAi (7 days high sugar diet), replicate 1


title: 13047_ΔpmrAB_RNA-seq

value: phoPQ KO


title: 86-J9

city: Paris

first: James

last: Di Santo

address: 28 Rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Bioinformatic  analyses were performed using Sequana RNA-Seq pipeline. Cokelaer et al.  'Sequana' a set of snakemake NGS pipelines. J Open Source Soft 2, 10.21105/joss.00352 (2017)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -O -s 2)
Differential analysis was performed using DESeq2 R package using default parameters
Functional analysis was performed using the Camera method from the limma package using default parameters
Genome_build: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips
Supplementary_files_format_and_content: table is in cvs format, with rows corresponding to each gene and coloumns corresponding to each sample as described above. The numbers correspond to the read counts per gene per sample

organism: Macaca fascicularis

source_name: PBMC samples collected after immunization

extract_protocol:
total RNA was extracted from PBMCs using the RNeasy extraction kit (Qiagen)
The library was prepared using the NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific)

value: peripheral blood mononuclear cells

tag: day after immunization

tag: treatment


title: L44-J9


title: 26-J7


title: 26-J9


title: L44-J7


title: 106-J9


title: 106-J7


title: sample12, non-cancerous tissue,male

city: Shanghai

first: ZHUOAN

last: CHENG

state: Shanghai

address: 2200 Nong, Xietu road

institute: Shanghai Jiaotong University

description: Gene expression data from the corresponding non-cancerous  tissue

hyb_protocol: The labeled cRNA targets were then hybridized in the slides

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, limma package the R program.
Significant differential expressed transcripts were screened by fold change ≥ 2 or ≤ -2 and p value ≤ 0.05.

source_name: the correponding non-cancerous tissues

label_protocol: RNA samples were then used to generate fluorescence labeled cRNA targets for the SBC human ceRNA array V1.0（4´180K, designed by Shanghai Biotechnology corporation, and made by Agilent technologies), which contains 88371 circRNA probes, 77103 lncRNA probes, and 18853 mRNA probes.

extract_protocol: Total RNAs were isolated from the paired tissues samples of 5 LUSC patients by TRIzol reagent (Invitrogen) and purified by RNeasy Mini Kit (Qiagen).

tag: subject id

value: normal lung tissue

tag: gender

value: Male

tag: age


title: sample50,cancer tissue,male

description: Gene expression data from the lung squamous cell carcinoma

source_name: The lung squamous cell carcinoma tissues

value: lung squamous cell carcinoma


title: sample22, non-cancerous tissue,male


title: RNAi_5: OGT RNAi (7 days high sugar diet), replicate 5

tag: diet

tag: genotype/variation


title: sample32, non-cancerous tissue,male

tag: tissue


title: sample32,cancer tissue,male


title: sample6,cancer tissue,male


title: sample6, non-cancerous tissue,male


title: sample50, non-cancerous tissue,male


title: RNAi_4: OGT RNAi (7 days high sugar diet), replicate 4


title: sample12,cancer tissue,male


title: sample22,cancer tissue,male


title: 86-J7

tag: cell type


title: 86-J4


title: L44-J4


title: Rhizobia 6hr Replicate 3

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

description: NimbleGen gene expression array data for custom-design array based on the Medicago truncatula v3.5 genome

hyb_protocol: Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen hybridization station.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

organism: Medicago truncatula

source_name: 18 day old A17 Medicago roots, rhizobia-inoculated, 6hr 5mM NH4NO3 treated

label_protocol: cDNA was synthesised from RNA using the Ovation Pico WTA System (NuGEN Technologies Inc., San Carlos, CA, USA) and purified using Qiagen Qiaquick PCR purification kit. dscDNA was labelled with Cy3 using the Nimblegen one-color DNA labeling kit.

growth_protocol: Seeds were germinated then grown for 4 days on 0.8% agar-modified nitrogen-free Fahräeus medium (MFM) plates before being mock- or rhizobia inoculated with 2mL of OD600=0.02 of Sinorhizobium meliloti 1021 overnight culture. Plants were grown for a further 14 days before treating. All plant growth was in long day (16hr light/8hr dark) constant 25 oC conditions in a Sanyo growth chamber (MLR251).

extract_protocol: Root samples were harvested then total RNA extracted using the Qiagen plant RNeasy kit. Total RNA samples were then treated with the TURBO DNA-free kit (Life Technologies) to remove residual DNA.

treatment_protocol: At dawn on day 14 post inoculation (14 dpi) roots were treated with 2ml liquid MFM supplemented with 5mM NH4NO3 (nitrogen-replete treatment) or liquid MFM supplemented with 0.1mM NH4NO3 (nitrogen-deplete treatment) then sampled at 2hr, 6hr or samples were taken at the point of treatment 0hr.

tag: genotype

value: root


title: L44-J2


title: 26-J4


title: H4tm3

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

data_processing:
RNA-seq: the cDNA library with a fragment length range of 300 bp (±25 bp) was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500).
Filtering: Adapter sequences were removed,higher N rate sequences, and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the SeqPrep and Sickle software.
Gene annotation: National Centre of Biotechnology Information (NCBI) non-redundant (NR) and SWISS-Prot database were used to annotated all the unigenes using DIAMOND v0.8.37.99 (E-value <1E-5). The predicted protein sequences were subjected to protein domain searches using HMMER v3.1b2 against the Pfam protein family database (http://pfam.xfam.org/).
Gene Expression Analysis: Gene expression levels were measured in the RNA-Seq analysis as fragments per kilobase of exon model per million mapped reads (FPKM). The DEseq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR < 0.01).
Supplementary_files_format_and_content: The excel file contain the gene name, fpkm value, the number of total reads

organism: Boehmeria nivea

source_name: Huangzhu No 4

growth_protocol: The ramie plants were growing at 25 ± 1°C with a 12 h photoperiod，75% ± 1 RH, under light intensity of 5000 lux, in a greenhouse of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science (IBFC, CAAS). To prepare shoots for cutting propagation, tops of the main stem were removed (topping) when the plants were about 80 to 100 cm in height. Lateral branches were allowed to grow in feaf axil on the main stem, and were cut when they were 10 to 15 cm in length.

extract_protocol:
To prepare samples for Illumina sequencing, total RNA of each sample was extracted using an EASYspin plus Total RNA kit (Aidlab, Beijing, China) following the protocol. Quality and yield of RNA were determined by agarose gel electrophoresis and Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.
Total RNA was extracted from the stem samples with TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified with Plant RNA Purification regent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The concentration and purity of total RNA was determined using NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was examined by Agilent2100 bioanalyzer (Agilent, Santa Clara, CA, USA).Illumina sequencing was performed at Majorbio Bio-pharm Technology Co. Ltd, Shanghai, China (http://www.majorbio.com/). For transcriptome sequencing, eight individual libraries (Yy97ck1, Yy97ck2, Yy97tm1, Yy97tm2, Hdck1, Hdck2, Hdtm1 and Hdtm2) were constructed using 5 μg of total RNA. Briefly, poly (A) mRNA was extracted from the total RNA sample using Oligo (dT) magnetic beads. mRNA was fragmented into 200–500 nt pieces by adding a fragmentation buffer. First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random hexamer primers. After generation of second-strand cDNA, the double-strand cDNA was end-repaired, and a single ‘A’ base and indexed adapters were ligated to the fragments. The cDNA library was constructed with the Illumina Paired End Sample Prep kit (Illumina, USA), quantified by TBS380 (Picogreen, Invitrogen, USA) and was then sequenced on the Illumina HiSeqTM2500 (2×150 bp read length) platform.

treatment_protocol: Then the branches were inserted into conical flask (100 ml) with 100 ml autoclaved tap-water, one branch in one flask, and there were about 4 to 5 cm of the stem were submerged in the water.The tap-water was renewed every two days. The root primordia formation (RAF) and lateral roots development were monitored every day.

tag: cultivar

value: Huazhu no 4 (H4)

value: stem

tag: developmental stage

value: early stage of adventitious root formation


title: 106-J2


title: Day 15 Naive

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

institute: KI

data_processing:
Sequencing was analyzed using the Ataqc pipelines of the Kundaje lab (https://github.com/kundajelab/ataqc). Differential sequencing analysis was performed with DiffBind
Genome_build: mm9
Supplementary_files_format_and_content: bed file format

source_name: Lung and Airways

extract_protocol:
ATAC-Seq was performed using a previously described optimization of the original protocol of Corces et al. (Nature Genetics, 2017). T helper cells were sorted using a BD FACSAria Fusion from the lungs (indlucing airways) of mice 15 days after sensitization and challenge with HDM. Four populations were sorted – Th2 cells (CD3+CD4+CD44+ST2+CD30L+), Non-Th2 memory cells (CD3+CD4+CD44+ST2-CD30L+), Treg (CD3+CD4+CD25hiCD30L-) and naïve T helper cells (from mLN, CD3+CD4+CD44loCD62Lhi). Three biological replicates were sorted for each population.
In total, 1000 of each T helper cell subset was purified from the combined lung and airway tissue. Cells were sorted directly into 25 µl of Tn5 transposase buffer (TD Buffer, 0.02 % Digitonin, Nextera DNA Library Prep Kit, Illumina). Immediately after sorting, 2.5 µl Tn5 transposase was added to each well on ice and mixed thoroughly by pipetting. The plate was next sealed and incubated at 37 oC for 30 minutes on a standard thermocycler. The reaction was stopped by adding 300 µl ERC buffer (QIAGEN MinElute Reaction Clean up kit) and fragmented DNA was isolated by column purification (QIAGEN, MinElute). Total fragmented DNA was subjected to PCR amplification (NEBNext PCR master mix, New England Biolabs) with illumina adapters (indexes 1-12) for 16 cycles (for indexes see Corces et al.). Final libraries were size-selected with Ampure XP magnetic beads (Beckman Coulter) and pooled for sequencing on a Hiseq2500 on high output mode with paired-end 2x 125 reads (Illumina).

tag: model

value: HDM

value: Lung

tag: condition

value: asthma


title: H4tm2

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science


title: H4tm1


title: 86-J2


title: 106-J4


title: L44-J14


title: Day 15 Other Effector


title: Rhizobia 6hr Replicate 1


title: Rhizobia 2hr Replicate 3

source_name: 18 day old A17 Medicago roots, rhizobia-inoculated, 2hr 5mM NH4NO3 treated


title: Day 15 Treg


title: H4ck2


title: H4ck3


title: Rhizobia 2hr Replicate 2


title: Day 15 Th2


title: Rhizobia 2hr Replicate 1


title: H4ck1


title: Rhizobia 0hr Replicate 3

source_name: 18 day old A17 Medicago roots, rhizobia-inoculated, 0hr sample


title: Rhizobia 0hr Replicate 1


title: 86-J14


title: Rhizobia 0hr Replicate 2


title: Mock 6hr Replicate 2

source_name: 18 day old A17 Medicago roots, mock-inoculated, 6hr control treatment


title: Mock 2hr Replicate 3

source_name: 18 day old A17 Medicago roots, mock-inoculated, 2hr control treatment


title: KO-Rep2-RNAseq

city: Barcelona

first: Maria

last: Vila-Casadesús

address: Carrer del Dr. Aiguader, 88

institute: CRG

data_processing:
RNAseq was aligned with STAR and genome annotation Gencode M17.
Annotation was done using STAR --genecounts option.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated with deeptools

source_name: ESCs

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. UMI-4C libraries were purified with AmpureXP beads.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library Preparation Kit. UMI-4C libraries were prepared according stardard NEBNext DNA libaray preparation instructions.

value: ESCs


title: Mock 6hr Replicate 3


title: Z2_tm3

source_name: Zhongzhu No2

value: Zhongzhu no 2 (Z2)


title: Mock 2hr Replicate 2


title: 26-J14


title: KO-Rep1-RNAseq


title: Z2_tm2


title: WT-Rep2-RNAseq


title: L44-J0


title: 26-J0


title: 106-J14


title: Z2_tm1


title: 106-J0


title: WT-Rep1-RNAseq


title: Hi-pancM

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

data_processing:
The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (Illumina Inc, San Diego, CA) producing a 275 bp fragment including adapters in average size. In the final step before sequencing, eight individual libraries were normalized and pooled together using the adapter indices supplied by the manufacturer.
Pooled libraries have then been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3—cBot—HS(Illumina Inc) sequencing was then performed as 50 bp, single reads and 7 bases index read on an Illumina HiSeq2500 instrument using the TruSeq SBS Kit HS- v3 (50-cycle) (Illumina Inc.).
RNA-Seq reads from mouse samples were aligned to the mouse genomes respectively using the STAR Aligner v2.5.2a  with their corresponding Ensembl 84 reference genomes. Sequenced read quality was checked with FastQC v0.11.2  and alignment quality metrics were calculated using the RNASeQC v1.1
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the FPKM as well as read counts from the feature counts software package
FPKM values were log transformed and mean centered prior to filtering for large changes.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HI-Panc progression model_metastatic (HI-Panc-M)

growth_protocol: Cell lines developed by us were cultered in  DMEM supplemented with 10 % FBS.

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

treatment_protocol: We performed the RNA-seq analysis of hypoxic cell models. For this purpose, PDAC models were treated with cobalt chloride (100ng/ml) for 24h.

value: K-rasG12D/p16-/- transgenic

value: Liver

tag: Stage

value: metastatic (HI-Panc-M)


title: Z2ck3


title: Z2ck2


title: 86-J0


title: Mock 2hr Replicate 1


title: Hi-pancL

source_name: HI-Panc progression model_localized (HI-Panc-L)

value: Body wall

value: localized (HI-Panc-L)


title: Z2ck1


title: G44-J9

value: peripheral blood mononuclear cells


title: Hi-panci

source_name: HI-Panc progression model_invaise  (HI-Panc-I)

value: pancreatic tissue

value: invaise  (HI-Panc-I)


title: 37-J9


title: DNA input_EXP#3

city: Leuven

first: Pierre

last: Vanderhaeghen

address: O&N4 Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
all ChIP-seq experiments and sequencing datasets were pooled and aligned to mm10 mouse genome assembly using Bowtie
Peaks were called using MACS with standard parameters and default cutoff P value <10e-5.
Target genes associated with peaks were identified by GREAT version 3.0
Search for an enrichment of Bcl6 matrices in the MACS-called ChIP peaks was performed using i-cisTarget using a promoter-only database.
Genome_build: mm10
Supplementary_files_format_and_content: gene list associated with Chip-seq.txt

source_name: cortical progenitor cells

growth_protocol: The A2 lox.Cre Bcl6 cell lines, tetracyclin-inducible Bcl6 ICE (A2lox.Cre) mouse Embryonic Stem Cells were routinely propagated on irradiated mouse embryonic fibroblasts in DMEM supplemented with 15% ESC-certified fetal bovine serum (vol/vol), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 50 U.ml−1 penicillin/ streptomycin and 10E3 U.ml−1 mouse Leukemia Inhibitor Factor. For differentiation, A2 lox.Cre Bcl6 mouse ESCs were plated at low density (20 × 10E3 ml−1) on gelatin-coated 5-cm dishes (day -1). At day 0, the ES medium was changed to DDM medium. At day 2, DDM was supplemented with cyclopamine (400 ng/mL) and the medium was replenished every 2 days. After 10 days, medium was switched back to DDM (Gaspard et al., 2009).

extract_protocol:
A2 lox.Cre Bcl6 cells were fixed with 1% formaldehyde in phosphate-buffered saline and then lysed, sonicated, and immunoprecipitated as described previously (Castro et al., 2011).
ChIP libraries were prepared according to the standard Illumina ChIP-seq protocol and were sequenced with the Genome Analyzer IIx (Illumina)

treatment_protocol: differentiation day 12, 24h Bcl6 induction using 1 µg.ml−1 Doxycline treatment

tag: cell types

value: ES-cell derived A2 lox.Cre Bcl6 progenitor cells

tag: differentiation day

value: day 12

tag: chip antibody


title: Mock 6hr Replicate 1

value: root


title: Mock 0hr Replicate 1

source_name: 18 day old A17 Medicago roots, mock-inoculated, 0hr sample


title: Mock 0hr Replicate 3


title: Mock 0hr Replicate 2


title: 23-J9

source_name: PBMC samples collected after immunization

tag: day after immunization

tag: treatment


title: sunn 1 Rhizobia 6hr Control Replicate 3

source_name: 18 day old sunn-1 Medicago roots, rhizobia-inoculated, 6hr control treated

value: hypernodulating mutant SUPERNUMERARY NODULES (Medtr4g070970, sunn-1)


title: sunn 1 Rhizobia 6hr Control Replicate 2


title: JNB5-1

city: Wuxi

first: Xuewei

last: Pan

address: 1800, Lihu Avenue

institute: Jiangnan University

description: processed data file: ZK66-VS-JNB5-1.GeneDiffExp.txt

data_processing:
Use software FastQC (v0.10.1) to control of raw data's quality.
Use Cutadapt (version 1.9.1) to filtering low-quality data, removing contamination and joint sequence.
Use bowtie2 (v2.1.9) software to compare with reference sequence.
Software (V 0.6.1) Htseq was used to calculate gene expression, the software used FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method to calculate gene expression.
Differentially expressed genes between samples JNB5-1 and ZK66 were screened based on differentially expressed genes. KEGG_B_Class function enrichment analysis were performed for significant difference genes.
Genome_build: S. marcescens WW4 (NC_020211.1)
Supplementary_files_format_and_content: ZK66-VS-JNB5-1.GeneDiffExp.txt: Tab-delimited text file includes FPKM values for each sample.

organism: Serratia marcescens

source_name: Bacterial culture

growth_protocol: Bacterial cultures were routinely incubated in LB medium at 30℃.

extract_protocol:
The collected cells were treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis.
The total RNA extracted from the bacteria were subjected to rRNA removing to obtain mRNA. The mRNA was used as templates for DNA synthesis. Illumina Hiseq platform was used for the cDNA libraries sequencing.

treatment_protocol: S. marcescens JNB5-1 and ZK66 cells were grown in LB medium for 12 h before harvesting.

tag: strain

value: Wild type (parent)


title: Bcl6 ChIP-seq_EXP#3

value: Bcl6 (Santa Cruz Biotechnology; Cat# sc-858, RRID:AB_2063450)


title: DNA input_EXP#2


title: 51-J9


title: G44-J7


title: Bcl6 ChIP-seq_EXP#2


title: 37-J7


title: ZK66

value: metR mutant


title: DNA input_EXP#1


title: Bcl6 ChIP-seq_EXP#1


title: 23-J7


title: 51-J7


title: gc-CTRL rep3

city: Changchun

first: Yun

last: Zhao

state: Jilin

address: Xi'an Road

department: College of Animal Sciences

institute: Jilin University

data_processing:
Primary sequencing data produced using the Illumina HiSeqTM 2500 system were considered raw reads
Raw sequencing data generally feature clean reads, reads with a sequencing primer, tags containing N, and adapter sequences. Raw reads were filtered into clean reads, and low-quality regional data were removed for downstream analysis (quality control)
When the alignment results passed quality control, downstream analysis was performed, including analyses of gene expression levels, DEGs, Gene Ontology (GO) enrichment, and pathway enrichment. Gene expression levels were calculated by fragments per kilo bases per million mapped reads (FPKM).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism: Sus scrofa

source_name: ovary

growth_protocol: The culture medium consisted of DMEM/F12 with 10% FBS and 1% penicillin-streptomycin. The cells were incubated under humidified atmosphere containing 5% CO2 at 37°C for 24 h, and then washed with PBS to remove any unattached cells.

extract_protocol:
Total RNA was extracted from GCs of the pLVX-RBP4 group and the CTRL group with TRIzol reagent according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GCs were infected with lentiviral particles for 72 h

value: landraces

value: ovary

value: granulosa cell


title: gc-CTRL rep2


title: sunn 1 Rhizobia 6hr Nitrogen Replicate 2

source_name: 18 day old sunn-1 Medicago roots, rhizobia-inoculated, 6hr 5mM NH4NO3 treated


title: 37-J4


title: sunn 1 Mock 6hr Control Replicate 2

source_name: 18 day old sunn-1 Medicago roots, mock-inoculated, 6hr control treated


title: gc-CTRL rep1


title: sunn 1 Mock 6hr Control Replicate 3


title: sunn 1 Rhizobia 6hr Nitrogen Replicate 3


title: 24h_reversal_Rep1

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

hyb_protocol: 6ug of labeled Cy3 or Cy5 cDNA were hybridized to human 385K NimbleGen Gene Expression microarrays according to manufacturer’s instructions.

scan_protocol: NimbleGen MS200 array scanner and NimbleScan software were used to scan the arrays and generate pair files as per manufacuturer's instructions.

data_processing: Pair-files were analyzed using Array star software using defualt parameters (RMA normlalization).

source_name: human ESC (H9)

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, 1 ug of cDNA was  Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: H9 hESCs were cultured under feeder-free conditions in suspension in StemPro (Thermo Fisher, A1000701) culture media per Schilz et al. 2012.

extract_protocol: Total RNA was harvested and purified with Qiagen’s RNeasy (74104) mini kit. Poly-A mRNA was converted to cDNA using Superscript III (Thermofisher 18080).

treatment_protocol: Differentiation towards Definitive Endoderm for 6, 12, 24 and 48 h time-points were carried out as per Schulz et al., 2012. Briefly, hESC cultures at 70% confluency were washed 2x with cold PBS and stimulated to differentiate by the addition of RPMI (Invitrogen), 50ng/ml Wnt (CellGS, GFM77), 100ng/ml Activin A (CellGS, GFH6). 24 hours after stimulation, media was replaced with RPMI containing 0.2% FBS, and 100 ng/ml Activin A.

tag: tag

value: 24 hours+24 hours reversal

tag: replicate


title: sunn 1 Rhizobia 6hr Control Replicate 1


title: 23-J4


title: 24h_reversal_Rep2


title: sunn 1 Rhizobia 6hr Nitrogen Replicate 1


title: gc-RBP4 rep3


title: 51-J4


title: sunn 1 Mock 6hr Control Replicate 1


title: 48h_reversal_Rep1

value: 48 hours+24 hours reversal


title: sunn 1 Mock 6hr Nitrogen Replicate 2

source_name: 18 day old sunn-1 Medicago roots, mock-inoculated, 6hr 5mM NH4NO3 treated


title: gc-RBP4 rep2


title: 12h_reversal_Rep2

value: 12 hours+24 hours reversal


title: 12h_reversal_Rep1

value: 12 housr+24 hours reversal


title: 48h_reversal_Rep2


title: 6h_reversal_Rep2

value: 6 hours+24 hours reversal


title: G44-J4

value: peripheral blood mononuclear cells


title: G44-J2


title: sunn 1 Mock 6hr Nitrogen Replicate 3


title: gc-RBP4 rep1


title: 37-J2


title: 6h_reversal_Rep1


title: A17 Rhizobia 6hr Control Replicate 2

source_name: 18 day old A17 Medicago roots, rhizobia-inoculated, 6hr control treated


title: 23-J2


title: 51-J2


title: Mock2

city: Wuhan

first: Junjing

last: Wu

address: No.1 Nanhu Yaoyuan, Nanhu Road

institute: Hubei Provincial Academy of Agricultural Sciences

data_processing:
Data filtering, raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Mapping, clean data were aligned to the porcine reference genome using TopHat v2.0.9.
Transcriptome assembly, the mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach.
Coding potential analysis, transcripts predicted with coding potential by  CNCI v2, CPC v0.9-r2, Pfam-scan v1.3, and phyloCSF v20121028 were filtered out, and those without coding potential were our candidate set of lncRNAs.
Quantification of gene expression level, Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: porcine reference genome
Supplementary_files_format_and_content: cufflinks.gtf files were generated using  Cuffdiff (v2.1.1)

source_name: mock_alveolar macrophages

extract_protocol:
Total RNAs of the PAMs were isolated using the miRNeasy Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PRRSV groups were infected with PRRSV-WUH3 at a MOI of 0.1, Mock groups were treated with RPMI-1640 culture medium

tag: sample group

value: culture medium treated

value: lung

value: primary alveolar macrophages


title: Mock3

tag: tissue


title: sunn 1 Mock 6hr Nitrogen Replicate 1

value: root


title: Mock1

tag: cell type


title: PRRSV3

source_name: PRRSV_alveolar macrophages

value: PRRSV infected


title: 48h_Rep1

value: 48 hours


title: 37-J14


title: 48h_Rep2


title: A17 Rhizobia 6hr Control Replicate 3

tag: genotype


title: PRRSV2


title: A17 Rhizobia 6hr Nitrogen Replicate 3

source_name: 18 day old A17 Medicago roots, rhizobia-inoculated, 6hr 5mM NH4NO3 treated


title: 24h_Rep1

value: 24 hours


title: 12h_Rep2

value: 12 hours


title: PRRSV1


title: A17 Rhizobia 6hr Control Replicate 1


title: G44-J0


title: 51-J14


title: 24h_Rep2


title: G44-J14


title: A17 Mock 6hr Control Replicate 2

source_name: 18 day old A17 Medicago roots, mock-inoculated, 6hr control treated


title: 6h_Rep2

value: 6 hours


title: 37-J0


title: A17 Mock 6hr Control Replicate 1


title: RawRL-CD137 rep3

city: Tianjin

address: 94 Weijin Road

institute: Nankai University

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to mm10 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values and statistics for each comparison

source_name: RAW264.7 cell line

extract_protocol:
4 mg total RNA from each sample was extracted by TRIzol reagent.
RNA libraries were prepared for sequencing using  oligo-dT beads

tag: gene expression

value: Renilla luciferase, Cd137(mus)

value: monocyte/macrophage cell line

tag: cell line


title: A17 Rhizobia 6hr Nitrogen Replicate 2


title: 23-J14


title: 6h_Rep1


title: 23-J0


title: RawRL-CD137 rep2


title: A17 Rhizobia 6hr Nitrogen Replicate 1


title: 12h_Rep1


title: A17 Mock 6hr Nitrogen Replicate 3

source_name: 18 day old A17 Medicago roots, mock-inoculated, 6hr 5mM NH4NO3 treated


title: RawRL-CD137 rep1

description: Con_1 vs CD137_1.xls


title: 51-J0


title: RawRL-Con rep2

value: Renilla luciferase


title: Yeast_total_RNA_rep1

city: Ann Arbor

first: mehmet

last: tardu

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Illumina data processing pipeline was used for base calling.
FastQC (v0.11.8) was used to evaluate the initial quality of the raw reads.
cutadapt (v1.18) was used to obtain high quality clean reads with the arguments -u 10 -m 15 -q 10.
All downstream analyses were based on clean, high quality data. Bowtie2 (v2.3.4.3) was used to align reads to Saccharomyces cerevisiae reference genome. Following alignment, mmquant  (v0.1.0) was used to count the number of mapped reads for each transcript. Then, gene_biotype feature in GTF file was used to classify RNA species as mRNA, rRNA, tRNA, etc. Afterthat, percentage of mapped reads to each RNA species was calculated.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Microsoft Office Excel Spreadsheet  (mmquant calculated read counts for all samples)

organism: Saccharomyces cerevisiae BY4741

source_name: exponentially growing (OD600 = 0.6) Saccharomyces cerevisiae cells

growth_protocol: Individual yeast colony was inoculated into 10 mL of YPD media and grown overnight at 30 °C with agitation (200 rpm).

extract_protocol:
Total RNA was extracted from 10 mL of yeast cells (OD600 = 0.6) using a standard hot acidic phenol method. Total RNA samples were treated with RNase-free DNase I (1 U/µg) to remove residual genomic DNA. poly(A) RNA isolation was performed in two sequential steps. In the first step oligo-dT magnetic beads were used to selectively bind poly-adenylated RNAs; these beads hybridize to the poly(A) sequence terminating the 3’ end of eukaryotic mRNAs. In the second step, we used a commercial rRNA depletion kit (RiboZero Gold) to remove the residual 5S, 5.8S, 18S and 28S rRNAs from our samples.
After quality and quantity measurements by using 2100 BioAnalyzer, 50 ng of total RNA and poly(A) RNA were fragmented using fragmentation buffer with the TruSeq mRNA Sample Preparation Kit according to manufacturer's instructions. Briefly, fragmented RNAs fragments were used for the first-strand cDNA synthesis using random hexamer-primer, and then the second strand was synthesized by using DNA polymerase I and RNase H. The double strand cDNAs were purified with AMPure XP beads and eluted with resuspension buffer followed by end-repair and 3’end adenine nucleotide addition. Finally, indexing adaptors were ligated to the fragments and cDNA fragments were enriched by 14-cycles of PCR amplification. Single-end sequencing was performed for the two cDNA libraries (two biological replicates) for each sample (poly(A) RNA and total RNA) using the Illumina HiSeq 4000 sequencing platform.  All sequence data are SE 50 bp.  Image processing, base calling, and quality value calculation were performed by the Illumina data processing pipeline. Raw reads were saved in FASTQ format.

treatment_protocol: Cells were then diluted to OD600 = 0.05 into 100 mL of YPD media and grown to an OD600 of 0.6.

value: wild type


title: 09-J9


title: A17 Mock 6hr Nitrogen Replicate 2


title: H9ESC_Rep1

value: ESC


title: Yeast_polyA_RNA_rep2


title: 53-J9


title: RawRL-Con rep1

description: Con_1 vs CD137_1.xls


title: Yeast_total_RNA_rep2


title: PKD_FP_rep2

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
Low quality reads was filtered using internal software SOAPnuke
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Mouse kidney

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

value: kidney


title: 41-J9

source_name: PBMC samples collected after immunization


title: skin from fish given DnaK taken 6 weeks post treatment biological rep6

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using the TrimGalore! software version 0.5.0. This software was used to trim low-quality ends from reads and for Illumina adapter removal.
Bowtie2 version 2.3.4.2 was used for alignment of reads to the channel catfish transcriptome using the alignment parameters as recommended by the eXpress software.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.5.1.
Genome_build: RefSeq transcripts from the channel catfish genome (assembly IpCoco_1.2)
Supplementary_files_format_and_content: tab-delimited text files of effective read counts, rounded to the nearest whole number

organism: Ictalurus punctatus

source_name: skin explant

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

value: rDNAK immunized

tag: time

value: 6 week

value: skin


title: H8_3_RNA-Seq

first: Chao-Tao

last: Tang

address: Shan Dong Middle road 145

institute: Renji hospital

data_processing:
For RNA sequencing, RNA samples from 6 biological replicates were separated into two independent pools, each comprised of three distinct samples at equal amounts.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina HiSeq X Ten instrument by the commercial service of Genergy Biotechnology Co. Ltd.
The raw data was delieved into NCBI’s Gene Expression Omnibius, and was handled by Perl and data quality was checked by FastQC v0.11.2. Clean reads were aligned to the chicken genome (release: Gallus gallus 4.0) from NCBI using Bowtie, with one mismatch allowed.
the expression of the transcript was calculated by FPKM using Perl.
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

source_name: Human Umbilical Vein Endothelial Cell

growth_protocol: HUVEC was cultured in the Endothelial Cell Medium （ECM）（ScienCell, USA）, supplemented with 10% fetal bovine serum (FBS; Gibco). Both of them were in the incubator at 37 °C and in a 5% CO2 humidified environment.

extract_protocol:
Total RNA was isolated from each thymic sample using the standard TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EGFL6 shRNAs,Transfection reagent was FuGENE® HD Transfection Reagent (32043, Active Motif, USA).

value: Human Umbilical Vein Endothelial Cell

tag: egfl6 expression

value: Depletion


title: Yeast_polyA_RNA_rep1


title: H9ESC_Rep2


title: H8_2_RNA-Seq


title: A17 Mock 6hr Control Replicate 3

value: root


title: 31-J9

address: 28 Rue du Dr Roux

institute: Institut Pasteur

data_processing:
Bioinformatic  analyses were performed using Sequana RNA-Seq pipeline. Cokelaer et al.  'Sequana' a set of snakemake NGS pipelines. J Open Source Soft 2, 10.21105/joss.00352 (2017)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -O -s 2)
Differential analysis was performed using DESeq2 R package using default parameters
Functional analysis was performed using the Camera method from the limma package using default parameters
Genome_build: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips
Supplementary_files_format_and_content: table is in cvs format, with rows corresponding to each gene and coloumns corresponding to each sample as described above. The numbers correspond to the read counts per gene per sample

extract_protocol:
total RNA was extracted from PBMCs using the RNeasy extraction kit (Qiagen)
The library was prepared using the NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific)

value: peripheral blood mononuclear cells


title: PKD_FP_rep1


title: A17 Mock 6hr Nitrogen Replicate 1


title: H8_1_RNA-Seq


title: K562-shHNRPDL-rep3

city: Suzhou

first: Xiuyan

last: Zhang

address: 199 Ren'ai Road

institute: Soochow University

description: Gene expression of shHNRPDL virus infected K562 cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction buffer containing Agilent fragmentation agent and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, same volume of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-074348 Human LncRNA Oligo Microarrays (v6 4X180K) for 17 hours at 65°C in a rotating hybridization oven (Agilent, G2545A) with a speed of 10rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3μm, Dye channel is set to Green).

data_processing: After generating the microarray scan images, the .tif images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028680_D_20199527) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: K562 cells_shHNRPDL

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, 5190-2305) according to the manufacturer's instructions, followed by RNAeasy mini spin column purification (QIAGEN, 74106). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: The cells were cultured with RPMI 1640 medium supplemented with 10% fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Rneasy mini kit (QIAGEN, 74104) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 UV-VIS spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: K562 cells were infected with Scramble and shHNRPDL virus, and after 72 hours GFP+ cells were sorted for RNA extraction.

value: chronic myeloid leukemia (CML) cell line

tag: genotype/variation

value: HNRPDL silenced


title: PKD_DMSO_rep2


title: skin from fish given DnaK taken 6 weeks post treatment biological rep5


title: 09-J7

first: James

last: Di Santo


title: skin from fish given DnaK taken 6 weeks post treatment biological rep4


title: Hn_3_RNA-Seq

value: Normal


title: K562-shHNRPDL-rep2


title: Hn_2_RNA-Seq


title: PKD_DMSO_rep1


title: 53-J7


title: K562-scramble-rep2

description: Gene expression of scramble virus infected K562 cells

source_name: K562 cells_scramble

value: scramble control


title: skin from fish given DnaK taken 6 weeks post treatment biological rep3


title: K562-scramble-rep3


title: K562-scramble-rep1


title: skin from fish given DnaK taken 6 weeks post treatment biological rep2


title: Hn_1_RNA-Seq


title: WT_DMSO_rep2


title: WT_DMSO_rep1


title: 53-J4


title: WT_FP_rep1


title: 09-J4


title: 31-J7


title: 41-J7


title: PD-2

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

data_processing:
Illunima Casava 1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads  containing adapter, reads containing poly-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using STAR and paired-end  clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the  method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Tab-delimited xls files include FPKM values for all Samples

source_name: A2780 cell lines

extract_protocol:
RNAs were isolated from A2780 cells using the TRIzol (Invitrogen) reagent by following the company manual. RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0  Flurometer (Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: A2780 cells were treated with DMSO, Olaparib, Palbociclib, and their combination (Ola/PD) for 24 hours.

value: ovarian carcinoma

tag: morphology

value: Epithelial

value: Palbociclib - treated


title: Ola+PD-1

value: Ola/PD - treated


title: skin from fish given DnaK taken 6 weeks post treatment biological rep1


title: skin from fish given DnaK taken 1 week post treatment biological rep6

value: 1 week


title: Ola+PD-2


title: 41-J4

city: Paris


title: skin from fish given DnaK taken 1 week post treatment biological rep5


title: K562-shHNRPDL-rep1


title: skin from fish given DnaK taken 1 week post treatment biological rep4


title: PD-1


title: skin from fish given DnaK taken 1 week post treatment biological rep3


title: 09-J2


title: 53-J2


title: skin from fish given DnaK taken 1 week post treatment biological rep1


title: V-2

value: DMSO - treated


title: 41-J2


title: skin from fish given sham treatment biological rep6

value: control


title: V-1


title: 31-J2


title: skin from fish given sham treatment biological rep5


title: hypoxia 24h, biological rep3

city: Chongqing

first: Xin

last: Zhou

state: Chongqing

address: Xinqiao Road, Sha Ping Ba District

department: Department of Plastic and Cosmetic Surgery, Xinqiao Hospital

institute: Army Medical University

description: Gene expression data from hacat cells from hypoxia treament for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom D Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: epidermal cell

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

growth_protocol: After the HaCaT cells were inoculated into the culture dish, the normoxic group was placed in a conventional incubator, and the hypoxic group was placed in a hypoxic incubator.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment was performed in the normoxic group, and the hypoxic group was treated in a hypoxic incubator for 0.5, 1, 3, and 24 hours, respectively.

value: HaCaT

value: hypoxia treament for 24h


title: 09-J14