title: day_18_3D_Matrigel+ascorbic_acid

city: Neuherberg

first: Simon

middle: Thomas

last: Rosowski

state: bayern

address: Ingolstädter Landstr 1

department: HPC

country: Germany

institute: Helmholtz Zentrum München

data_processing:
For the alignment of reads we used the sequences and annotation files for the human genome (GRCh38) from Ensembl (release 99).
The Cell Ranger (from 10X Genomics, Pleasanton, CA, version 3.1.0) pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices.
The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly.
AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy  (version 1.4.4). The alignment files (bam) were sorted by barcode using samtools (version 1.10) and Velocyto (version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Genome_build: hg19
Supplementary_files_format_and_content: count matrices (.mtx) with genes and cell barcodes (.tsv)

source_name: hiPSCs

growth_protocol: 1. 2D hiPSC cell culture: HiPSCs were cultured on hESC Matrigel-precoated 6-plates according to manufacturer’s recommendations (Corning) in mTeSR1 medium (Stemcell Technologies) at 5% CO2, 5% O2, and 37°C with daily medium change and split twice a week in a 1:6 ratio using 0.05% Trypsin-EDTA (Sigma).  2. 3D suspension culture: For the transfer into a 3D hiPSC cell culture, the medium was aspirated, cells were washed with 2 mL PBS -/- and 500 µL Accutase were added. During incubation at 37 °C for 3 to 7 min, cells detached while adding 2.5 mL mTeSR stopped the reaction. The well was washed with 1 mL mTeSR before centrifugation for 5 min at 200 x g and resuspended in 500 µL mTeSR with Rock inhibitor (1:1000) and 1% Penicillin/Streptomycin (P/S, Thermo). The cells were incubated in ultra-low attachment plates at 37°C and 100 rpm (Fisher).

extract_protocol:
Matrix-free samples were washed with PBS, resuspended in Accutase and incubated for cell detachment at 37°C for 30 min. The reaction was stopped by adding five volumes of media. Afterward, cells were washed once with PBS. Prior to this process, Matrigel embedded samples were washed with PBS, incubated with 0.5 mL Collagenase/Dispase Solution (1:100 to a final concentration of 1 mg/mL in StemPro34) for around 4 h, until organoids detached from the Matrigel. The enzymatic reaction was stopped with 1 mL Neutralisation Buffer (1%BSA, 1%P/S in DMEM:F12). The single cells were cryo-preserved in DMEM with 10% heat-inactivated FBS (Thermo Fisher Scientific) and 10% DMSO based on a previously described scRNA-seq sample preparation protocol(Guillaumet-Adkins et al., 2017). For sequencing, cryo-preserved cells were thawed in DMEM:F12.
RNA libraries were generated using Chromium Single Cell 3’ library and gel bead kit v3.1 (10x Genomics). The amplified cDNA library was sequenced on a NovaSeq 6000 S2 flow cell from Illumina.

treatment_protocol: 3. 3D suspension culture differentiation to ECs: At day -1 of the differentiation, cells were transferred into low attachment 6 well plates in order to form embryonic bodies (1.5 x 106 cells/well). Differentiation was performed according to(Olmer et al., 2018; Patsch et al., 2015). Briefly, from day 0 to 3 N2B27 medium supplemented with BMP4 (25 ng/mL) and CHIR (7.5 µM) was used without media exchange. Media was changed daily from day 3 to 7 using StemPro 34 with VEGFA (200 ng/mL) and forskolin (2 µM). Afterward, StemPro 34 with VEGFA (30 ng/mL) and FGF2 (30 ng/mL) was used with exchange after two days. 4. 3D microwell chip: For matrix-free cultivation, the microwell chip platform, described by Wiedenmann et al., was used to allow the growth of 1196 aggregates in parallel(Wiedenmann et al., 2021). The chip was coated with 10 % Pluronic F 127 (Sigma) overnight and seeded with approximately 1x106 cells. StemPro 34 with VEGFA (100 ng/mL), FGF2 (100 ng/mL), and FBS (15%) was used for cultivation. The medium was exchanged every second day. 5. Hydrogel cell culture: For cultivation in 24 well plates, 100 µL Matrigel were added into each well of the plate that whole ground is covered and incubated at 37°C for 1 h. Aggregates were centrifuged at 800 rpm for 5 min at 4°C, resuspended in 80 µL of Matrigel and spread on top of the first layer. Gel polymerization was done at 37°C inside a container with a bit of ice to allow a slow temperature adjustment. After one hour 0.5 mL media were added. Media composition complies with microwell chip incubation. +AA samples contained 60 µg/mL ascorbic acid. For imaging, the aggregates were embedded in ibidi slides with a number of 10 to 20 per well. The amount of Matrigel and media was adjusted to the smaller volume.

tag: experiment

tag: days of differentiation

tag: specification

value: + ascorbic acid from day 12 on

tag: culture method

value: 3D Matrigel


title: RNAseq_NCU00412_N7990

status: Public on Mar 08 2022

type: SRA

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

country: USA

institute: University of Oregon

description: RNA-seq

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using STAR program (version 2.7.3a)
Total aligned reads per neurospora gene were calculated using RSEM software (version 1.3.1) and normalized using DESeq2 software (version 1.24.0)
Batch effect were corrected using R package, limma (version 3.44.1).
FDR < 0.05 and log2 fold-change > 2 were used as a threshold to identify significantly up- or downreagulated genes.
neurospora crassa genome (OR74A)
tab-deliminated text files of gene ID and expected read count obtained from RSEM calculation

molecule: total RNA

organism: Neurospora crassa

source_name: nuclei from germinated condia

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq kit (KAPA Biosystems).

treatment_protocol: Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature.

tag: sample type

value: nuclei


title: Colorectal Cancer Cells - HCT116_NIVO+sPDL1_24h_rep1

city: Napoli

first: Luigi

last: Portella

address: M. Semmola

department: Research Department

country: Italy

institute: Istituto Nazionale Tumori di Napoli - IRCCS fondazione "Pascale"

data_processing:
RNAseq FASTQ sample sequences were mapped on HG38 genome (Dec. 2013 assembly) with STAR software (v. 2.7.3a) and default options
The resulting BAM files were then processed with feature Countsfunction present into the Rsubread R/Bioconductor package (v.2.4.2) on Ensembl HG38 GTF (v. 102) to produce a count matrix of 64252 genes and 46 samples
To remove lowly expressed genes a proportion test has been performed by the aid of the filtered.data function present into the NOISeq R/Bioconductor package (v. 2.34.0) resulting in 16842 genes for the 46 samples matrix
Samples were then divided for cell line and normalized with RUVs procedure present in the RUVSeq R/Bioconductor package (v.1.24.0).
A different "k" parameter is chosen for each cell line on the best normalization afforded for each case (Cell Line HCT116 k=3, HT29 k=5, PES43 k=1).
Then, for each cell line to test differentially expressed genes, the glmQLFit combined with glmQLFTest from the edgeR R/Bioconductor package (v. 3.32.0).
Functional enrichment analysis was then performed with gProfiler2 R package (v. 0.2.0).
Genome_build: HG38 genome (Dec. 2013 assembly)

organism: Homo sapiens

source_name: Colorectal Cancer Cells

growth_protocol: Human colon cancer cells HCT116 were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco BRL, Grand Island, NY). HT29 were cultured in RPMI (Invitrogen, San Diego, CA, USA). PES43 human melanoma cancer cells (Scala, 2006) were cultured in IMDM. Each medium was supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/mL), streptomycin (100 μg/mL) (Invitrogen, Carlsbad, CA). All the cells were maintained in an incubator with a humidified atmosphere of 5% CO2 at 37°C and were proved mycoplasma-free.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to manufacture protocol
Total RNA was quantified using the Qubit fluorometer (ThermoFisher) with Qubit™ RNA HS Assay Kit (ThermoFisher). Polyadenylated RNA libraries were prepared using QIAseq Stranded mRNA Select Kit (Qiagen). The mRNA Enrichment was obtained starting from 1ug of total RNA using Oligo-dT probes attached to the surface of magnetic beads. Fragmentation was then performed at the reaction temperature of 95°C to obtain an insert size of ~350 bp. Double-stranded cDNA was achieved by a reaction with Rnase H-Reverse Transcriptase in combination with random primers followed by a second-strand synthesis, end repair, and A-addition step. The dual index technology was used to sequence multiple samples thanks to the ligation of Illumina-compatible adapters. Finally, the last amplification step was performed on the purified libraries using the CleanStart PCR Mix, also able to degrade contaminating material. QIAseq Beads were used for reaction cleanups between protocol steps. The quality control and quantification of libraries were performed using the Agilent 2100 Bioanalyzer instrument and High Sensitivity DNA Kit (Agilent). Each QIAseq Stranded library was diluted to a concentration of 4 nM. Then, the libraries with different sample indexes were pooled in equimolar amounts. The pooled libraries at concentration of 1.6 pM were sequenced on Illumina NGS NextSeq 500 platform using 2x 150 bp paired-end mid-output sequencing kit (Illumina).

treatment_protocol: HT29 and HCT116 cells treated with NIVO, sPD-L1 and combination sPD-L1 + NIVO for 6-24 hours and compared to PES43 cells

tag: tissue

value: Colon

tag: disease

value: Colorectal carcinoma

tag: treatment

value: NIVO+sPDL-1 for 24h


title: Colorectal Cancer Cells - HCT116_sPDL1_24h_rep2

value: solubile-PDL-1 (sPDL-1) for 24h


title: day_18_3D_Matrigel

molecule: polyA RNA


title: RNAseq_NCU00412_N7992

description: RNA-seq


title: LAN4_6h_post_stress_2

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
RNA-seq raw data analysis was performed using nf-core rnaseq v3.3. Cleaned reads were aligned to Salmo salar genome SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2). Fragments mapping were counted using featureCounts (subread v1.5.1) and differentially expressed genes (DEGs) were estimated using SARTools R package (v1.7.3). Significant DEGs were determined when the adjusted p-value (padj) was < 0.05. ShinyGO v0.741 was used to perform the enrichment analysis and functional classification of DEGs. Term categories (FDR < 0.05) were displayed and sorted by fold enrichment (minGSSize =2).
Genome_build: Salmo salar genome SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2)
Supplementary_files_format_and_content: Counts of sequencing reads for the features of interest (.counts.txt)

organism: Salmo salar

growth_protocol: For this study, 540 Atlantic salmon (35 g) coming from the same genetic line (Gain) and provided by AquaGen AS (Trondheim, Norway) were distributed in nine tanks (60 fish per tank). Then, fish were fed one of three experimental diets (three tanks per diet) for 7 weeks using automatic belt feeders for feed distribution 6 hours a day with a feeding level of 2% of body weight, adjusted by the average feed consumption in each tank over the last seven days with a 10% excess per day.

extract_protocol:
Gill samples from CD and LAN4 groups (3 fish per diet and sampling time: initial control without stress, 1h post-stress and 6h post-stress) were used to determine the gene expression by RNA sequencing (RNA-seq). Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the supplier’s instructions and then, each RNA sample was quantified using a NanoDrop TM 8000 spectrophotometer (Nanodrop Technologies). RNA integrity was measured by Agilent Bioanalyzer 2100 (all samples showed a RNA integrity number ≥ 7)
Library preparation and RNA-sequencing were performed by the Norwegian Sequencing Center, using TruSeq Stranded mRNA library prep and Illumina Novaseq 6000 System (150 bp paired-end)

treatment_protocol: After 7 weeks of feeding period, 42 Atlantic salmon per diet group were divided into seven tanks with 6 fish per tank. Fish were acclimatized and continued to be fed with the same diets for one week until exposure to stress test. Water temperature was controlled around 15 °C and flow rate was adjusted to maintain the oxygen saturation at 80% and dissolved oxygen concentration at around 7.5 - 8 mg L-1. Then, hypoxia stress consisted of netting the fish out of the experimental tanks for 1 minute, and afterwards placing them back into their respective tanks. Then, for each dietary group, six fish per sampling time: initial control without stress, 0 hour (immediately after stress), 1, 3, 6, 12- and 24-hours post-stress exposure, were taken out, sedated (15 mg L-1 MS222) and sampled for blood. Approximately 1 mL blood was withdrawn from the caudal vein using 2 mL heparinized syringes. The blood samples were separated by centrifugation at 3000 × g for 7 min. Plasma was aliquoted and placed in sterile Eppendorf tubes to be further stored at -80 ºC

value: gill

tag: diet

tag: group

value: LAN4_6h post stress

tag: stress

value: 6h post stress


title: Melanoma Cancer Cells - PES43_NIVO_6h_rep2

source_name: Melanoma Cancer Cells

value: Skin

value: Melanoma

value: NIVOLUMAB (NIVO) for 6h


title: Colorectal Cancer Cells - HCT116_NIVO_24h_rep2

value: NIVOLUMAB (NIVO) for 24h


title: CD-B-ATAC

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

library_source: genomic

data_processing:
peak
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited txt files; data show differential peak and expression between the two groups

molecule: genomic DNA

organism: Mus musculus

source_name: Liver tissue

extract_protocol: ChIP-seq, RNA-seq, ATAC-seq

treatment_protocol: mouse fed a high fat diet (60% kcal fat) or a control diet (18% kcal fat) for 10 weeks

tag: strain

value: mouse fed a control diet (18% fat)


title: LAN4_6h_post_stress_3


title: LAN4_1h_post_stress_3

value: LAN4_1h post stress

value: 1h post stress


title: Colorectal Cancer Cells - HCT116_sPDL1_24h_rep1


title: RNAseq_crf4_2_N8017

description: RNA-seq


title: day_12_3D_Matrigel


title: day_12_3D_suspension_culture

value: 3D suspension culture


title: LAN4_6h_post_stress_1


title: Colorectal Cancer Cells - HCT116_NIVO_24h_rep1


title: day_9_2_3D_suspension_culture


title: IP_DMSO_p65_1

city: Dundee

first: Dimitrinka

last: Ditsova

state: Scotland

address: 64 Atholl Street

department: Division of Gene Regulation and Expression

country: United Kingdom

institute: University of Dundee

data_processing:
Sequencing was performed with a read length of 2 x 100bp using Illumina NovaSeq 6000.
Quality of the reads was assessed with fastqc.
Adapters were trimmed using cutadapt (Martin, 2011).
Trimmed sequences were aligned to human genome assembly hg38 using STAR 2.7.5.
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
The bigWig files were generated by deepTools (Ramírez et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files showed the reads per kilobase per million (RPKM) of ChIP read densities within the 10bp windows of genomic region for triplicate of samples. The 3 replicates for each condition were merged

source_name: Jurkat cells

growth_protocol: Jurkat cells were grown in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% FBS, 0.5 μM β-mercaptoethanol, 50 units/ml penicillin and 50µg/ml streptomycin. Jurkats wer cultured in flasks or dishes at 37oC with 5% CO2.

extract_protocol:
Cells were cross-linked with 1% parafolmaldehyde for 10 minutes and glycine was added to quench the reaction. The cell lysates were prepared as described (Varshney et al., 2018). The chromatin was sonicated in Bioruptor (Diagenode) at high power for 40 min (30 s on/off). 40 micrograms of the sonicated chromatin were used for each IP. 5% of each extract used in the IPs were taken as inputs.For p65, 7.5ug of anti-p65 rabbit polyclonal (Invitrogen; 51-0500) or Rabbit IgG Isotype Control (ThermoFisher; 02-6102) antibody were added to samples and incubated overnight at 4oC, before incubation with 30ul Protein G Dynabeads (Life Technologies) for an additional 2h. Beads were eluted as desribed by Varshney et al before Proteinase K treatment and reverse crosslinking at 42oC overnight. Eluted DNA was purified by QIAquick PCR purification kit (QIAGEN).
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos (Index Primers Set 1) for Illumina.

treatment_protocol: For two of our experimental conditions Jurkat cells were stimulated with 200ng/ml PMA and 300ng/ml ionomycin for 3 hours. All cells were permeabilized with 0.05% Tween-20 in PBS for 10 minutes. Some of the stimulated cells were further treated with 2mg/ml PureLink RNase A (ThermoFisher) for 30 minutes at room temperature.

value: untreated

tag: antibody


title: RNAseq_crf4_3_N7966

description: RNA-seq

value: nuclei


title: RNAseq_NCU09388_N7989

description: RNA-seq


title: Liver WT rep1 [CON14L]

city: shanghai

first: Fei

last: Mao

state: State...

address: Fudan university

country: China

institute: Fudan University

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by thesoftware of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Hisat2.
HTSeq(0.9.1) statistics were used to compare the Read Count values on each gene as theoriginal expression of the gene, and then used FPKM to standardize the expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Liver

extract_protocol:
Livers, WAT,muscles were all removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

tag: age

tag: genotype

value: wild type

value: control


title: day_18_reaggregated_3D_suspension_culture


title: Colorectal Cancer Cells - HCT116_ctr_24h_rep2

value: Colon

value: Colorectal carcinoma


title: LAN4_1h_post_stress_2

value: gill


title: LAN4_initial_control_3

value: LAN4_control w/o stress

value: Initial control (without stress)


title: LAN4_initial_control_2


title: Colorectal Cancer Cells - HCT116_sPDL1_6h_rep2

value: solubile-PDL-1 (sPDL-1) for 6h


title: day_3_3D_suspension_culture


title: day_9_1_3D_suspension_culture_


title: RNAseq_NCU09388_N7988

description: RNA-seq


title: day_6_3D_suspension_culture


title: LAN4_1h_post_stress_1


title: Colorectal Cancer Cells - HCT116_ctr_24h_rep1


title: RNAseq_crf4_1_N6171

description: RNA-seq


title: RNAseq_crf4_3_N8018

description: RNA-seq


title: Colorectal Cancer Cells - HCT116_NIVO+sPDL1_6h_rep2

value: NIVO+sPDL-2 for 6h


title: Colorectal Cancer Cells - HCT116_NIVO+sPDL1_6h_rep1

value: NIVO+sPDL-1 for 6h


title: LAN4_initial_control_1


title: H3K27me2me3_crf4_1_N6170

description: chip-seq

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with default option.
Reads with low mapping quality (MapQ < 10) and from repetitive seuqnces were discarded.
Pileup score were calculated using Homer software (version 4.10.1).
ChIP-seq scores correspond to the total number of mapped tags after normalizing to 10 million reads.
neurospora crassa genome (OR74A)
bigwig of pileup graph

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC

extract_protocol:
Lysates were cleared by centrifugation and 1/20th input was saved. H3K27me2/3 antibody was added (Active Motif, 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the Qiagen MinElute PCR purification kit and eluted in 30 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions. AMPure XP beads (Beckman Coulter A63881) were used for size selection of ~200-800 bp fragments. Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 3x 10 min with a cycle of 30 sec on followed by 30 sec off, at high power.


title: BRD4_3hrIAA_3hrNutlin_rep2

city: Vienna

first: Vanja

last: Haberle

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

description:
BRD4_3hrIAA_3hrNutlin.ps.bw
BRD4_3hrIAA_3hrNutlin.ns.bw
Brd4_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

data_processing:
Library strategy: PRO-seq
UMI removal and adapter trimming: Sequenced reads consist of a 10nt long UMI (for counting unique RNA molecules), followed by PolII active site-associated RNA sequence and potentially a part of the Illumina sequencing adapter (in cases where RNA was shorter than 22nt). Prior to mapping, the UMI sequence (10nt at the 5' end of the read) was removed and noted for later counting. Illumina adapter was trimmed off with cutadapt v1.18.
Read alignment: All reads longer than 15nt after adapter trimming were mapped to a merged reference consisting of hg19 and dm3 (spike-in) genome using Bowtie version 0.12.9 allowing 2 mis-matches. Reads mapping to multiple positions were randomly assigned to one mapping position.
Genomic coverage:  5' ends of mapped reads (the last nucleotide transcribed by PolII) were counted per genomic position taking into account only unique UMIs. Coverage was generated separately for positive and negative strands. Coverage was normalized to tags per million and scaled by a factor obtained from relative spike-in abundance. Coverage was generated with GenomicRanges v1.34.0 package in R and exported into bigWig format with rtracklayer v1.42.2.
Quantification and differential analysis:  5' ends of mapped, UMI-collapsed reads overlapping promoter+pause region (from +1 to +150bp downstream of the TSS) and gene body region (from +150bp to annotated gene end) were counted for each individual sample/replicate. Gene annotation from Ensembl v83 was used, and annotated TSSs were corrected to nearest CAGE-defined TSS from FANTOM5 collection. Provided raw counts were used for downstream differential analysis between different conditions with DEseq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of a referent set of 21115 genes/transcripts with Ensembl v83 gene/transcript IDs, gene names, TSS positions corrected by CAGE and annotated transcription end sites. For each gene raw counts in each individual replicate are provided, separately for promoter+pause region (from +1 to +150bp downstream of the TSS) and gene body region (from +150bp to annotated gene end).  BigWig files contain spike-in normalized genome-wide coverage of PRO-seq reads, separately for positive and negative strands (the values for negative strand are shown as negative).

molecule: nuclear RNA

source_name: HCT116 cells

extract_protocol:
After treatment the cells were harvested and nuclei were isolated. Spike-in control (D. melanogaster S2 cell nuclei; 1% of total human HCT116 cells/nuclei) were added at the level of nuclei permeabilization step. Nuclear-run-on was performed for 3min at 37°C with biotin labeled CTPs (Perkin Elmer #NEL542001EA) followed by RNA extraction and base hydrolysis. Biotin-tagged nuclear-run-on RNA was enriched via M280 streptavidin beads (Invitrogen #112.06D) and precipitated via Phenol-Chloroform treatment.
3’ RNA adapters were ligated to isolated RNA and second biotin RNA enrichment followed by RNA 5’ cap modification via TAP (Biozym #187005) treatment was performed. Furthermore, 5’ hydroxyl repair via PNK (NEB #M0201S) treatment and subsequent 5’ adapter ligation was carried out. Afterwards, cDNA was generated from enriched RNA via reverse transcription (Super Script III Reverse Transcriptase, Invitrogen #18080-044). 10µl of the cDNA library was amplified via KAPA Amplification reaction (Roche #7959028001) on a qPCR machine (Biorad CFX Connect RealTime System). KAPA reaction: 10µl cDNA, 1µl forward primer 35µM (RP1-RP20), 1µl of reverse primer 35µM (RP1: 5’-AATGATACGGCGACCACCGAGATCTACAGTTCAGAGTTCTACAGTCCGA-3’), 25µl 2x KAPA SYBER master mix, 13µl water. PCR program: 98°C - 45 sec, 98°C - 15 sec, 60°C - 30 sec, 72°C - 30 sec, 72°C - 10 sec. Samples were removed from the qPCR machine after 12-15 cycles and cleaned with Ampure beads (Beckman #A63881) in a 1:1.4 (DNA:beads) ratio. DNA bound to the beads was eluted in 11µl of water and subjected to single-end deep sequencing.

treatment_protocol: 1x10^7 WT or COF-AID tagged cells per replicate were treated as follows:   1. Control:  water (mock) treatment for 3h [MED14- and BRD4-AID-tagged cells] or 12h [MED14-AID-tagged cells], or DMSO treatment for 3h [WT]  2. Nutlin:  10µM Nutlin 3a (Sigma# SML0580) treatment for 3h [WT, MED14- and BRD4-AID-tagged cells] or 6h [MED14-AID-tagged cells]  3. Auxin:  500µM auxin (IAA) treatment for 3h [MED14- and BRD4-AID-tagged cells] or 12h [MED14-AID-tagged cells]  4. Auxin + Nutlin: 500µM auxin (IAA) treatment for 3h and subsequent 10µM Nutlin 3a treatment for 3h [MED14- and BRD4-AID-tagged cells] or 500µM auxin (IAA) treatment for 12h and subsequent 10µM Nutlin 3a treatment for 6h [MED14-AID-tagged cells]

tag: cell line

tag: cell type

value: CRISPR/Cas9 edited cells

value: auxin (IAA) +Nutlin-3a


title: CD_6h_post_stress_2

value: Control Diet

value: CD_6h post stress

value: 6h post stress


title: Colorectal Cancer Cells - HCT116_NIVO_6h_rep1

value: NIVOLUMAB (NIVO) for 6h


title: Colorectal Cancer Cells - HCT116_sPDL1_6h_rep1


title: day_0_3D_suspension_culture

tag: experiment

value: 3D suspension culture


title: H3K27me2me3_crf4_1_N6171

description: chip-seq

value: nuclei


title: H3K27me2me3_NCU00412_N7990

description: chip-seq


title: CD_6h_post_stress_3


title: CD_6h_post_stress_1


title: H3K27me2me3_NCU00412_N7992

description: chip-seq


title: Colorectal Cancer Cells - HCT116_ctr_6h_rep2

value: untreated


title: BRD4_3hrIAA_3hrNutlin_rep1


title: RNAseq_crf4_2_N8016

description: RNA-seq


title: BRD4_3hrIAA_0hrNutlin_rep2

description:
BRD4_3hrIAA_0hrNutlin.ps.bw
BRD4_3hrIAA_0hrNutlin.ns.bw
Brd4_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: auxin (IAA) +DMSO


title: H3K27me2me3_crf4_3_N8018

description: chip-seq


title: H3K27me2me3_crf4_3_N7966

description: chip-seq


title: CD_1h_post_stress_2

value: CD_1h post stress

value: 1h post stress


title: BRD4_3hrIAA_0hrNutlin_rep1

value: auxin (IAA)  +DMSO


title: Colorectal Cancer Cells - HCT116_ctr_6h_rep1

value: Colon

value: Colorectal carcinoma


title: Colorectal Cancer Cells - HT29_NIVO+sPDL1_24h_rep2

value: Colorectal Adenocarcinoma

value: NIVO+sPDL-2 for 24h


title: CD_1h_post_stress_3

value: gill


title: BRD4_0hrIAA_3hrNutlin_rep2

description:
BRD4_0hrIAA_3hrNutlin.ps.bw
BRD4_0hrIAA_3hrNutlin.ns.bw
Brd4_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: CRISPR/Cas9 edited cells

value: water (mock) +Nutlin-3a


title: CD_1h_post_stress_1

value: Control Diet


title: H3K27me2me3_NCU09388_N7989

description: chip-seq


title: RNAseq_crf4_1_N6170

description: RNA-seq


title: Colorectal Cancer Cells - HT29_NIVO+sPDL1_24h_rep1

value: NIVO+sPDL-1 for 24h


title: BRD4_0hrIAA_3hrNutlin_rep1


title: H3K27me2me3_NCU09388_N7988

description: chip-seq


title: CD_initial_control_3

value: CD_control w/o stress

value: Initial control (without stress)


title: BRD4_0hrIAA_0hrNutlin_rep2

description:
BRD4_0hrIAA_0hrNutlin.ps.bw
BRD4_0hrIAA_0hrNutlin.ns.bw
Brd4_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: water (mock) +DMSO


title: Colorectal Cancer Cells - HT29_sPDL1_24h_rep2

value: solubile-PDL-1 (sPDL-1) for 24h


title: H3K27me2me3_crf4_2_N8017

description: chip-seq

value: nuclei


title: CD_initial_control_2


title: Colorectal Cancer Cells - HCT116_NIVO_6h_rep2

value: NIVOLUMAB (NIVO) for 6h


title: H3K27me2me3_crf4_2_N8016

description: chip-seq


title: CD_initial_control_1


title: cells B hsa-miR-130a targeted chimeric eCLIP_2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
For targeted miR-130a datasets, reads that did not contain the primer sequence (CAGUGCAAUGUUAAAAGGGCAU) were filtered out.
For total chimeric eCLIP datasets, 10nt from the 3'end of Read1 was trimmed with umi_tools. Args: -u -9
Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.7.6a) against a human genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species (hg19) --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
To capture chimeric reads, trimmed fastqs were converted to fasta and collapsed into unique sequences using seqtk seq (1.3-r106) and ctk fasta2collapse.pl (v1.0.8)
Collapsed sequences were indexed and used to map mature miRNA (miRBase) using bowtie2 (v2.2.6)
Sequences that mapped to miRs whose mRNA portion were at least 18nt were re-assigned according to their original read ID, and mapped to the human genome as previously described.
Genome_build: hg19
Supplementary_files_format_and_content: gk.Au9.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.bed and gk.Au13.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.bed contain enriched regions from the miR-130a targeted chimeric eCLIP dataset
Supplementary_files_format_and_content: cellsB_rep1.vs.cellsB_rep2.bed contains reproducible total chimeric eCLIP peaks across replicates
Supplementary_files_format_and_content: BigWig files contain RPM-normalized read densities

source_name: CD34+ cord blood

growth_protocol: Several vials of Lineage-depleted (Lin-) human cord blood (CB) cells were thawed and sorted to collect CD34+ CB cells. Kasumi-1 cells were maintained in RPMI  supplemented with 20% FBS, Pen/Strep and L-glutamine at 37o C with 5% CO2. Cells were maintained at a density of 3x10^5-1x10^6 cells/ml.

extract_protocol:
CB replicates of (~5M million cells) and Kasumi-1 cells (~2.5 million cells) were treated with 400mJ of UV using the Hoefer UVC500 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with AGO2 bound Dynabeads. Subsequent protocol was followed exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina Novaseq 6000 paired end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.

treatment_protocol: Sorted CD34+ CB cells and Kasumi-1 cells were UV cross-linked (254 nm; 400 mJ/cm2) and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). AGO2 antibody employed for immunoprecipitation was Santa Cruz, clone 4F9.

value: CD34+ cord blood

value: Lineage-depleted human cord blood cells

tag: rip antibody

value: AGO2 clone 4F9 (Santa Cruz, sc-53521)

tag: inline barcode1

value: Inline barcode1:Ril19


title: Colorectal Cancer Cells - HT29_sPDL1_24h_rep1

value: Colon

value: Colorectal Adenocarcinoma


title: BRD4_0hrIAA_0hrNutlin_rep1


title: Med14_3hrIAA_3hrNutlin_rep2

description:
Med14_3hrIAA_3hrNutlin.ps.bw
Med14_3hrIAA_3hrNutlin.ns.bw
Med14_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: auxin (IAA) +Nutlin-3a


title: Colorectal Cancer Cells - HT29_NIVO_24h_rep2

value: NIVOLUMAB (NIVO) for 24h


title: RNA-seq: V6.5-OsRDR1

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: mm10, hg38
Supplementary files format and content: Gene expression matrix

source_name: V6.5-OsRDR1 stable cell line

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme).

tag: cell type and treatment

value: V6.5 with OsRDR1 consistent expression

value: V6.5-OsRDR1 stable cell line


title: H3K27me2me3_WT_N3753

description: chip-seq

tag: sample type


title: Med14_3hrIAA_3hrNutlin_rep1

value: CRISPR/Cas9 edited cells


title: Colorectal Cancer Cells - HT29_NIVO_24h_rep1

tag: tissue


title: Med14_3hrIAA_0hrNutlin_rep2

description:
Med14_3hrIAA_0hrNutlin.ps.bw
Med14_3hrIAA_0hrNutlin.ns.bw
Med14_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: auxin (IAA) +DMSO


title: Colorectal Cancer Cells - HT29_ctr_24h_rep2

tag: disease

value: untreated


title: H3K27me2me3_WT_N3752

description: chip-seq


title: RNA-seq: NIH/3T3-OsRDR1(+)Dox

source_name: NIH/3T3-OsRDR1 stable cell line

value: NIH/3T3-OsRDR1 with Dox induction for 6 days

value: NIH/3T3-OsRDR1 stable cell line


title: Colorectal Cancer Cells - HT29_ctr_24h_rep1

tag: treatment


title: Med14_3hrIAA_0hrNutlin_rep1

value: auxin (IAA)  +DMSO


title: MNaseSeq_crf4-1_N6171

description: MNase-seq

data_processing:
Paired-end sequence reads were aligned to the neurospora crassa genome (OR74A) using Bowtie2 (version 2.3.3) with the option “-q -p 4 -X 250 --no-discordant --no-mixed --no-unal” (Paired-end alignment reads with maximum 250bp distance gap between them were used in subsequent analysis. This length correspond to mono-nucleosome)
Only correctly aligned paired-end alignment reads were filtered using samtools (version 1.5) commands “samtools view –hf 0x2 input.bam | grep –v “XS:i:” “
Dyad Coverage was calculated using the scripts (03_PNA_SDE.R) from Baldi et al (Baldi, S. et al. Genome-wide Rules of Nucleosome Phasing in Drosophila. Mol. Cell 72, 661-672.e4 (2018))
The spectral density (SD) score correspond to periods of 182bp was calculated using the scripts (cov2spec.R) from Baldi et al. SD score was normalized as Z-score :  (log2(SD score) – average) / standard deviation.
Regions with the average Z-score threshold of 2 were defined as the domain of a regular nucleosome array.
neurospora crassa genome (OR74A)
bigwig of dyad coverage and spectral density

growth_protocol: A 50 ml culture of Vogel’s solution plus 1.5% sucrose was inoculated with 2.5E7 cells, harvested from freshly grown conidia, and grown at 32oC with shaking for ~3.5 hours, until at least 70% of conidia have germinated as determined by microscopy

extract_protocol:
Cells were treated with 2 mg of zymolyase (100T) in a 1 ml solution of spheroplast buffer (1M sorbitol, 50mM Tris pH 7.5, 10mM BME) for 15 minutes while rotating at room temperature. Cells were pelleted at full speed and resuspended in 100 ul MNase digestion buffer (1M sorbitol, 50mM NaCl, 10mM Tris pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.075% (v/v) IGEPAL (Sigma), 0.5mM spermidine and 1mM BME). Exonuclease III (NEB) (30 units) and micrococcal nuclease (Takara) were added to samples and rapidly mixed. Digestion proceeded for 10 minutes at 37oC and was quenched with final concentration of 5mM EGTA and 5mM EDTA (from 50mM/50mM stock). MNase concentration was optimized for each strain to yield ~80-90% mononucleosomes (20 units for N3752, N3753, N7966, N8018, N7990, N7992, N7988, N7989; 60 units for N4718; and 80 units for N4730, N6170, N6171, N8016, N8017). RNase (40 ug) treatment was for 1.5 hours at 42C and proteinase K (200 ug) treatment was for 1 hour at 65 C.
10 ug of gel-purified (minelute, Qiagen) mononucleosome DNA was prepared for high-throughput sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: Cells were crosslinked by addition of fresh formaldehyde for a final concentration of 1%, then shaken at room temperature for 10 minutes. The crosslinking reaction was quenched by the addition of 6.8 ml of 1M Tris-HCl pH 8 to a final concentration of 125mM for 10 minutes, shaking at room temperature. Conidia were then harvested by centrifugation.

value: nuclei


title: Colorectal Cancer Cells - HT29_NIVO+sPDL1_6h_rep2

value: NIVO+sPDL-2 for 6h


title: RNA-seq: NIH/3T3-AtRDR1(+)Dox

source_name: NIH/3T3-AtRDR1 stable cell line

value: NIH/3T3-AtRDR1 with Dox induction for 6 days

value: NIH/3T3-AtRDR1 stable cell line


title: Med14_0hrIAA_3hrNutlin_rep2

description:
Med14_0hrIAA_3hrNutlin.ps.bw
Med14_0hrIAA_3hrNutlin.ns.bw
Med14_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: water (mock) +Nutlin-3a


title: Med14_0hrIAA_3hrNutlin_rep1


title: RNA-seq: NIH/3T3-OsRDR1(-)Dox

value: NIH/3T3-OsRDR1 without Dox induction


title: Colorectal Cancer Cells - HT29_NIVO+sPDL1_6h_rep1

value: Colon

value: Colorectal Adenocarcinoma

value: NIVO+sPDL-1 for 6h


title: MNaseSeq_crf4-2_N8017

description: MNase-seq


title: RNA-seq: NIH/3T3-AtRDR1(-)Dox

value: NIH/3T3-AtRDR1 without Dox induction


title: RNA-seq: NIH/3T3-WT

value: WT


title: Med14_0hrIAA_0hrNutlin_rep2

description:
Med14_0hrIAA_0hrNutlin.ps.bw
Med14_0hrIAA_0hrNutlin.ns.bw
Med14_3hrIAA_3hrNutlin_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: CRISPR/Cas9 edited cells

value: water (mock) +DMSO


title: Colorectal Cancer Cells - HT29_sPDL1_6h_rep2

value: solubile-PDL-1 (sPDL-1) for 6h


title: Colorectal Cancer Cells - HT29_sPDL1_6h_rep1


title: MNaseSeq_crf4-3_N7966

description: MNase-seq


title: Med14_0hrIAA_0hrNutlin_rep1


title: Colorectal Cancer Cells - HT29_NIVO_6h_rep2

value: NIVOLUMAB (NIVO) for 6h


title: MNaseSeq_crf4-3_N8018

description: MNase-seq


title: PyMT/Jagged1-rep-2

first: Hanqiu

last: Zheng

address: Qinghuayuan Sub-District, Haidian District

department: School of Medicine

institute: Tsinghua University

description:
Single cell RNA
10X Genomics
P-J-barcodes.tsv
P-J-features.tsv
P-J-matrix.mtx

data_processing:
CellRanger software package (v3.0.2) was used for alignment, filtering, barcode reading and demultiplexing, prior to analysis in R.
Genome_build: not provided
Supplementary_files_format_and_content: *-barcodes.tsv: 10X Genomics Filtered Gene BC Barcodes.
Supplementary_files_format_and_content: *-features.tsv: 10X Genomics Filtered Gene BC Genes.
Supplementary_files_format_and_content: *-matrix.mtx: 10X Genomics Filtered Gene BC Matrix.

source_name: Mammary tumor

extract_protocol:
Mammary tumor were removed, digested to single cell. Sorting immune cell infiltrated in the tumor using FACs. Chromium Next GEM Single Cell 3' Reagent Kits v3.1 was used with 8000 immune cells for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: FVB/NJ

value: mammary tumor

value: 12 weeks old


title: Colorectal Cancer Cells - HT29_NIVO_6h_rep1


title: Kasumi-1 total chimeric eCLIP size-matched input

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
For targeted miR-130a datasets, reads that did not contain the primer sequence (CAGUGCAAUGUUAAAAGGGCAU) were filtered out.
For total chimeric eCLIP datasets, 10nt from the 3'end of Read1 was trimmed with umi_tools. Args: -u -9
Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.7.6a) against a human genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species (hg19) --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
To capture chimeric reads, trimmed fastqs were converted to fasta and collapsed into unique sequences using seqtk seq (1.3-r106) and ctk fasta2collapse.pl (v1.0.8)
Collapsed sequences were indexed and used to map mature miRNA (miRBase) using bowtie2 (v2.2.6)
Sequences that mapped to miRs whose mRNA portion were at least 18nt were re-assigned according to their original read ID, and mapped to the human genome as previously described.
Genome_build: hg19
Supplementary_files_format_and_content: gk.Au1.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.bed contains total chimeric eCLIP normalized peaks
Supplementary_files_format_and_content: BigWig files contain RPM-normalized read densities

tag: antibody manufacturer

value: AGO2 clone 4F9, Santa Cruz

tag: antibody catalog #

value: t(8;21) AML cell line


title: RNA-seq: V6.5-EGFP

source_name: V6.5-EGFP stable cell line

value: V6.5 with EGFP consistent expression

value: V6.5-EGFP stable cell line


title: MNaseSeq_crf4-1_N6170

description: MNase-seq

value: nuclei


title: MNaseSeq_NCU00412_N7990

description: MNase-seq


title: PyMT-rep-2

description:
Single cell RNA
10X Genomics
PYMT-barcodes.tsv
PYMT-features.tsv
PYMT-matrix.mtx

value: PyMT


title: MNaseSeq_NCU09388_N7988

description: MNase-seq


title: PyMT-rep-1


title: Kasumi-1 total chimeric eCLIP


title: Colorectal Cancer Cells - HT29_ctr_6h_rep1

value: Colon

value: Colorectal Adenocarcinoma

value: untreated


title: MNaseSeq_NCU09388_N7989

description: MNase-seq


title: cells B hsa-miR-130a targeted chimeric eCLIP

extract_protocol:
CB replicates of (~5M million cells) and Kasumi-1 cells (~2.5 million cells) were treated with 400mJ of UV using the Hoefer UVC500 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with AGO2 bound Dynabeads. Subsequent protocol was followed exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina Novaseq 6000 paired end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

value: CD34+ cord blood

value: Lineage-depleted human cord blood cells sorted to collect CD34+ CB cells

value: AGO2 clone 4F9 (Santa Cruz, sc-53521)


title: Am-rep-2

description:
Am-4
PyMT-A-Vector-and-PyMT-A-Jagged1-raw_counts.txt.gz

data_processing:
Illumina adapter sequences have been trimmed off the reads, which were subsequently mapped against the mm10 mouse reference using STAR (version 2.6.0c).
The counts for each gene were obtained by using featureCounts (version 1.6.2), and the minimum mapping quality score were set to 30.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: PyMT-A-Vector-and-PyMT-A-Jagged1-raw_counts.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.

source_name: mammary tumor cell line

growth_protocol: PyMT-A-Vector and PyMT-A-Jagged1 cell lines were cultured in DMEM plus 10%FBS and 1%P/S.

extract_protocol:
The tumor cell lines RNA were harvested using Trizol reagent. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490) was used with 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Infected with PMSCV-Jagged1 Virus


title: PGCLC_rep2

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

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

description: Human PGCLCs, biological replicate #2

data_processing:
Sequenced reads were trimmed with Trimmomatic.
Sequenced reads were mapped to the human reference genome using STAR.
Mapped reads on respective genetic features were counted using featureCounts.
Genome_build: Hg38
Supplementary_files_format_and_content: Expression read count matrix (csv)

source_name: PGCLCs, biological replicate #2

extract_protocol:
RNeasy Micro Kit (QIAGEN)
SMART-Seq HT Kit (Takara)

value: PGCLCs


title: MNaseSeq_crf4-2_N8016

description: MNase-seq


title: cells B total chimeric eCLIP size-matched input, rep 1


title: PGCLC_rep1

description: Human PGCLCs, biological replicate #1

source_name: PGCLCs, biological replicate #1


title: Acon-rep-2

description:
Acon-3
PyMT-A-Vector-and-PyMT-A-Jagged1-raw_counts.txt.gz

value: FVB/NJ

value: Infected with PMSCV-puro Virus


title: Am-rep-1

description:
Am-2
PyMT-A-Vector-and-PyMT-A-Jagged1-raw_counts.txt.gz

value: mammary tumor


title: MNaseSeq_set-7_N4718

description: MNase-seq


title: cells B total chimeric eCLIP, rep 2


title: MNaseSeq_WT_N3752

description: MNase-seq


title: Acon-rep-1

description:
Acon-1
PyMT-A-Vector-and-PyMT-A-Jagged1-raw_counts.txt.gz


title: PyMT/Jagged1-rep-1

value: 12 weeks old


status: Public on Mar 07 2022

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 24h, replicate number 3

data_processing:
Gene expression was quantified with RSEM using the Trinity utility
Mapped counts were statistically tesed with DESeq2 and transcripts with FDR < 0.05 and absolute fold change > 2 were determined as differentially expressed genes.
Genome_build: Pv11_5.2 (SUB8069519)
Supplementary_files_format_and_content: TPM expression matrix.

organism: Polypedilum vanderplanki

source_name: Pv11 cell line

growth_protocol: Pv11 cells were cultured in IPL-41 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 2.6 g/L tryptone phosphate broth (Becton, Dickinson and Company, Franklin Lakes, NJ), 10% (v/v) fetal bovine serum (MP Biomedicals, Santa Ana, CA), and 0.05% (v/v) of an antibiotic and antimycotic mixture (penicillin, amphotericin B, and streptomycin; Merck KGaA, Darmstadt, Germany).

extract_protocol:
At each time point cells were collected at each time point by centrifugation at 8,000g for 2 minutes (4˚C), and the culture medium was removed. Cells were suspended in 500µL of RNAiso Plus (Takara) and incubated for 5 minutes.
The total RNA was extracted with Nucleospin RNA clean-up and the TruSeq RNA Sample Prep Kit -v8 following the manufacturer's protocol.

treatment_protocol: 5x10^6 Pv11 cells were resuspended in 2mL IPL-41 medium and were submitted to the following stresses; 0.5% (V/W) NaCl, 600mM Mannitol, 600mM Trehalose, 20µM Paraquat, and 15 minute 42˚C heat shock and was sampled at for 1, 3 and 24 hours post exposure.

tag: stress


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 72h, replicate number 2


title: iPSC_rep1

description: Human iPSCs, biological replicate #1

source_name: iPSCs, biological replicate #1

value: iPSCs


title: MNaseSeq_WT_N3753

description: MNase-seq

source_name: nuclei from germinated condia


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 72h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 24h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 24h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 12h, replicate number 3


title: Colorectal Cancer Cells - HT29_ctr_6h_rep2

source_name: Colorectal Cancer Cells


title: cells C hsa-miR-130a targeted chimeric eCLIP

value: t(8;21) AML cell line Kasumi-1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 72h, replicate number 3


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 12h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 12h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 03h, replicate number 3


title: MNaseSeq_NCU00412_N7992

description: MNase-seq


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 03h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 00h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 00h, replicate number 3


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 03h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, Rehydration condition sampled at 00h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 48h, replicate number 3


title: cells B total chimeric eCLIP size-matched input, rep 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 48h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 48h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 36h, replicate number 3


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 36h, replicate number 2


title: MNaseSeq_set-7_N4730

description: MNase-seq


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 24h, replicate number 3


title: iPSC_rep2

description: Human iPSCs, biological replicate #2

source_name: iPSCs, biological replicate #2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 24h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 36h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 24h, replicate number 1


title: cells B total chimeric eCLIP, rep 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 12h, replicate number 3


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 12h, replicate number 2


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 12h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 00h, replicate number 3


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 00h, replicate number 1


description:
Pv11_Trehalose_3h_rep1
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 3h, replicate number 1


description:
From DDBJ Study DRA008948
Transcriptome sequencing of Pv11 cells submitted to desiccation time course, PreCondTre condition sampled at 00h, replicate number 2


description:
Pv11_Trehalose_3h_rep3
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 3h, replicate number 3


description:
Pv11_Trehalose_24h_rep3
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 24h, replicate number 3


title: Skeletal_muscle_streptozotocin_bezafibrate_rep4

type: RNA

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
STZ_BEZ_46
Gene expression data from skeletal muscle from streptozotocin/bezafibrate-treated mice, biological replicate 4

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

label: biotin

source_name: Skeletal muscle from streptozotocin/bezafibrate-treated mice

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Animals per housed under spf conditions

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: To induce type 1 diabetes, 65 mg/kg of streptozotocin (STZ) was injected i.p. into 10-16 weeks old mice on 5 consecutive days while respective controls were mock-injected with citrate buffer. BEZ treatment for 8 weeks started 2 weeks after STZ injection. BEZ (B7273, Sigma-Aldrich) was mixed to standard mouse chow in 0.25% or 0.5% (w/w) concentration (BEZ food) by the supplier (R/M-H, Ssniff, Germany); control animals received untreated placebo food (standard diet, SD food).

tag: strain

value: 5-6 months

tag: gender

value: male

value: wildtype

value: streptozotocin/bezafibrate-treated

value: skeletal muscle


title: Skeletal_muscle_streptozotocin_bezafibrate_rep1

description:
STZ_BEZ_43
Gene expression data from skeletal muscle from streptozotocin/bezafibrate-treated mice, biological replicate 1

tag: age


title: Skeletal_muscle_streptozotocin_bezafibrate_rep3

description:
STZ_BEZ_45
Gene expression data from skeletal muscle from streptozotocin/bezafibrate-treated mice, biological replicate 3

tag: genotype


title: Skeletal_muscle_streptozotocin_bezafibrate_rep2

description:
STZ_BEZ_44
Gene expression data from skeletal muscle from streptozotocin/bezafibrate-treated mice, biological replicate 2


title: Skeletal_muscle_streptozotocin_bezafibrate_rep5

description:
STZ_BEZ_49
Gene expression data from skeletal muscle from streptozotocin/bezafibrate-treated mice, biological replicate 5


title: Skeletal_muscle_streptozotocin_rep2

description:
STZ_30
Gene expression data from skeletal muscle from streptozotocin-treated mice, biological replicate 2

source_name: Skeletal muscle from streptozotocin-treated mice

value: streptozotocin-treated


title: Skeletal_muscle_streptozotocin_rep1

description:
STZ_29
Gene expression data from skeletal muscle from streptozotocin-treated mice, biological replicate 1


title: Skeletal_muscle_streptozotocin_rep5

description:
STZ_42
Gene expression data from skeletal muscle from streptozotocin-treated mice, biological replicate 5


title: Skeletal_muscle_streptozotocin_rep4

description:
STZ_40
Gene expression data from skeletal muscle from streptozotocin-treated mice, biological replicate 4


title: Skeletal_muscle_streptozotocin_rep3

description:
STZ_32
Gene expression data from skeletal muscle from streptozotocin-treated mice, biological replicate 3


description:
Pv11_Trehalose_1h_rep2
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 1h, replicate number 2

tag: cell line


description:
Pv11_ROS_3h_rep3
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 3h, replicate number 3


title: Skeletal_muscle_control_rep7

description:
Ctrl_07
Gene expression data from skeletal muscle from control mice, biological replicate 7

source_name: Skeletal muscle from control mice

value: control


description:
Pv11_Trehalose_24h_rep2
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 24h, replicate number 2


description:
Pv11_Trehalose_24h_rep1
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 24h, replicate number 1


description:
Pv11_Trehalose_1h_rep3
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 1h, replicate number 3


title: Skeletal_muscle_control_rep5

description:
Ctrl_05
Gene expression data from skeletal muscle from control mice, biological replicate 5


description:
Pv11_ROS_3h_rep2
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 3h, replicate number 2


description:
Pv11_ROS_3h_rep1
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 3h, replicate number 1


description:
Pv11_Trehalose_1h_rep1
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 1h, replicate number 1


title: Skeletal_muscle_control_rep6

description:
Ctrl_06
Gene expression data from skeletal muscle from control mice, biological replicate 6


title: Skeletal_muscle_control_rep4

description:
Ctrl_04
Gene expression data from skeletal muscle from control mice, biological replicate 4


title: Skeletal_muscle_control_rep1

description:
Ctrl_01
Gene expression data from skeletal muscle from control mice, biological replicate 1


description:
Pv11_ROS_24h_rep1
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 24h, replicate number 1


description:
Pv11_Trehalose_3h_rep2
Transcriptome sequencing of Pv11 cells submitted to Trehalose and sampled at 3h, replicate number 2


title: Skeletal_muscle_control_rep3

description:
Ctrl_03
Gene expression data from skeletal muscle from control mice, biological replicate 3


title: Skeletal_muscle_control_rep2

description:
Ctrl_02
Gene expression data from skeletal muscle from control mice, biological replicate 2


description:
Pv11_ROS_1h_rep3
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 1h, replicate number 3


description:
Pv11_ROS_24h_rep3
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 24h, replicate number 3


title: Visceral_fat_streptozotocin_bezafibrate_rep4

description:
STZ_BEZ_46
Gene expression data from visceral fat from streptozotocin/bezafibrate-treated mice, biological replicate 4

source_name: Visceral fat from streptozotocin/bezafibrate-treated mice

value: visceral fat


description:
Pv11_ROS_24h_rep2
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 24h, replicate number 2


title: E1E2-4

city: Liverpool

first: William

middle: Anderson

last: Paxton

state: England

address: 8 West Derby Street, Ronald Ross Building

department: IVES

institute: University of Liverpool

description:
rawcounts.csv
DiffExpGenes.csv

data_processing:
Barcoding using Oxford Nanopore Guppy software (version 3.2.4)
Demultiplex and trimming of adapters and barcodes using Porechop (https://github.com/rrwick/Porechop)
Mapping to human genome (GCA_000001405.15) using Minimap2
Mapped reads were assigned to genomic features using featureCounts
Normalisation of raw read counts was performed using EdgeR “trimmed mean M-values (TMM)” method
Differential gene expression between E1E2 or pCDNA transfected cells was determined using the R package Limma, using the “voom” method with a cut off of p=0.05

source_name: HEK293T cells

growth_protocol: HEK293T cells grown in Advanced DMEM supplemented with FBS, penstrep and L-glutamine, seeded onto a 6 well plate to achieve 50-60% confluency at point of transfection

extract_protocol:
Total RNA was extracted usign Qiagen RNAeasy Plus kit. All of the extracted RNA was used as input for PolyA+ RNA purification using Dynabeads mRNA purification kit.
Library was produced according to Oxford Nanopore cDNA sequencing protocol SQK-PCS-109 and barcoding protocol SQK-PCB-109

treatment_protocol: Cells were transfected using lipofectamine reagent with either a plasmid expressing the HCV (genome 1a) envelope glycoprotein E1E2 or with an empty vector plasmid, pCDNA. Cells were incubated for 2 days following transfection prior to extraction

value: Transfected with E1E2 expressing plasmid

tag: cell type

value: Embryomic kidney cells


title: Visceral_fat_streptozotocin_bezafibrate_rep2

description:
STZ_BEZ_44
Gene expression data from visceral fat from streptozotocin/bezafibrate-treated mice, biological replicate 2


title: E1E2-6

description:
rawcounts.csv
DiffExpGenes.csv


title: E1E2-5

description:
rawcounts.csv
DiffExpGenes.csv


title: E1E2-3

description:
rawcounts.csv
DiffExpGenes.csv


description:
Pv11_ROS_1h_rep1
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 1h, replicate number 1


title: Visceral_fat_streptozotocin_rep6

description:
STZ_42
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 6

source_name: Visceral fat from streptozotocin-treated mice


title: Visceral_fat_streptozotocin_bezafibrate_rep3

description:
STZ_BEZ_45
Gene expression data from visceral fat from streptozotocin/bezafibrate-treated mice, biological replicate 3


description:
Pv11_ROS_1h_rep2
Transcriptome sequencing of Pv11 cells submitted to ROS and sampled at 1h, replicate number 2


title: Visceral_fat_streptozotocin_bezafibrate_rep5

description:
STZ_BEZ_49
Gene expression data from visceral fat from streptozotocin/bezafibrate-treated mice, biological replicate 5


title: pCDNA-3

description:
rawcounts.csv
DiffExpGenes.csv

value: Transfected with pCDNA


title: pCDNA-4

description:
rawcounts.csv
DiffExpGenes.csv


title: E1E2-1

description:
rawcounts.csv
DiffExpGenes.csv


description:
Pv11_NaCl_3h_rep3
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 3h, replicate number 3


title: Visceral_fat_streptozotocin_bezafibrate_rep1

description:
STZ_BEZ_43
Gene expression data from visceral fat from streptozotocin/bezafibrate-treated mice, biological replicate 1


title: pCDNA-2

description:
rawcounts.csv
DiffExpGenes.csv


title: pCDNA-1

description:
rawcounts.csv
DiffExpGenes.csv


description:
Pv11_NaCl_3h_rep1
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 3h, replicate number 1


title: Visceral_fat_streptozotocin_rep5

description:
STZ_40
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 5


title: Visceral_fat_streptozotocin_rep4

description:
STZ_32
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 4


title: Visceral_fat_streptozotocin_rep3

description:
STZ_31
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 3


title: Visceral_fat_streptozotocin_rep2

description:
STZ_30
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 2


description:
Pv11_NaCl_3h_rep2
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 3h, replicate number 2


title: Visceral_fat_streptozotocin_rep1

description:
STZ_29
Gene expression data from visceral fat from streptozotocin-treated mice, biological replicate 1


description:
Pv11_NaCl_24h_rep3
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 24h, replicate number 3


title: E1E2-2

description:
rawcounts.csv
DiffExpGenes.csv


description:
Pv11_NaCl_24h_rep1
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 24h, replicate number 1


title: MDAMB231 Omomyc mini-protein biological replica 5

city: Barcelona

first: Mariano

middle: F

last: Zacarias-Fluck

address: Natzaret, 115-117

department: Preclinical and Translational Research Program

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description: Clariom S, human HT

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Clariom S Human HT (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol. The samples were scanned in three diferent plates since they were part of a bigger experiment, hence the batches 1-2-3

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Partek Genomic Suite followed by GSEA 3.0 software from Broad Institute.

label: Biotin

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: Cells were grown at 37ºC, 5% CO2 in DMEM/F12 supplemented with glutamine and 10% FBS

extract_protocol: Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were plated and after overnight incubation, vehicle or 12.8 µM Omomyc treatement were added

tag: agent

value: Omomyc mini-protein

tag: tumor type

value: Triple negative breast cancer


title: MDAMB231 Omomyc mini-protein biological replica 3

description: Clariom S, human HT


title: Visceral_fat_control_rep7

description:
SD_07
Gene expression data from visceral fat from control mice, biological replicate 7

source_name: Visceral fat from control mice


title: MDAMB231 Omomyc mini-protein biological replica 4

description: Clariom S, human HT


description:
Pv11_NaCl_1h_rep3
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 1h, replicate number 3


description:
Pv11_NaCl_1h_rep2
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 1h, replicate number 2


description:
Pv11_NaCl_1h_rep1
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 1h, replicate number 1


title: Visceral_fat_control_rep6

description:
SD_06
Gene expression data from visceral fat from control mice, biological replicate 6


title: MDAMB231 Omomyc transgene biological replica 4

description: Clariom S, human HT

value: Omomyc transgene


title: MDAMB231 Omomyc transgene biological replica 5

description: Clariom S, human HT


title: MDAMB231 Omomyc mini-protein biological replica 2

description: Clariom S, human HT


title: Visceral_fat_control_rep5

description:
SD_05
Gene expression data from visceral fat from control mice, biological replicate 5


title: Visceral_fat_control_rep3

description:
SD_03
Gene expression data from visceral fat from control mice, biological replicate 3


description:
Pv11_NaCl_24h_rep2
Transcriptome sequencing of Pv11 cells submitted to NaCl and sampled at 24h, replicate number 2


title: MDAMB231 Omomyc transgene biological replica 1

description: Clariom S, human HT


title: 24 h, P .putida + nZVI, 2

city: Liberec

first: Alena

last: Sevcu

state: Liberec

address: Bendlova 1409/7

department: Applied Biology

country: Czech Republic

institute: Technical University of Liberec

data_processing:
The first 15 nucleotides of the reads of the adapters were trimmed, and the adapters were aligned to the P. putida KT2440 reference genome (GenBank Accession no. AE015451.2) using STAR aligner and assessed for transcript level (ht-seq count).
The differential gene expression for each condition was illustrated using the relative log expression function in the DESEQ2 package, and statistical analysis was performed through the p.adjust function in R software.
Genes showing log2 (fold change) of ≥1.0 or ≤ −1.0 and adjusted P-value < 0.05 were considered to be significantly expressed. Clustering and visualization of the dissimilarity matrix was achieved using pheatmap. PCA was performed based on the PCAtools package
Genome_build: Pseudomonas putida KT2440
Supplementary_files_format_and_content: gene-clustering-genes-with-highest-variance.xlsx
Supplementary_files_format_and_content: most-changed-genes1.xlsx

organism: Pseudomonas putida

source_name: bacterial pellet exposed to nZVI

growth_protocol: P. putida was grown in 10 mL tryptone soy medium (7 h at 30°C, 150 rpm), to obtain the mid-log exponential growth phase of cells (approximately 3.3 × 10^8 cells/mL). The cells were subsequently harvested, pelleted down, and transferred to reservoir water as an exposure medium for the nZVI toxicity studies.

extract_protocol:
Samples treated with nZVI particles were removed by a KV-70-70-25-N dimensional nickel-plated block magnet (UNIMAGNET, Czech Republic) before RNA extraction. The RNA was harvested after 0, 3, 6, and 24 h from nZVI-exposed cells and after 0 and 24 h from dissolved iron-exposed cells using an Isolate II RNA Mini Kit (Bioline, Canada). Cell pellets were obtained through centrifugation at 21,000 × g, 4°C for 15 min and added immediately 1 mg/mL of lysozyme and incubated at 37°C for 10 min prior to the addition of RNA lysis buffer. The subsequent DNase treatments and RNA washing steps were then treated as described in the manufacturer's protocol. The integrity of the total RNA (RIN) was determined with an Agilent RNA ScreenTape by 2200 TapeStation system (Agilent Technologies, Germany) and Qubit™ RNA Broad Range Assay Kit using Qubit 2.0 fluorometer (Life Technologies, USA) was for RNA concentration quantification.
To prepare for whole transcriptome sequencing of the RNA-seq library, triplicate biological flasks containing starting material with at least 700 ng of total RNA (RIN > 7) were depleted of rRNA using a NEBNext rRNA depletion kit for bacteria (New England Biolabs, USA) following the manufacturer’s instructions. Then, the RNA was prepared using a NEBNext® Ultra™ II RNA Library Prep kit for Illumina® (New England Biolabs). The resulting cDNA libraries were pooled and were sequenced using an Illumina NextSeq system with an 85-bases read length in the forward direction

treatment_protocol: Natural reservoir water from a local reservoir in Czech Republic (50.7702097N, 15.0755733E) was collected to a depth of 10 cm from a surface point in a spade on November 18, 2018 and was used as the NP exposure medium in the current study. P. putida from its mid-log phase was pelleted down and added into the reservoir water, and exposed to 100 mg/L nZVI or 44.5 µg/L dissolved iron), a flask without nanoparticle was served as control condition

value: exposed to 100 mg/L nZVI

tag: time


title: Visceral_fat_control_rep4

description:
SD_04
Gene expression data from visceral fat from control mice, biological replicate 4


title: MDAMB231 Vehicle biological replica 5

description: Clariom S, human HT

value: Vehicle


title: 24 h, P. putida + nZVI, 3


description:
Pv11_Mannitol_3h_rep3
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 3h, replicate number 3


title: 8 d2

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
All sequencing reads from RNA-seq were mapped to the mouse reference genome (GRCm38.84) using hisat2-2.10 (Kim et al., 2015).
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.1 (Trapnell et al., 2012) using default parameters for gene expression levels. We used htseq-count (Anders et al., 2015) to count reads on genes. Differential expression analysis was performed using DESeq2 (R package, (Love et al., 2014)). Genes were considered differentially expressed if FPKM >=1 in at least one sample and |fold change| >= 2, adjusted p-value < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: liver

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

value: liver

value: post hepatectomy day 2

value: wild type


title: MDAMB231 Vehicle biological replica 4

description: Clariom S, human HT


title: 24 h, P. putida + nZVI, 1


description:
Pv11_Mannitol_3h_rep2
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 3h, replicate number 2


title: MDAMB231 Omomyc transgene biological replica 2

description: Clariom S, human HT


title: Visceral_fat_control_rep2

description:
SD_02
Gene expression data from visceral fat from control mice, biological replicate 2

value: 5-6 months

value: male

value: wildtype


title: MDAMB231 Vehicle biological replica 3

description: Clariom S, human HT


title: Visceral_fat_control_rep1

description:
SD_01
Gene expression data from visceral fat from control mice, biological replicate 1


title: MDAMB231 Omomyc transgene biological replica 3

description: Clariom S, human HT


title: MDAMB231 Vehicle biological replica 2

description: Clariom S, human HT


title: MDAMB231 Vehicle biological replica 1

description: Clariom S, human HT


title: 24 h, P. putida + dissolved iron, 3

description: 24hr_dissolved iron_3

source_name: bacterial pellet exposed to dissolved iron

value: exposed to 44.5 µg/L dissolved iron


title: 24 h, P. putida + dissolved iron, 1

description: 24hr_dissolved iron_1


title: 24 h, P. putida + dissolved iron, 2

description: 24hr_dissolved iron_2


description:
Pv11_Mannitol_24h_rep3
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 24h, replicate number 3


description:
Pv11_Mannitol_3h_rep1
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 3h, replicate number 1


title: 24 h, P. putida, 1

source_name: bacterial pellet

value: nanoparticle free


title: 6 h, P. putida + nZVI, 2

value: 6 h


title: 2 d14

value: post hepatectomy day 14


title: 6 h, P. putida, 3


title: 6 h, P. putida + nZVI, 3


title: 7 TVR d2


description:
Pv11_Mannitol_24h_rep1
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 24h, replicate number 1


title: 2 d1


description:
Pv11_Mannitol_1h_rep3
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 1h, replicate number 3


title: 3 d2


title: 24 h, P. putida, 3


description:
Pv11_Mannitol_24h_rep2
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 24h, replicate number 2


title: 24 h, P. putida, 2


title: 6 d14


title: Control.2

value: 10 weeks


description:
Pv11_Mannitol_1h_rep1
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 1h, replicate number 1


title: 0 h, P. putida, 3

value: 0 h  (at immediate exposure and instant sampling without prolonged incubation)


description:
Pv11_Mannitol_1h_rep2
Transcriptome sequencing of Pv11 cells submitted to Mannitol and sampled at 1h, replicate number 2


title: 6 h, P. putida, 1


title: Control.1


title: High-Grade Serous Carcinoma s949

city: Los Angeles

first: Kate

last: Lawrenson

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

description:
s949
ATAC-seq of a high-grade serous carcinoma

data_processing:
ATAC-seq Sequence Analysis: The paired-end 42 bp sequencing reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
ATAC-seq “Peak Finding”: Since both reads (tags) from paired-end sequencing represent transposition events, both reads are used for peak-calling. Unlike ChIP-seq, where in-silico extension is performed to represent the length of the fragment bound by the protein of interest, ATAC-Seq aims to identify enrichment of transposome accessibility, thus no in-silico extension is performed. Rather, the 42 bp length of the reads is used for peak-calling. The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The peak caller used for ATAC-Seq at Active Motif is MACS2 (Zhang et al., Genome Biology 2008, 9:R137), using both PE reads from each aligned fragment.
ChIP-seq data was processed using ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline).
ChIP-seq Sequence Analysis: Map reads with BWA, mark duplicates Picard, and remove duplicates. Estimate library complexity and calculate NRF (non-redundant fraction), PBC1, PBC2 (PCR bottleneck coefficient). Calculate cross-correlation analysis with spp/phantompeakqualtools. Generate p-value and fold-over-control signal tracks for each replicate and replicates pooled with MACS2.
ChIP-seq "Peak Finding": Call peaks with MACS2. Calculate and report overlapping peaks from both replicates.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: Processed files are peak files in narrowPeak format.
Supplementary_files_format_and_content: ATAC-seq: Processed files are peak files in BED format.

source_name: Epithelial Ovarian Cancer

extract_protocol:
H3K27ac ChIP-seq: 5mm punch biopsies were taken from frozen tissue blocks, and were pulverized using the Covaris CryoPrep system (Covaris, Woburn, MA), then fixed using 1% formaldehyde (Thermo fisher, Waltham, MA) diluted in Phosphate-buffered saline solution (10 min at room temperature) and quenched with 125 mM glycine (10 min at room temperature). Cells were lysed in ice cold lysis buffer (50 mM Tris, 10 mM EDTA, 1% SDS with protease inhibitor; 10 min) and rinsed with ice-cold phosphate-buffered saline solution. The Covaris E210 sonicator was used to shear chromatin to 300–500 base pairs (AFA: 5% duty cycle, 5 intensity, 200 cycles/burst; 10 min). Chromatin samples were diluted with 5 vol of dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris–HCl pH 8.1) and incubated overnight at 4°C with 1 µg H3K27ac antibody (DiAGenode, C15410196, Denville, NJ; as a ratio of 1:600) coupled with protein A and protein G beads (Life Technologies, Carlsbad, CA). Chromatin samples were washed five times with RIPA washing buffer (0.05 M HEPES pH 7.6, 1 mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5 M LiCl), once with TE buffer (pH 8.0) and were resuspended in elution buffer (50 mM Tris, 10 mM EDTA, 1% SDS). Samples were treated with RNase (30 min at 37 °C) and incubated overnight with proteinase K (65 °C).
H3K27ac ChIP-seq: DNA was isolated using the Qiagen Qiaquick kit, and libraries prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics, Ann Arbor, MI).
ATAC-seq: Epithelial-rich regions of flash frozen tumors were biopsied using a 5mm biopsy punch. Primary Fallopian tube tissues were subjected to enzymatic digest using Pronase and DNase1 for 48-72 hours and the epithelial-enriched cells viably frozen down in 10% DMSO/90% fetal bovine serum. In one instance, Fallopian epithelial cells were cultured on collagen-coated plates prior to profiling.
ATAC-seq was performed by Active Motif, using paired end 42bp reads, and sequenced to a depth of ~40M reads.

value: High-Grade Serous Carcinoma

value: untreated


title: 0 h, P. putida, 1


title: High-Grade Serous Carcinoma s3263

description:
s3263
ATAC-seq of a high-grade serous carcinoma


description:
Pv11_Control_3h_rep3
Transcriptome sequencing of control Pv11 cells and sampled at 3h, replicate number 3

source_name: Pv11 cell line


title: treated soma_Rep6

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

institute: Università di Pisa

data_processing:
Library QC: Library preparation was checked by calculating ribosomal content
Raw data quality: Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw data set was determined using third-party (FastQC v0.11.9, MultiQC v1.12)  QC tools
Data trimming: Sequence reads were trimmed to remove possible adapter sequences using fastp v0.20.1
Mapping of reads: The reads were mapped to the reference sequence using a short read aligner STAR v2.7.08a with default settings
Feature counting: Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a gene was determined with HTSeq v0.13.5
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts of the overlap of reads with annotation features/genes obtained using HTSeq v0.13.5

source_name: cells dissociated from hippocampi

growth_protocol: Newborn animals (P1) were sacrificed and both hippocampi were harvested in a solution of D-glucose 6.5 mg/ml in D-PBS (Cell isolation was performed by chemical digestion and mechanical dissociation. After this step, cells were seeded in high-glucose DMEM with 10% fetal bovine serum, 100 IU ml-1 penicillin, 100 µg ml-1 streptomycin and 2 mM Glutamax (DIV0). The medium was replaced four hours later by cell culture medium (Neurobasal-A medium modified with B27, 2 mM Glutamax, 50 IU ml-1 penicillin, 50 µg ml-1 streptomycin, 2.5 μM. Half of the medium was replaced every 2-3 days.

extract_protocol:
NucleoSpin RNA PLUS XS Kit was used for RNA extraction. Samples from axonal compartment and somatodendritic compartment were collected in lysis solution and incubated at 4° (protocol adapted from Bio-protocol 9(14): e3312, DOI:10.21769/BioProtoc.3312). Then, lysed samples were treated to digest the DNA and the RNA that was eluted in RNAse-free water. Quant-iT RiboGreen RNA Kit was used for the quantification of total RNA. RQN was >=9.7 for all samples.
The NEBNext Low Input RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Low Inputr RNA Library Prep Kit for Illumina" (NEB #E6420S/L). Briefly, cDNA was syntesized and amplified from poly A tailed mRNA. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a peak between 200-400 bp).
Low input sample preparations including unique dual indexing and unique molecular identifiers (UMIs). RNA sequencing (polyA enriched) of 24 totalRNA samples (mouse), using Illumina NovaSeq6000 sequencing, Paired-End, 150 bp. Per sample ~9 Gb, 30 million Paired-End reads.

treatment_protocol: Cells we seeded on Poly-D-Lysine and laminin coated microfluidic chambers (XONA, #RD150). A differential coating was performed (poly-D-Lysine 100 ug/ml and laminin 1 ug/ml in the soma side; poly-D-Lysine 500 ug/ml and laminin 10 ug/ml in the axonal side). At DIV0, 200.000 cells were seeded in the soma side. Four hours later, the medium was replaced with cell growth medium modified with 5 µg ml-1 MNPs. In the stretched growth, the stimulus was applied from DIV1 to DIV6.

value: total cell culture

value: MNP+50 T/m magnetic field gradient


title: 6 h, P. putida + nZVI, 1

value: exposed to 100 mg/L nZVI


description:
Pv11_Control_3h_rep2
Transcriptome sequencing of control Pv11 cells and sampled at 3h, replicate number 2


title: treated soma_Rep8


title: 6 h, P. putida, 2


title: treated soma_Rep5


title: High-Grade Serous Carcinoma s2640

description:
s2640
ATAC-seq of a high-grade serous carcinoma


title: High-Grade Serous Carcinoma s2722

description:
s2722
ATAC-seq of a high-grade serous carcinoma


title: High-Grade Serous Carcinoma s1382

description:
s1382
ATAC-seq of a high-grade serous carcinoma


description:
Pv11_Control_3h_rep1
Transcriptome sequencing of control Pv11 cells and sampled at 3h, replicate number 1


title: treated soma_Rep4


title: treated soma_Rep2


description:
Pv11_Control_24h_rep3
Transcriptome sequencing of control Pv11 cells and sampled at 24h, replicate number 3


title: 0 h, P. putida, 2


title: treated soma_Rep1


description:
Pv11_Control_24h_rep2
Transcriptome sequencing of control Pv11 cells and sampled at 24h, replicate number 2


title: Fallopian Tube 64090

description:
FT64090
ATAC-seq of a Fallopian tube sample

source_name: Fallopian Tube

value: Fallopian Tube


description:
Pv11_Control_24h_rep1
Transcriptome sequencing of control Pv11 cells and sampled at 24h, replicate number 1


title: Clear Cell Ovarian Cancer 511

description:
511
ATAC-seq of a Clear Cell Ovarian Cancer

value: Clear Cell Ovarian Cancer


title: High-Grade Serous Carcinoma s1015

description:
s1015
ATAC-seq of a high-grade serous carcinoma


title: Fallopian Tube 19155

description:
FT19155
ATAC-seq of a Fallopian tube sample


description:
Pv11_Control_1h_rep3
Transcriptome sequencing of control Pv11 cells and sampled at 1h, replicate number 3


title: High-Grade Serous Carcinoma s2904

description:
s2904
ATAC-seq of a high-grade serous carcinoma


title: treated axon_Rep6

value: pure axonal preparation


title: Fallopian Tube 19123 - side A

description:
FT19123_sideA_pre_culture
ATAC-seq of a Fallopian tube sample


title: Fallopian Tube 19123 - side B

description:
FT19123_sideB_pre_culture
ATAC-seq of a Fallopian tube sample


title: treated axon_Rep8


description:
Pv11_Control_1h_rep2
Transcriptome sequencing of control Pv11 cells and sampled at 1h, replicate number 2


title: Fallopian Tube 19123 - side B - cultured

description:
FT19123_sideB_post_culture
ATAC-seq of a Fallopian tube sample after cell culturing

value: cultured cells


title: Stroma 589

description:
Endometrioid_589-St
H3K27ac ChIP-seq of a stroma sample

source_name: Stroma

value: Stroma

tag: chip antibody


title: treated axon_Rep2


title: Stroma 375

description:
Endometrioid_375-Str
H3K27ac ChIP-seq of a stroma sample


title: Endometriosis 589

description:
Endometrioid_589-Endo
H3K27ac ChIP-seq of an endometriosis sample

source_name: Endometriosis

value: Endometriosis


title: Endometriosis 375

description:
Endometrioid_375-Endo
H3K27ac ChIP-seq of an endometriosis sample


title: treated axon_Rep4


description:
Pv11_Control_1h_rep1
Transcriptome sequencing of control Pv11 cells and sampled at 1h, replicate number 1


title: High-Grade Serous Carcinoma s1070

description:
s1070
ATAC-seq of a high-grade serous carcinoma


description:
Pv11_42C_3h_rep3
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 3h, replicate number 3


title: 092817M_ReCirc

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description:
CD8 TILs
Moffitt_BG_CD103_CD69

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by featureCounts (version 1.5.3) using RefSeq transcript annotations for human
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: Surgically removed High Grade Serous Ovarian Cancer tumor tissue

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically dissociated and single cell suspensions were prepared after debris removal. TRM and re-circulating CD8+ TILs were FACs sorted in Aria-sort
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

tag: cancer type

value: HGSOC

value: Re-circulating CD8+ TILs


title: 092608M_TRM

description:
CD8 TILs
Moffitt_BH_CD103

value: TRM CD8+ TILs


description:
Pv11_42C_3h_rep2
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 3h, replicate number 2


title: High-Grade Serous Carcinoma s1048

description:
s1048
ATAC-seq of a high-grade serous carcinoma

tag: tissue


title: 092817M_TRM

description:
CD8 TILs
Moffitt_BG_CD103


description:
Pv11_42C_3h_rep1
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 3h, replicate number 1


title: High-Grade Serous Carcinoma s1040

description:
s1040
ATAC-seq of a high-grade serous carcinoma


title: treated axon_Rep1


description:
Pv11_42C_24h_rep3
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 24h, replicate number 3


description:
Pv11_42C_24h_rep2
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 24h, replicate number 2


title: 042017M_TRM

description:
CD8 TILs
Moffitt_AC_CD103


title: Darmouth051110_TRM

description:
CD8 TILs
Darmouth_AE_CD103


title: Darmouth051110_ReCirc

description:
CD8 TILs
Darmouth_AE_CD103_CD69


title: control soma_Rep5

value: MNP + null magnetic field gradient


title: control soma_Rep4


title: control soma_Rep6