title: A375-TP-472, 10uM- replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

source_name: A375 cell line

growth_protocol: A375 were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: A375 cells treated with either DMSO, 5 uM and 10 uM of TP-472 and these cells were used to prepare the total RNA and to perfrom RNA Seq.


title: A375-control DMSO- replicate 3

status: Public on Dec 23 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: control DMSO


title: A375-TP-472, 10uM- replicate 2


title: A375-TP-472, 5uM- replicate 3


title: A375-TP-472, 10uM- replicate 1


title: A375-TP-472, 5uM- replicate 1


title: A375-control DMSO- replicate 2


title: A375-TP-472, 5uM- replicate 2


title: Cas13d, +CUG1, gRNA, rep1

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
pseudoalignment (transcript level), kallisto 0.43.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated values, TPM estimates from kallisto 0.43.0 for each sample

source_name: HeLa

growth_protocol: HeLa cells were maintained in 10% FBS growth medium (Dulbecco’s modified eagle medium (DMEM) + 10% fetal bovine serum (FBS) + 1% penicillin/streptomycin) in a humidity-controlled 5% CO2 incubator at 37°C.

extract_protocol:
RNA was extracted with 300 uL TRIzol and purified using the Direct-zol RNA Miniprep Kit.
Ribosomal RNA was depleted from 300 ng total RNA using the NEBNext rRNA Depletion Kit (NEB, #E6310L), and libraries were generated for next-generation sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L) according to the manufacturer protocol. Libraries were multiplexed with Illumina i5 and i7 barcoding primers, pooled at 4 nM, and sequenced in a 2x76 bp paired-end format on an Illumina NextSeq 500. >14 million paired end reads were sequenced per library and recorded in FASTQ format.

treatment_protocol: Cells were passaged to 12-well tissue culture plates at a density of 1.5×10^5 cells/well (3.9×10^4 cells/cm2) and transfected with 500 ng plasmid DNA using 2 uL of TransIT-X2 transfection reagent (Mirus Bio, #MIR6005) and 100 uL Opti-MEM I reduced serum medium (ThermoFisher Scientific, #31985088) according to the manufacturer’s protocol. Cells were incubated with transfection reagent for 20 hr, after which the culture medium was aspirated and replaced with 10% FBS growth medium. Cells were then incubated for an additional 48 hr for 3-day experiments, followed by RNA isolation for further analysis.

value: HeLa

tag: approach

tag: target seq

value: CUGn

tag: rep


title: LN-pLPLUC +Nutlin ChIP Seq Input

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

library_source: genomic

data_processing:
alignment to hg19 genome using Bowtie2
peak calling using macs2 (Q<0.05)
Genome_build: hg19
Supplementary_files_format_and_content: BED file

molecule: genomic DNA

source_name: LNCaP cell line

growth_protocol: LNCaP-derived cells were cultured in hormone proficient media

extract_protocol:
ChIP was performed as previously described (McNair et al 2018)
Swift BioSciences  ACCEL-NGS 2S Plus DNA Library

treatment_protocol: Nutlin 3 treated cells were treated at 10 µM for 24 hoours

tag: transduced

value: transduced with pLenti-pLPLUC

value: Complete media, Hormone proficient + Nutlin 3 at 10 µM 24 hours


title: LN-R237H ChIP Seq Input

value: transduced with pLenti-R273H

value: Complete media, Hormone proficient


title: LN-pLPLUC ChIP Seq Input


title: 7

city: changsha

first: Zhaoyu

last: Yang

address: 87 of xiangya road

country: China

institute: xiangya hospital

description: tiRNA and tRF

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: Human NCBI genome build 36 (NCBI36)
Supplementary_files_format_and_content: Sample_All_Comparisons_of_Expresseds_tDR.xlsx: Excel file includes tag count and TPM values for each Sample.
Supplementary_files_format_and_content: *_human_novoalign_alignment_tRNA_raw.txt

source_name: myocardial papilla

extract_protocol:
Total RNAs were extracted according to the manufacturer’s instruction (Qiagen, USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

tag: tissue

value: myocardial papilla

tag: diagnosis

value: RHD with AF


title: LNp53KO-R237H ChIP Seq Input

value: CRISPR mediated p53KO and transduced with pLenti-R273H


title: LNp53KO-R237C ChIP Seq Input

value: CRISPR mediated p53KO and transduced with pLenti-R273C


title: LNp53KO-R273H ChIP Seq Rep 2


title: LNp53KO-R237H ChIP Seq Rep 1


title: LNp53KO-R237C ChIP Seq Rep 2


title: LNp53KO-R237C ChIP Seq Rep 1


title: A375-control DMSO- replicate 1


title: LN-pLPLUC+Nutlin ChIP Seq Rep 2


title: LN-R273H ChIP Seq Rep 2


title: LN-R237C ChIP Seq Input

value: transduced with pLenti-R273C


title: LN-pLPLUC +Nutlin ChIP Seq Rep 1


title: dUTP strand-specific RNA-seq log-phase cells of Kluyveromyces lactis grown in BMW

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Kluyveromyces lactis

source_name: log-phase cells

growth_protocol: We conducted RNA-seq on the following 11 Ascomycota yeast species: Candida albicans, Candida glabrata, Kluyveromyces lactis, Kluyveromyces waltii, Saccharomyces bayanus, Naumovozyma castellii, Saccharomyces cerevisiae, Schizosaccharomyces japonicus, Schizosaccharomyces octosporus, Schizosaccharomyces pombe, Yarrowia lipolytica. Each of the 11 species was grown in BMW medium, chosen to minimize cross-species growth differences, as previously described (Thompson et al., 2013). N. castellii was grown at 25℃ while the rest of the species were grown at 30℃.

extract_protocol:
RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) were used to isolate total RNA from log-phase cells by mechanical lysis using the manufacturer instructions as previously described (Thompson et al., 2013).
dUTP strand-specific RNA-seq libraries were constructed as previously described (Yassour et al., 2010) with the following modifications. (1) The polyA+-selected RNA was fragmented in a 40 µl reaction containing 1x Fragmentation Buffer (Affymetrix) by heating at 80℃ for 4 minutes followed by cleanup via ethanol precipitation for all libraries (except Y. lipolytica, S. pombe, S. japonicus, and S. octosporus; for these species, the conditions described previously were used (Yassour et al., 2010)), followed by cleanup via 1.8x RNAClean XP beads (Beckman Coulter Genomics). (2) For C. glabrata, K. lactis, S. bayanus, S. pombe, S. japonicus, and S. octosporus libraries, the adapter ligation was performed overnight at 16℃. For the rest, this was done at 16 degrees for 2 hours as described previously (Yassour et al., 2010). (3) Normalization was carried out based on the cDNA input and pooling of selected Illumina barcoded-adaptor-ligated cDNA products followed by gel size selection occurred as follows: range of 275 to 575 bp for pooled C. albicans, K. polysporus, K. waltii, and N. castellii libraries, and 375 to 575 bp for C. glabrata, K. lactis, and S. bayanus libraries. For the other libraries, no pooling was performed before gel size-selection – range of 310 to 510 bp for Y. lipolytica and 350 to 550 bp for S. pombe, S. japonicus, and S. octosporus. (4) The final PCR product was purified by 1.8x AMPure XP beads (Beckman Coulter Genomics) followed by a second gel size-selection for the range of 300 to 575 bp for C. albicans, K. polysporus, K. waltii, and S. castellii libraries, but no gel size-selection was performed for the other libraries. The pooled final library was sequenced on one to four lanes of HiSeq2000 (Illumina) with 68 base (Y. lipolytica had 76 base) paired-end reads and 8 base index reads.

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: LN-R237H ChIP Seq Rep 1


title: LN-R273C ChIP Seq Rep 2


title: LN-R237C ChIP Seq Rep 1


title: LN-pLPLUC ChIP Seq Rep 2


title: PAC0140_plasma

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

description: Maternal Plasma

data_processing:
All sequencing data was firstly assessed for quality using FastQC [] to identify any failed and low-coverage samples.
Alignment and analysis processed from raw FASTQ files using the bcbio-nextgen pipeline (Pantano, Estivill, and Martí 2009). Briefly, adapter detection and trimming were performed using Atropos (Didion, Martin, and Collins 2017). Alignment performed using STAR (Dobin et al. 2013) (hg19 build GRch37). Micro RNA were clustered and collapsed using SeqCluster (Pantano, Estivill, and Martí 2011), and detected using SeqBuster (Pantano, Estivill, and Martí 2009). Micro RNA were annotated using the miraligner (Pantano, Estivill, and Martí 2009) tool with miRBase version 21.0 (Griffiths-Jones et al. 2006; Kozomara and Griffiths-Jones 2014) (http://www.mirbase.org) as the reference miRNA database.
Analysis was limited to gene counts greater than 2.5 counts per million (CPM) in at least 29 samples (i.e. the size of the smallest sample group).
Differential gene expression (DGE) was carried out using edgeR (Robinson, McCarthy, and Smyth 2009) within the R/Bioconductor statistical framework, relying on sample-weight transformation contained in the voom functions (Law et al. 2014). Linear models were then fitted with limma (Law et al. 2014) along with empirical Bayes moderation (Smyth GK 2004).
Genome_build: GRCh37
Supplementary_files_format_and_content: counts

source_name: Blood Plasma

extract_protocol:
Placental villous tissue was collected from women who were undergoing elective pregnancy terminations (6-23+6 weeks’ gestation). All placenta tissue was collected post termination and processed as soon as possible after collection and placed into RNALater (Thermo Fisher) within 15 minutes. Total RNA was isolated using a modified protocol of the RNeasy mini plus kit (Qiagen, Hilden, Germany) whereby the RW1 buffer, a proprietary component of the RNeasy Kit, is replaced with 100% ethanol, that then underwent size fractionation for small RNAs before sequencing. For plasma, samples of peripheral blood (6-9 mL) were collected from the same women into standard EDTA blood tubes at the time of termination and stored on ice until processed. Whole blood underwent centrifugation at 800 x g for 15 minutes at 4°C before plasma removal and then spun for a further 15 minutes. All samples were stored at -80°C until further processing. Micro RNA was isolated from 200 μL plasma samples using the QIAGEN miRNA serum/plasma kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Sequencing library preparation and sequencing was performed by Qiagen (Valencia, CA) using the QIAseq miRNA Library Kit and QIAseq miRNA 48 Index IL kits as per manufacturer’s instructions. Amplified cDNA libraries underwent single-end sequencing by synthesis (Illumina 1.9).

value: Blood Plasma

tag: subject id

tag: gestational age

tag: Sex

value: Female


title: PAC0139_plasma

description: Maternal Plasma

value: Male


title: Bursa from IBDV infected three weeks old chick

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat. To remove low quality cells and likely multiple captures, which is a major concern in microdroplet-based experiments, we applied a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2-fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers.
Principal component analysis (PCA) was performed to reduce the dimensionality with RunPCA function in Seurat . Graph-based clustering was performed to cluster cells according to their gene expression profile using the FindClusters function in Seurat [56]. Cells were visualized using a 2-dimensional t-distributed stochastic neighbor embedding (t-SNE) algorithm with the RunTSNE function in Seurat [56]. We used the FindAllMarkers function (test.use = bimod) in Seurat [56] to identify marker genes of each cluster. For a given cluster, FindAllMarkers identified positive markers compared with all other cells. Then, we used the R package SingleR, a novel computational method for unbiased cell type recognition of scRNA-seq, with the reference transcriptomic datasets(Immgen: The Immunological Genome Project: networks of gene expression in immune cells)
Genome_build: Immgen: The Immunological Genome Project: networks of gene expression in immune cells
Supplementary_files_format_and_content: matrix.mtx, features.tsv, barcodes.tsv

molecule: polyA RNA

organism: Gallus gallus

source_name: IBDV infection 72 h (Bursa from three weeks)

extract_protocol:
1×PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/ml) was added and then centrifugation at 300 x g for 5 min at room temperature. The cell pellet was suspended in 1ml red blood cell lysis buffer and incubated for 10 min at 4℃. The samples were then resuspended in 1ml PBS containing 0.04% BSA and filtered over Scienceware Flowmi 40-µm cell strainers (VMR).
Single cell sequencing libraries were prepared using the Chromium Single Cell 3’Reagent Kit (10× Genomics) according to manufacturer’s protocol. Samples were sequenced on the Illumina Novaseq6000 with 28-bp read ,8-bp i7 index and 98-bp read 2 for the gene-expression library.

tag: group

tag: age

value: three weeks old

tag: infection

value: IBDV

value: Bursa of Fabricius

tag: cell type

value: total bursa cells


title: LN-pLPLUC ChIP Seq Rep 1

value: transduced with pLenti-pLPLUC

tag: treatment


title: Bursa from Control three weeks old chick

source_name: untreated (Bursa from Control three weeks)

value: untreated


title: PAC0131_plasma

description: Maternal Plasma


title: PAC0134_plasma

description: Maternal Plasma


title: Bursa from IBDV infected two weeks old chick

source_name: IBDV infection 72 h (Bursa from two weeks)

value: two weeks old


title: Bursa from Control two weeks old chick

source_name: untreated (Bursa from Control two weeks)


title: PAC0129_plasma

description: Maternal Plasma


title: PAC0124_plasma

description: Maternal Plasma


title: PAC0127_plasma

description: Maternal Plasma


title: Δppk logarithmic rep 4 cisplatin treated 15 min ; cisplatin paired- RNA -seq

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

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

department: Biological Chemistry

institute: University of Michigan

description:
rRNA substracted RNA
combined_logfc.csv
results_fordppk_time15_vs_time0_sleuth_output.csv
results_genotypedppk:time.fTime15_sleuth_output.csv
results_time.fTime15_sleuth_output.csv

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were subject to quantitation using kallisto v0.43 and differential expression calling using sleuth 0.30.0
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth

organism: Escherichia coli

source_name: Culture lysate

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C.  The lysate (600 μl) was mixed 1:1 with 2X IP buffer (200 mM Tris, pH 8.0, 600 mM NaCl; 4% v/vTriton X-100; 2X protease inhibitors) and 1X molecular grade BSA (NEB #S9000S). We prepared NEB protein G beads (50 μl per sample) by washing them with 1 ml of 1X IP buffer without protease inhibitors but including 1X molecular grade BSA, and resuspending them in a final volume of 50 μl/ sample. Washed beads were incubated with lysates at 4°C with rocking for two hours. Using a magnetic stand, beads were removed, and pre-cleared lysates were placed into fresh tubes.  As an input control, 50 μl of pre-cleared lysates were mixed with 450 μl of ChIP Elution Buffer (50 mM Tris, pH 8.0, 10 mM EDTA; 1% w/v SDS) and placed at 65°C for no more than 16 hours for crosslink reversal. DNA extraction will be described below. To the remainder of the lysate / IP buffer mixture, we added 5 μl of mCherryChIP antibody (mCherry Monoclonal Antibody: ThermoFisher Cat #M11217) and incubated the samples at 4°C overnight on a tube rocker. The next morning, we prepared a new batch of NEB protein G beads (50 μl/ sample), distributed into antibody and lysate mixtures and incubated at 4°C with rocking for two hours. The mixtures were then washed in the following series with 1 ml washes for each buffer and mixing by inversion. After each inversion, the tubes were placed on a magnetic stand to remove wash, and new wash was added. The following wash buffers were used n series:  1X Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% v/vTriton X-100; 1 mM EDTA); 1X Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% v/v Triton X-100; 0.1% w/v sodium deoxycholate; 1 mM EDTA); 1X Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% v/v Triton X-100; 1 mM EDTA);  1X TE (10 mM Tris, pH 8.0; 1 mM EDTA). After the last wash, beads were resuspended in 500 μl of ChIP Elution Buffer (recipe above) and incubated at 65°C for 30 min with vortexing every 5-10 minutes. The tubes were then placed on a magnetic stand, the supernatant placed in a fresh tube, placed at 65°C for no more than 16 hours for crosslink reversal. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).  RNA samples: NEBNext Ultra 2 Directional RNA kit

tag: strain

tag: genotype

value: MOPs minimal media + glucose

value: logarithmic phase


title: PAC0120_plasma

description: Maternal Plasma


title: PAC0118_plasma

description: Maternal Plasma


title: PAC0117_plasma

description: Maternal Plasma


title: Normal post-auricular skin tissue circRNA 3

type: RNA

city: Changsha

first: Wei

last: Liu

state: China

address: The Second Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha

institute: The Second Xiangya Hospital, Central South University of China

description: circRNA expression data from Homo sapiens normal post-auricular skin tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: Normal post-auricular skin tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Acquired middle ear cholesteatoma and normal post-auricular skin tissues

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

treatment_protocol: Tissues from acquired middle ear surgury were promptly frozen in liquid nitrogen.

value: Normal post-auricular skin tissue

tag: gender

value: male


title: PAC0114_plasma

description: Maternal Plasma


title: Normal post-auricular skin tissue circRNA 4

value: female


title: Normal post-auricular skin tissue circRNA 2


title: Normal post-auricular skin tissue circRNA 1


title: Δppk logarithmic rep 2; cisplatin paired- RNA -seq


title: Δppk logarithmic rep 3; cisplatin paired- RNA -seq


title: Acquired middle ear cholesteatoma tissue circRNA 1

description: circRNA expression data from Homo sapiens acquired middle ear cholesteatoma tissue


title: Acquired middle ear cholesteatoma tissue circRNA 6


title: Acquired middle ear cholesteatoma tissue circRNA 2


title: Δppk logarithmic rep 1; cisplatin paired- RNA -seq


title: Δppk logarithmic rep 3 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: Δppk logarithmic rep 2 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: Δppk logarithmic rep 4; cisplatin paired- RNA -seq


title: PAC0109_plasma

description: Maternal Plasma


title: PAC0111_plasma

description: Maternal Plasma


title: Acquired middle ear cholesteatoma tissue circRNA 3


title: Δppk logarithmic rep 1 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: PAC0108_plasma

description: Maternal Plasma


title: PAC0122_plasma

description: Maternal Plasma


title: Acquired middle ear cholesteatoma tissue circRNA 4


title: PAC0105_plasma

description: Maternal Plasma


title: PAC0107_plasma

description: Maternal Plasma


title: WT logarithmic rep 3 cisplatin treated 15 min ; cisplatin paired- RNA -seq

value: wild type


title: Acquired middle ear cholesteatoma tissue circRNA 5


title: WT logarithmic rep 2 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: WT logarithmic rep 4; cisplatin paired- RNA -seq


title: PAC0103_plasma

description: Maternal Plasma


title: PAC0102_plasma

description: Maternal Plasma


title: PAC0100_plasma

description: Maternal Plasma


title: WT logarithmic rep 3; cisplatin paired- RNA -seq


title: PAC0099_plasma

description: Maternal Plasma


title: WT logarithmic rep 2; cisplatin paired- RNA -seq


title: WT logarithmic rep 4 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: WT logarithmic rep 1; cisplatin paired- RNA -seq


title: PAC0098_plasma

description: Maternal Plasma


title: PAC0097_plasma

description: Maternal Plasma


title: Δppk hfq-PAmCherry mcherry chip rep2

description:
dppk_hfqmc_mchip_vs_inp.lograt.bed
dppk_hfqmc_mchip.bed
dppk_hfqmc_mchip_peaks.bed

value: delta_ppk hfq-PAmCherry


title: WT logarithmic rep 1 cisplatin treated 15 min ; cisplatin paired- RNA -seq


title: PAC0091_plasma

description: Maternal Plasma

value: Blood Plasma


title: WT hfq-PAmCherry mcherry chip rep1

description:
WT_hfqmc_mchip_vs_inp.lograt.bed
WT_hfqmc_mchip.bed
WT_hfqmc_mchip_peaks.bed

value: hfq-PAmCherry


title: PAC0088_plasma

description: Maternal Plasma

value: Female


title: Δppk hfq-PAmCherry input rep2


title: WT hfq-PAmCherry mcherry chip rep2


title: Δppk hfq-PAmCherry input rep1


title: Δppk hfq-PAmCherry mcherry chip rep1


title: PAC0087_plasma

description: Maternal Plasma

value: Male


title: PAC0086_plasma

description: Maternal Plasma


title: PAC0084_plasma

description: Maternal Plasma


title: PAC0083_plasma

description: Maternal Plasma


title: PAC0078_plasma

description: Maternal Plasma


title: WT mcherry chip rep 2


title: WT hfq-PAmCherry input rep2


title: WT hfq-PAmCherry input rep1


title: WT mcherry chip rep 1


title: WT input rep 1


title: PAC0093_plasma

description: Maternal Plasma


title: Δppk Δhfq logarithmic rep 1- RNA -seq

description:
rRNA substracted RNA
sleuth_table_genotypedhfqdppk_HA.tsv

value: delta_ppk delta_hfq


title: PAC0077_plasma

description: Maternal Plasma


title: PAC0074_plasma

description: Maternal Plasma


title: PAC0075_plasma

description: Maternal Plasma


title: PAC0076_plasma

description: Maternal Plasma


title: PAC0072_plasma

description: Maternal Plasma


title: Δhfq logarithmic rep 1- RNA -seq

description:
rRNA substracted RNA
sleuth_table_genotypedhfq_HA.tsv


title: PAC0071_plasma

description: Maternal Plasma


title: Δppk logarithmic rep 2- RNA -seq

description:
rRNA substracted RNA
sleuth_table_genotypedppk_HA.tsv


title: PAC0069_plasma

description: Maternal Plasma


title: PAC0070_plasma

description: Maternal Plasma


title: PAC0064_plasma

description: Maternal Plasma


title: PAC0065_plasma

description: Maternal Plasma


title: WT logarithmic rep 1- RNA -seq

description:
rRNA substracted RNA
sleuth_table_genotypedhfq_HA.tsv
sleuth_table_genotypedppk_HA.tsv
sleuth_table_genotypedhfqdppk_HA.tsv


title: PAC0063_plasma

description: Maternal Plasma


title: WT logarithmic rep 2- RNA -seq


title: WT input rep 2


title: PAC0062_plasma

description: Maternal Plasma


title: PAC0058_plasma

description: Maternal Plasma


title: PAC0059_plasma

description: Maternal Plasma


title: PAC0060_plasma

description: Maternal Plasma


title: PAC0057_plasma

description: Maternal Plasma


title: Δppk Δhfq logarithmic rep 2- RNA -seq


title: PAC0055_plasma

description: Maternal Plasma


title: PAC0056_plasma

description: Maternal Plasma


title: PAC0053_plasma

description: Maternal Plasma


title: PAC0054_plasma

description: Maternal Plasma


title: Δhfq logarithmic rep 2- RNA -seq


title: PAC0051_plasma

description: Maternal Plasma


title: PAC0049_plasma

description: Maternal Plasma


title: PAC0047_plasma

description: Maternal Plasma


title: Δppk logarithmic rep 1- RNA -seq


title: PAC0050_plasma

description: Maternal Plasma


title: PAC0052_plasma

description: Maternal Plasma


title: PAC0048_plasma

description: Maternal Plasma


title: PAC0043_plasma

description: Maternal Plasma


title: PAC0044_plasma

description: Maternal Plasma


title: PAC0042_plasma

description: Maternal Plasma


title: PAC0038_plasma

description: Maternal Plasma


title: PAC0041_plasma

description: Maternal Plasma


title: PAC0039_plasma

description: Maternal Plasma


title: PAC0040_plasma

description: Maternal Plasma


title: PAC0037_plasma

description: Maternal Plasma


title: PAC0035_plasma

description: Maternal Plasma


title: PAC0033_plasma

description: Maternal Plasma


title: PAC0034_plasma

description: Maternal Plasma


title: PAC0027_plasma

description: Maternal Plasma


title: PAC0029_plasma

description: Maternal Plasma


title: PAC0031_plasma

description: Maternal Plasma


title: PAC0046_plasma

description: Maternal Plasma


title: PAC0025_plasma

description: Maternal Plasma


title: PAC0024_plasma

description: Maternal Plasma


title: PAC0022_plasma

description: Maternal Plasma


title: PAC0021_plasma

description: Maternal Plasma


title: PAC0045_plasma

description: Maternal Plasma


title: PAC0020_plasma

description: Maternal Plasma


title: PAC0018_plasma

description: Maternal Plasma


title: PAC0023_plasma

description: Maternal Plasma


title: PAC0016_plasma

description: Maternal Plasma


title: PAC0015_plasma

description: Maternal Plasma


title: PAC0017_plasma

description: Maternal Plasma


title: PAC0014_plasma

description: Maternal Plasma


title: PAC0011_plasma

description: Maternal Plasma


title: PAC0012_plasma

description: Maternal Plasma


title: PAC0010_plasma

description: Maternal Plasma


title: PAC0009_plasma

description: Maternal Plasma


title: PAC0036_plasma

description: Maternal Plasma


title: PAC0008_plasma

description: Maternal Plasma


title: PAC0032_plasma

description: Maternal Plasma


title: PAC0007_plasma

description: Maternal Plasma


title: PAC0030_plasma

description: Maternal Plasma


title: PAC0026_plasma

description: Maternal Plasma


title: PAC0006_plasma

description: Maternal Plasma


title: PAC0139_tissue

description: Placental Chorionic Villous Tissue

source_name: Chorionic Villous

value: Chorionic Villous


title: PAC0140_tissue

description: Placental Chorionic Villous Tissue


title: PAC0134_tissue

description: Placental Chorionic Villous Tissue


title: PAC0127_tissue

description: Placental Chorionic Villous Tissue


title: PAC0129_tissue

description: Placental Chorionic Villous Tissue


title: PAC0131_tissue

description: Placental Chorionic Villous Tissue


title: PAC0118_tissue

description: Placental Chorionic Villous Tissue


title: PAC0124_tissue

description: Placental Chorionic Villous Tissue


title: PAC0117_tissue

description: Placental Chorionic Villous Tissue


title: PAC0122_tissue

description: Placental Chorionic Villous Tissue


title: PAC0013_plasma

description: Maternal Plasma


title: PAC0109_tissue

description: Placental Chorionic Villous Tissue


title: PAC0114_tissue

description: Placental Chorionic Villous Tissue


title: PAC0108_tissue

description: Placental Chorionic Villous Tissue


title: PAC0111_tissue

description: Placental Chorionic Villous Tissue


title: PAC0100_tissue

description: Placental Chorionic Villous Tissue


title: PAC0103_tissue

description: Placental Chorionic Villous Tissue


title: PAC0102_tissue

description: Placental Chorionic Villous Tissue


title: PAC0099_tissue

description: Placental Chorionic Villous Tissue


title: PAC0105_tissue

description: Placental Chorionic Villous Tissue


title: PAC0098_tissue

description: Placental Chorionic Villous Tissue


title: PAC0093_tissue

description: Placental Chorionic Villous Tissue


title: PAC0107_tissue

description: Placental Chorionic Villous Tissue


title: PAC0091_tissue

description: Placental Chorionic Villous Tissue


title: PAC0097_tissue

description: Placental Chorionic Villous Tissue


title: PAC0088_tissue

description: Placental Chorionic Villous Tissue


title: PAC0087_tissue

description: Placental Chorionic Villous Tissue


title: PAC0084_tissue

description: Placental Chorionic Villous Tissue


title: PAC0078_tissue

description: Placental Chorionic Villous Tissue


title: PAC0086_tissue

description: Placental Chorionic Villous Tissue


title: PAC0083_tissue

description: Placental Chorionic Villous Tissue


title: PAC0120_tissue

description: Placental Chorionic Villous Tissue


title: PAC0076_tissue

description: Placental Chorionic Villous Tissue


title: P64W6-Outer-unloaded-IL1

city: Durham

first: Amy

last: McNulty

state: NC

address: 203 Research Dr

department: Orthopaedic Surgery

institute: Duke University

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W6-Outer-unloaded-IL1

data_processing:
Basecalling by Illumina RTA3
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis
Reads were mapped to the Sscrofa11.1v91 version of the pig genome and transcriptome using the STAR RNA-seq alignment tool.  Reads were kept for subsequent analysis if they mapped to a single genomic location
Gene counts were compiled using the HTSeq tool
Normalization and differential expression analysis was performed using the DeSeq2 BioConductor packge in the R statistical programming language
Genome_build: Sscrofa11.1v91
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and matrix table with DeSeq normalized counts for every gene and every sample

organism: Sus scrofa

source_name: medial meniscus

growth_protocol: Cells were isolated from the inner third or outer two-thirds of porcine medial menisci from skeletally mature female pigs by enzymatic digestion and frozen for future use. Cells from at least three separate menisci were pooled and expanded for one passage, then seeded onto collagen type I coated Bioflex® plates at a density of 250,000 cells/well.

extract_protocol:
RNA was column purified according to the Norgen RNA extraction kit protocol (Catalog # 48300; Norgen Biotek Corp.)
KAPA Stranded mRNA-Seq Kit--KK8421

treatment_protocol: Approximately 40 hours after seeding, fresh culture media with or without 0.1 ng/mL IL-1α was added and explants were subjected to 5% cyclic tensile stretch in a sine wave pattern at 0.5Hz, using using a FlexCell® FX600T™. Immediately following the loading session, cells were rinsed in phosphate buffered saline then RNA extraction was performed.

tag: zone

value: Outer

tag: treatment (load)

value: unloaded


title: P64W5-Outer-unloaded-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W5-Outer-unloaded-IL1


title: PAC0074_tissue

description: Placental Chorionic Villous Tissue

tag: tissue


title: P64W4-Outer-unloaded-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W4-Outer-unloaded-IL1


title: PAC0075_tissue

description: Placental Chorionic Villous Tissue


title: P63W6-Outer-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W6-Outer-unloaded


title: PAC0072_tissue

description: Placental Chorionic Villous Tissue


title: P63W5-Outer-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W5-Outer-unloaded


title: PAC0071_tissue

description: Placental Chorionic Villous Tissue


title: P63W4-Outer-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W4-Outer-unloaded


title: P62W6-Outer-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W6-Outer-5load-IL1

value: loaded


title: PAC0069_tissue

description: Placental Chorionic Villous Tissue


title: PAC0070_tissue

description: Placental Chorionic Villous Tissue


title: P62W5-Outer-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W5-Outer-5load-IL1


title: PAC0064_tissue

description: Placental Chorionic Villous Tissue


title: P62W4-Outer-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W4-Outer-5load-IL1


title: PAC0062_tissue

description: Placental Chorionic Villous Tissue


title: P61W5-Outer-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W5-Outer-5load


title: P61W4-Outer-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W4-Outer-5load


title: PAC0077_tissue

description: Placental Chorionic Villous Tissue


title: PAC0060_tissue

description: Placental Chorionic Villous Tissue


title: PAC0065_tissue

description: Placental Chorionic Villous Tissue


title: PAC0059_tissue

description: Placental Chorionic Villous Tissue


title: P64W3-Inner-unloaded-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W3-Inner-unloaded-IL1

value: Inner


title: P64W1-Inner-unloaded-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W1-Inner-unloaded-IL1


title: P64W2-Inner-unloaded-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P64W2-Inner-unloaded-IL1


title: P63W3-Inner-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W3-Inner-unloaded


title: P63W2-Inner-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W2-Inner-unloaded


title: P63W1-Inner-unloaded

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P63W1-Inner-unloaded


title: P62W3-Inner-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W3-Inner-5load-IL1


title: PAC0054_tissue

description: Placental Chorionic Villous Tissue


title: PAC0055_tissue

description: Placental Chorionic Villous Tissue


title: P61W6-Outer-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W6-Outer-5load


title: P62W2-Inner-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W2-Inner-5load-IL1


title: PAC0056_tissue

description: Placental Chorionic Villous Tissue


title: P61W3-Inner-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W3-Inner-5load


title: PAC0063_tissue

description: Placental Chorionic Villous Tissue


title: PAC0051_tissue

description: Placental Chorionic Villous Tissue


title: PAC0052_tissue

description: Placental Chorionic Villous Tissue


title: PAC0053_tissue

description: Placental Chorionic Villous Tissue


title: P61W2-Inner-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W2-Inner-5load


title: P61W1-Inner-5load

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P61W1-Inner-5load


title: PAC0048_tissue

description: Placental Chorionic Villous Tissue


title: PAC0047_tissue

description: Placental Chorionic Villous Tissue


title: PAC0046_tissue

description: Placental Chorionic Villous Tissue


title: PAC0057_tissue

description: Placental Chorionic Villous Tissue


title: Lung ctDNA methylation in rats with 10 Gy X-ray to lung

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Then, the clean reads were aligned to rat genome (UCSC RN5) using bismark software (v0.22.3) with default parameters. The methylation status of each C within the genome was extracted by bismark_methylation_extractor. Methylated regions (MRs) were identified by DSS software (v2.34.0) and then were annotated with home-made scripts. Software IGV was recommended to be used to visualize the NGS data.
Genome_build: UCSC RN5
Supplementary_files_format_and_content: Methylated_Region

organism: Rattus norvegicus

source_name: lung tissues

growth_protocol: SPF condition of rats.

extract_protocol:
Briefly, genomic DNA was extracted using DNeasy Mini Prep Kit (Qiagen) and ctDNA was extracted using the QIAamp Circulating Nucleic Acid Kit (QIAGEN) according to the manufacturer’s instructions.
Extracted DNA was quantified using a Qubit 3.0 Fluoromter (Thermo Fisher Scientific), and mixed with 0.05% artificially-synthesized unmethylated sequences, followed by sodium bisulfite conversion. Bisulfite conversion was performed using a EZ-DNA-Methylation-GOLD kit (Zymo Research). Then, Accel-NGS Methy-Seq DNA library kit (Swift Bioscience) was used to prepare the sequencing libraries. Libraries were qualified using 2100 bioanalyzer (Agilent) and sequenced on NovaSeq 6000 sequencer (Illumina) with 150bp paired end mode according to the manufacturer’s instructions.

treatment_protocol: SD rats were irradiated with local radaition to brain, lung or skin. Serum was collected and subjiected to ctDNA extraction. ctDNA were then treated by methylation-sensive bisulfite and sequencing. Brain was irradiated with 20 Gy electron beam. Lung was irradiated with 10 Gy X-ray. Skin was irradaited with 45 Gy electron beam.

value: 10 Gy X-ray to lung

value: lung tissues


title: Brain ctDNA methylation in rats with 20 Gy electron beam to brain

source_name: brain tissues

value: 20 Gy electron beam to brain

value: brain tissues


title: Serum ctDNA methylation in rats with 10 Gy X-ray to lung

source_name: serum

value: serum


title: PAC0045_tissue

description: Placental Chorionic Villous Tissue


title: PAC0044_tissue

description: Placental Chorionic Villous Tissue


title: Serum ctDNA methylation in rats with 20 Gy electron beam to brain


title: P62W1-Inner-5load-IL1

description:
2021-10-08 Cell Stretch RawCounts.xlsx
2021-12-20 Cell Stretch Normalized Counts.xlsx
P62W1-Inner-5load-IL1


title: Skin ctDNA methylation in rats with45 Gy electron beam to skin

source_name: skin tissues

value: 45 Gy electron beam to skin

value: skin tissues


title: Serum ctDNA methylation in rats with 45 Gy electron beam to skin


title: PAC0050_tissue

description: Placental Chorionic Villous Tissue


title: Serum ctDNA methylation in rats

value: Without treatment (control)


title: PAC0049_tissue

description: Placental Chorionic Villous Tissue


title: PAC0043_tissue

description: Placental Chorionic Villous Tissue


title: JJDD006C

city: Berkeley

first: Jamie

middle: H D

last: Cate

state: CA

address: 2151 Berkeley Way

department: Molecular and Cell Biology/Chemistry

institute: University of California

description: RNA-Seq of activated Jurkat cells, replicate 2

data_processing:
PAR-CLIP replicate 1 library adaptors have 3' sequence TCGTATGCCGTCTTCTGCTTG. This is preceded by a 5-nt UMI barcode for PCR deduplication. Finally, each eIF3 subunit sample is indicated by a 5-nt barcode.
Barcoding for PAR-CLIP samples: PA=TCACTNNNNN  PB=TCATCNNNNN  PD=TCCACNNNNN  P1=TCCGTNNNNN  P2=TCACTNNNNN where NNNNN is the UMI for PCR deduplication
Clusters of overlapping sequence reads mapped against the human genome version hg38 were generated using the PARalyzer software (Pubmed ID: 21851591) incorporated into the PARpipe pipeline (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/, (Pubmed ID: 30517751) with the settings below. Binding sites were categorized using the Gencode GRCh38.p12 GTF annotations (gencode.v21.annotation.gtf), https://www.gencodegenes.org/human/.
Settings used for PARpipe: Conversion = T>C;   Minimum read count per group = 5;   Minimum read count per cluster = 7;   Minimum read count for kde = 3;   Minimum cluster size = 11;   Minimum conversion locations for cluster = 2;   Minimum conversion count for cluster = 2;   Minimum read count for cluster inclusion = 1;   Minimum read length = 20;   Maximum number of non conversion mismatches = 1;
Genome_build: hg38
Supplementary_files_format_and_content: Excel spreadsheets with tabulated data from the PAR-CLIP experiment or RNA-Seq experiment.

growth_protocol: Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS (VWR Life Science Seradigm) and 0.01% Penicillin-Streptomycin (10,000 U/mL) (ThermoFisher).

extract_protocol: RNA samples were extracted from non-activated Jurkat cells or Jurkat cells activated for 5 hr with PMA + IONO, using the Direct-zol RNA Miniprep kit (Zymo Research). The libraries were prepared using TruSeq Stranded RNA LT Ribo-Zero Gold kit (Illumina) following the manufacturer’s instructions, with two biological replicates. Cutadapt (version 2.6) with a minimum read length of 20, 5’ end with a cutoff of 15 and the 3’ end with a cutoff of 10 in paired-end mode was used to remove adapters. RNA-seq reads were pseudoaligned using kallisto v.0.46.0 run in quant mode with default parameters to estimate transcript abundance (transcripts per million, TPM). The transcript index for kallisto was made with default parameters and GENCODE Release 32 (GRCh38.p13) FASTA file.

treatment_protocol: 50 µM of 4-thiouridine was determined as non-toxic to Jurkat cells over the time course of the PAR-CLIP experiments. Jurkat cells seeded at 8 x 10^5 cells ml-1 were treated with 50 µM of 4-thiouridine for 7 hours. Then, the cells were treated with or without 1X Cell Stimulation Cocktail, containing PMA and IONO (ThermoFisher, Cat. #: 00-4970-93) for 5 hours. Cells were then crosslinked on ice with 365 nm UV irradiation at an energy dose of 0.2 J cm-2.

value: T cell leukemia

tag: cell line

value: Jurkat Clone E6-1


title: PAC0042_tissue

description: Placental Chorionic Villous Tissue

value: Male


title: PAC0041_tissue

description: Placental Chorionic Villous Tissue

value: Female


title: JJDD005C

description: RNA-Seq of activated Jurkat cells, replicate 1


title: PAC0039_tissue

description: Placental Chorionic Villous Tissue

value: Chorionic Villous


title: BM cells, Case14_remission_sequencing

city: Perugia

first: Danika

last: Di Giacomo

state: Perugia

address: S.Andrea delle fratte

department: Medicine and Surgery

country: Italy

institute: University of Perugia

description: Case_14 (UPN#676)

data_processing:
FASTQ sequencing files were uploaded to SOPHiA DDM® platform version 4 and, following adapter trimming and quality filtering, reads were aligned to the human reference genome (hg19 assembly) through the artificial SOPHiA™ intelligence.
Variant calling of the resulted alignments was then performed using an in-house somatic variant caller
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including non-filtered annotated variants identified in each Sample

source_name: Unsorted Bone Marrow Cells

extract_protocol:
DNA was extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared using 200 ng of BM genomic DNA following manufacturer’s instructions (SOPHiA Genetics, Saint Sulpice, Switzerland).
probe-based targeted sequencing

value: bone marrow

tag: cytogenetics


title: PAC0038_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case14_post-HCT_sequencing

description: Case_14 (UPN#198)


title: BM cells, Case14_diagnosis_sequencing

description: Case_14 (UPN#546)


title: BM cells, Case13_remission_sequencing

description: Case_13 (UPN#687)


title: PAC0040_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case13_diagnosis_sequencing

description: Case_13 (UPN#606)


title: M3,ctrl

first: lixiaoping

middle: 李小平

last: li

address: 199 Ren'ai Road, Suzhou Industrial Park

department: IBMS

institute: suzhou university

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by tophat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format

source_name: Peripheral blood mononuclear cells

extract_protocol:
The PBMCs derived from asthmatic patient and healthy people blood were extracted and were resuspended in  Trizol plus reagent(Takara Biotechnology Co. LTD)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood mononuclear cells

tag: disease state

value: healthy volunteers


title: JJDD006B

description: RNA-Seq of nonactivated Jurkat cells, replicate 2


title: JJDD005B

description: RNA-Seq of nonactivated Jurkat cells, replicate 1


title: PAC0036_tissue

description: Placental Chorionic Villous Tissue

tag: subject id


title: PAC0037_tissue

description: Placental Chorionic Villous Tissue

tag: gestational age


title: PAC0035_tissue

description: Placental Chorionic Villous Tissue

tag: Sex


title: BM cells, Case12_diagnosis_sequencing

description: Case_12 (UPN#650)


title: CC24,ctrl


title: BM cells, Case11_diagnosis_sequencing

description: Case_11 (UPN#649)


title: PAC0058_tissue

description: Placental Chorionic Villous Tissue


title: 107,sick

value: Asthmatic patients


title: BM cells, Case10_remission_sequencing

description: Case_10 (UPN#684)


title: PAC0032_tissue

description: Placental Chorionic Villous Tissue


title: PAC0031_tissue

description: Placental Chorionic Villous Tissue


title: PAC0033_tissue

description: Placental Chorionic Villous Tissue


title: Con

hyb_protocol: Labeled controls and test samples labeled with  Cy3-dCTP were dissolved in 80μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent).

data_processing: To select the differentially expressed genes, we used thresholdvalues of>=2 and<=-2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA)

source_name: Con THP1

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, 2 and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 1 g total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with the T7 Oligo (dT) and T7 Oligo (dN).

growth_protocol: Human THP-1 cells were purchased from ATCC and cultured in RPMI-1640 medium (HyClone, Logan, Utah) with 10% FBS (Gibco, Hong Kong) and 1% penicillin-streptomycin solution and 0.05mM β-Mer (Invitrogen, Camarillo, CA, USA) at 37°C in a humidified 5% CO2 atmosphere.

treatment_protocol: DMSO and  LPS treated THP-1 cells for 48h were collected in Trizol plus reagent(Takara Biotechnology Co. LTD)

value: control


title: LPS

source_name: LPS THP1

value: LPS-stimulating


title: PAC0034_tissue

description: Placental Chorionic Villous Tissue


title: 69,sick


title: BM cells, Case10_diagnosis_sequencing

description: Case_10 (UPN#547)


title: 68,sick


title: PAC0030_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case9_remission_sequencing

description: Case_9 (UPN#683)


title: CC25,ctrl


title: PAC0029_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case9_diagnosis_sequencing

description: Case_9 (UPN#544)


title: PAC0027_tissue

description: Placental Chorionic Villous Tissue


title: PAC0026_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case8_diagnosis_sequencing

description: Case_8 (UPN#607)


title: PAC0025_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case6_remission_sequencing

description: Case_6 (UPN#686)


title: Lung AT2 cells DNp63 WT Pol2 ChIP-Seq

city: Tampa

first: Elsa

middle: Renee

last: Flores

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

description: AT2 WT Pol2

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the rat genome build UCSC rn6 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Differential regions were determined using the diffReps software using the G-test with significance achieved for a fold change > 2 and an FDR-adjusted q-value < 0.01.
Genome_build: rn6
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format

organism: Mus musculus

source_name: ΔNp63fl/fl and ΔNp63Δ/Δ mice

extract_protocol:
Cell pellets were spun down and flash frozen. Samples were sent on dry ice to Active Motif where they used their proprietary low-cell number ChIP-seq extraction protocol.
Sequencing librairies were prepared using Bioo Kit Option 2 protocol using 1.7-10 ng of DNA per sample.

treatment_protocol: Basal cells were isolated and grown on J2-3T3 feeders in MTEC-plus media. AT2 cells were isolated and grown with lung endothelial cells in BASC media. Cells were treated with either adenoviral-empty or adenoviral-cre for deletion of ΔNp63

value: lung

value: AT2 cells

value: DNp63 WT

tag: chip antibody

value: Pol2  (Active Motif, 39097)


title: PAC0024_tissue

description: Placental Chorionic Villous Tissue


title: Lung AT2 cells DNp63 Cre Pol2 ChIP-Seq

description: AT2 Cre Pol2

value: DNp63 Cre


title: Lung AT2 cells DNp63 Cre P63 ChIP-Seq

description: AT2 Cre p63


title: Lung AT2 cells Input ChIP-Seq

description: AT2 Input

value: Pooled

value: Input  (Active Motif, 39097)


title: BM cells, Case6_diagnosis_sequencing

description: Case_6 (UPN#543)

tag: age


title: Lung AT2 cells DNp63 WT P63 ChIP-Seq

description: AT2 WT p63


title: BM cells, Case5_remission_sequencing

description: Case_5 (UPN#685)


title: PAC0023_tissue

description: Placental Chorionic Villous Tissue


title: Lung AT2 cells DNp63 Cre H3K27ac ChIP-Seq

description: AT2 Cre H3K27ac

value: H3K27ac (Active Motif, 39134)


title: BM cells, Case5_diagnosis_sequencing

description: Case_5 (UPN#605)


title: PAC0021_tissue

description: Placental Chorionic Villous Tissue

value: Male


title: PAC0022_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case4_diagnosis_sequencing

description: Case_4 (UPN#542)


title: Lung AT2 cells DNp63 WT H3K27ac ChIP-Seq

description: AT2 WT H3K27ac


title: Lung Basal cells Input ChIP-Seq

description: Basal Input

value: basal cells

value: Input  (Active Motif, 39915)


title: PAC0020_tissue

description: Placental Chorionic Villous Tissue

value: Chorionic Villous


title: BM cells, Case2_remission_sequencing

description: Case_2 (UPN#675)

value: bone marrow


title: PAC0018_tissue

description: Placental Chorionic Villous Tissue


title: Lung Basal cells DNp63 Cre Pol2 ChIP-Seq

description: Basal Cre Pol2


title: PAC0017_tissue

description: Placental Chorionic Villous Tissue

value: Female


title: BM cells, Case2_diagnosis_sequencing

description: Case_2 (UPN#545)


title: BM cells, Case1_remission_sequencing

description: Case_1 (UPN#682)


title: Lung Basal cells DNp63 Cre P63 ChIP-Seq

description: Basal Cre p63

value: P63 (Santa Cruz, sc-8431)


title: BM cells, Case1_diagnosis_sequencing

description: Case_1 (UPN#540)


title: PAC0016_tissue

description: Placental Chorionic Villous Tissue


title: PAC0015_tissue

description: Placental Chorionic Villous Tissue


title: BM cells, Case3_diagnosis_sequencing

description: Case_3 (UPN#541)


title: Lung Basal cells DNp63 WT P63 ChIP-Seq

description: Basal WT p63


title: Lung Basal cells DNp63 WT Pol2 ChIP-Seq

description: Basal WT Pol2


title: non-Alzheimer's Disease_Biological replicate 10

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description: Transcriptome expression profiling of postmortem human hippocampus non-AD brain

data_processing:
Sequences were obtained by using HiSeq1500 (Rapid Mode).
The quality of RNA-Seq reads was checked and preprocessed using fastp (v0.20.1) with --detect_adapter_for_pe option. RNA-Seq reads (FASTQ format) were aligned to RefSeq human reference genome (hg19) using HISAT2 (v2.1.0) software (RRID:SCR_015530). PCR duplicates were removed by Samtools (RRID:SCR_005227). Total paired reads per sample was between 18 million (M) to 59 M reads and mapping efficacy was between 96.62% to 98.65%. For further analysis, StringTie (v2.1.4) was used. Annotation file was created by StringTie and merged with RefSeq Reference Genome Annotation based on human reference genome (hg19). Mapped reads were applied to StringTie (v2.2.1) using the merged annotation file including known transcript annotation and merged transcripts (novel annotations).
Genome_build: hg19
Supplementary_files_format_and_content: The resulting bam files were used to not only calculate gene and transcript expression profile by python script prepDE.py (https://github.com/gpertea/stringtie/blob/master/prepDE.py), but also to obtain TPM (Transcripts Per Kilobase  Million) values. Bioconductor package edgeR (v3.28.1) was used for differential expression analysis and three separate excel files were produced as processed files for all samples.

source_name: Postmortem human hippocampus brain

growth_protocol: Postmortem human hippocampus were cut out from each brain and preserved at −80 °C until RNA preparation. Written informed consent for all subjects was obtained from their families. Neuropathologic changes were examined as described previously (PMID: 20739649).

extract_protocol:
Total RNA was isolated using a combination of Isogen and the RNeasy Mini Kit, according to the manufacturer's instructions.
The libraries for polyA(+) RNA sequencing were prepared using TruSeq Rapid PE cluster Kit-HS (Illumina; PE-402-4001) and TruSeq Rapid SBS Kit-HS (Illumina; FC-402-4001) according to manufacturer's instructions.


title: Lung Basal cells DNp63 Cre H3K27ac ChIP-Seq

description: Basal Cre H3K27ac


title: non-Alzheimer's Disease_Biological replicate 9


title: Lung Basal cells DNp63 WT H3K27ac ChIP-Seq

description: Basal WT H3K27ac


title: SA4 [S4-SA-10-19_S48_L002]

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: SA control MSCs

extract_protocol:
Extracted bone marrow was enzymatically digested and sorted followed by RNA extraction using NucleoSpin RNA-XS kit.
Trio low-input RNA-seq library preparation kit

tag: strain/model

value: Townes Sickle

tag: mouse group

value: SA

value: bone marroow

value: Mesenchymal Stem Cells (MSCs)

tag: cell population

value: CD45-, Ter119-, CD31-, CD51+ and CD140a+ population


title: non-Alzheimer's Disease_Biological replicate 8


title: SA4 [S4-SA-10-19_S48_L001]

tag: cell type


title: PAC0011_tissue

description: Placental Chorionic Villous Tissue


title: C3-before

type: genomic

city: Linköping

first: Jyotirmoy

last: Das

address: Sandbäcksgatan

department: Department of Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description:
genomic DNA from PBMC
before BCG vaccination

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: GenomeStudio (version 1.8) Methylation module to detect cytosine methylation at single-base resolution.  Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Peripheral Blood Mononuclear Cells

label_protocol: Standard Illumina protocol

extract_protocol: DNA from HLA-DR, CD3 and PBMC cells was extracted using AllPrep DNA/RNA Mini Kit from Qiagen, Germany.

tag: sample type

value: PBMC


title: non-Alzheimer's Disease_Biological replicate 6

tag: gender


title: non-Alzheimer's Disease_Biological replicate 5


title: PAC0013_tissue

description: Placental Chorionic Villous Tissue


title: SA2 [S2-SA-10-19_S46_L002]


title: C6-after

description:
genomic DNA from PBMC
after BCG vaccination


title: PAC0012_tissue

description: Placental Chorionic Villous Tissue


title: non-Alzheimer's Disease_Biological replicate 4


title: C4-after


title: non-Alzheimer's Disease_Biological replicate 7


title: PAC0010_tissue

description: Placental Chorionic Villous Tissue


title: SA3 [S3-SA-10-19_S47_L002]


title: SA3 [S3-SA-10-19_S47_L001]


title: PAC0009_tissue

description: Placental Chorionic Villous Tissue


title: SA2 [S2-SA-10-19_S46_L001]


title: PAC0008_tissue

description: Placental Chorionic Villous Tissue


title: non-Alzheimer's Disease_Biological replicate 3


title: PAC0007_tissue

description: Placental Chorionic Villous Tissue


title: SA1 [S1-SA-10-19_S45_L002]


title: C7-before


title: non-Alzheimer's Disease_Biological replicate 2


title: PAC0006_tissue

description: Placental Chorionic Villous Tissue


title: C2-after


title: SA1 [S1-SA-10-19_S45_L001]


title: C8-after


title: C1-before


title: C5-before


title: PAC0014_tissue

description: Placental Chorionic Villous Tissue


title: SS4 [S4-SS-10-22_S51_L002]


title: 5038ET1

city: Nashville

first: Ian

last: Macara

address: 465 21st Ave South

institute: Vanderbilt University

data_processing:
Sample 1-10
Illumina HiSeq 3000 for basecalling
reads were filtered, sorted and aligned to the mm9 genome assembly
Data filtered with a p-value of either <.05, and FC >2 or <0.005
Sample 11-12
Illumina Nextseq 500 for basecalling
reads were filtered, sorted and aligned to the mm9 genome assembly using inDrop pipeline
Data filtered with a p-value of either <.05
Genome_build: mm9
Supplementary_files_format_and_content: h5ad
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Myoepithelial cells

growth_protocol: All cells were freshly sorted except for sample 12 - cultured for 72 hours

extract_protocol:
Mammary tissue was processed with Collagenase and Trypsin for single cells, stained with antibodies and FACS sorted.
Sample 1-Sample 10: libraries constructed using Illumina TruSeq RNA v2 Sample preparation protocol, Sample 11 and 12: libraries constructed as per Kelin et al 2015's CEL-Seq workflow.

treatment_protocol: Sample 12 was cultured for 72 hours

tag: strain

tag: developmental stage

tag: treatment

value: 72 hour culture


title: 4713ET1

source_name: Mammary epithelial cells

value: untreated


title: SS4 [S4-SS-10-22_S51_L001]

source_name: SS MSCs

value: SS

tag: tissue


title: Alzheimer's Disease_Biological replicate 7

description: Transcriptome expression profiling of postmortem human hippocampus AD brain


title: SS3 [S3-SS-10-22_S50_L002]


title: Alzheimer's Disease_Biological replicate 8


title: SS3 [S3-SS-10-22_S50_L001]


title: Alzheimer's Disease_Biological replicate 6


title: Alzheimer's Disease_Biological replicate 4


title: SS2 [SS1-10-28_S52_L002]


title: Alzheimer's Disease_Biological replicate 3


title: Alzheimer's Disease_Biological replicate 5


title: Alzheimer's Disease_Biological replicate 2


title: SS2 [SS1-10-28_S52_L001]


title: Lung Squamous AT2 cells DNp63 WT

description:
AT2_WT
R_11_9_AT2_DNp63_ad_empty_RNA

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include quantile normalized FPKM values for each Sample

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Sequencing libraries were prepared using the Illumina Truseq stranded total RNA kit using 1000 ng of RNA per sample.

value: lung

value: squamous AT2 cells

tag: genotype

value: DNp63 WT


title: Alzheimer's Disease_Biological replicate 1


title: SS1 [S1-SS-10-22_S49_L001]


title: non-Alzheimer's Disease_Biological replicate 1


title: Lung Squamous AT2 cells DNp63 CRE

description:
AT2_CRE
R_11_9_AT2_DNp63_ad_cre_RNA

value: DNp63 CRE


title: dUTP strand-specific RNA-seq log-phase cells of Candida albicans grown in BMW

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Candida albicans

source_name: log-phase cells

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: NBT_S288CdU_SCUra_R9

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 10
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints. This was not required for the designed library.
Promoters were aligned to themselves using Bowtie2 to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster. The designed library was aligned to the promoter sequences we ordered using Bowtie2, and only perfect matches were considered in further analysis.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP). For the designed library, we calculated expression for all promoters for which any reads were seen, but used only those for which we saw at least 100 reads for the analysis described in the publication (MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz).
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels, as well as sequence identifiers

organism: Saccharomyces cerevisiae

source_name: Designed promoter library

growth_protocol: Libraries were transformed into yeast (strain Y8205 or S288CdeltaUra3) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved (with the exception of the designed sequence library, where at least 100x coverage was obtained). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period. Cells were then grown continuously in log phase prior to cell sorting, diluting as necessary to keep the OD below 0.8. All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Plasmids were isolated using Qiagen spin miniprep kits, as adapted for yeast according to the manufacturer's website. Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins, done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SD-Ura and grown for 2-3 days, shaking at 30C until cultures reached saturation.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center.
OTHER: amplicon sequencing

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

value: SD-Ura

tag: libraryid

value: NBT/designed


title: NBT_S288CdU_SCUra_R8

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 11
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R7

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 12
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: LNp53KO-R273H microarray rep 3

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

institute: Thomas Jefferson University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA Normalization in R

label: biotin

source_name: LNCaP cell line

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction with sodium acetate re-precipitation

treatment_protocol: LNCaP-derived cells were cultured in hormone proficient media with no additional treatments

tag: viral transduciton

value: CRISPR mediated p53KO and transduced with pLenti-R273H


title: LNp53KO-R273H microarray rep 2


title: LNp53KO-R273C microarray rep 3

value: CRISPR mediated p53KO and transduced with pLenti-R273C


title: LNp53KO-R273C microarray rep 2


title: LNp53KO-R273H microarray rep 1


title: LNp53KO-pLPLUC microarray rep 3

value: CRISPR mediated p53KO


title: LNp53KO-R273C microarray rep 1


title: SS1 [S1-SS-10-22_S49_L002]

value: Townes Sickle

value: bone marroow

value: Mesenchymal Stem Cells (MSCs)


title: NBT_S288CdU_SCUra_R6

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 13
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: LNp53KO-pLPLUC microarray rep 2


title: LNp53KO-pLPLUC microarray rep 1


title: NBT_S288CdU_SCUra_R3

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 16
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R2

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 17
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R5

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 14
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R19

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 0
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: exosomes isolated from the plasma of the late-phase RIPC rats, rep3

city: Guangzhou

first: Danni

last: Li

address: No. 26 Yuancunerheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description:
RIPC-EXO_3
exosomes isolated from the plasma of the late-phase RIPC rats

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the Rat reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: rn6
Supplementary_files_format_and_content: miRNA_counts.csv

source_name: Rat plasma

extract_protocol:
Exosomes were prepared by differential centrifugation at 4°C as follows. Whole blood samples were centrifuged at 1,600 xg for 20 min to obtain plasma, then centrifuged at 2,000 xg for 45 min and 10,000 xg for 45 min to remove cells and platelets, and then twice at 110,000 xg for 70 min with a Type 100 Ti rotor (Beckman, Germany). After a series of differential centrifugation steps above, the final precipitation was considered as exosomes (n = 3 per group).
The miRNA library preparation and sequencing were conducted using an Illumina HiSeqTM 2500 platform (Ribobio, China). Both 3' and 5' adaptors were ligated with unique small RNA fractions to construct a small RNA sequencing library.

treatment_protocol: RIPC was induced by binding elastic rubber bands around the proximal ends of both hind limbs with a 4-cycle procedure (5 minutes of ischemia followed by 5 minutes of reperfusion) after the rats were anesthetized. After 48 h, the rats in both groups were anesthetized and the blood were drawn from the abdominal aorta.

value: Rat plasma

value: Plasma

tag: protocol

value: the late phase of RIPC

value: exosomes


title: LNp53WT_pLPLUC microarray rep 2

city: Philadelphia

value: transduced with pLenti-pLPLUC


title: NBT_S288CdU_SCUra_R18

first: Carl

last: de Boer

address: 415 Main St

institute: The Broad Institute

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 1
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R17

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 2
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: exosomes isolated from the plasma of the late-phase RIPC rats, rep2

description:
RIPC-EXO_2
exosomes isolated from the plasma of the late-phase RIPC rats

value: untreated


title: exosomes isolated from the plasma of the late-phase RIPC rats, rep1

description:
RIPC-EXO_1
exosomes isolated from the plasma of the late-phase RIPC rats


title: LNp53WT_pLPLUC microarray rep 1


title: LN-R237H microarray rep 1

value: transduced with pLenti-R273H


title: LN-R237H microarray rep 3


title: LN-R237C microarray rep 1

value: transduced with pLenti-R273C


title: LN-R237C microarray rep 3


title: SIG11_LPS_PSA_5

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

country: Germany

institute: University Hospital of Bonn

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and base call file conversion.
Sequenced reads were corrected for low-quality sequence, then mapped to mm10 whole genome with the ensembl gene annotation version 101 using STAR v2.7.3a with standard parameters.
Read count generation was performed using featureCounts/Subread v2.0.0 ignoring multimapping reads.
Batch effects were removed with R [v4.0.4 (R Core Team, 2021)] in RStudio [v1.3.1093 (RStudio Team, 2020) using the RUVSeq package [v1.22.0 (Risso et al, 2014)].
Differential expression analysis was performed using DESeq2 [v1.28.1 (Love et al, 2014)] with the individual groups as contrasts. The log2‐fold change (log2FC) shrinkage was performed using apeglm to preserve large effects of true positives [v1.10.0 (Zhu et al, 2019)]. Transcript annotations were retrieved using the Bioconductor package org.Mm.eg.db [v3.11.4 (Carlson, 2020)] and plots were created using ggplot2 [v3.3.3 (Wickham, 2016)]. Pathway enrichment analyses were performed using clusterProfiler [v3.16.1 (Yu et al, 2012)] and reactomePA [v1.34.0 (Yu & He, 2016)] with log2FC ≥ 0.5 and adjusted p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Brains were collected and divided into two halves. Left hemispheres were immediately homogenized in 1 ml QIAzol (QIAGEN) and RNA was isolated using the RNeasy RNA isolation kit (Quiagen GmbH).
Library preparation was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) with an input of 100 ng total RNA according to manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected daily, and repeatedly over 4 consecutive days, with either 100 µl lipopolysaccharides (LPS) (1 µg/gbw/day, Enzo Life Science, Salmonella abortus equi S-form, Cat # ALX-581-009-002) or 100 µl PBS/day as vehicle control together with either 10 μg/gbw low molecular weight polysialic acid (polySia avDP20) or PBS as vehicle control.

value: Brain

tag: age

value: 3 months

value: LPS injection

tag: treatment 2

value: PolySia avDP20 injection


title: LNp53WT_pLPLUC microarray rep 3


title: LN-R237C microarray rep 2


title: exosomes isolated from the plasma of the control rats, rep1

description:
Control-EXO_1
exosomes isolated from the plasma of the control rats

value: without RIPC


title: NBT_S288CdU_SCUra_R16

city: Cambridge

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 3
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz

value: SD-Ura

value: NBT/designed


title: NBT_S288CdU_SCUra_R15

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 4
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: LN-pLPLUC microarray rep 3


title: exosomes isolated from the plasma of the control rats, rep3

description:
Control-EXO_3
exosomes isolated from the plasma of the control rats


title: exosomes isolated from the plasma of the control rats, rep2

description:
Control-EXO_2
exosomes isolated from the plasma of the control rats


title: NBT_S288CdU_SCUra_R4

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 15
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: SIG11_LPS_PSA_4


title: NBT_S288CdU_SCUra_R13

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 6
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: NBT_S288CdU_SCUra_R14

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 5
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: Cd7_Stim_JB12

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Sequencing reads were aligned to the mouse reference genome (mm10) using subread (PMID: 30783653). Quantification of reads on transcripts annotated by RefSeq was done with featurecounts (PMID: 24227677). Gene expression values (RPKM) was caculated by in-house script.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file, from left to right represent Entrz ID, Gene Symbol, and expression value for each sample (log2(RPKM+1)+0.0001).

source_name: Spleen

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134).
Libraries were prepared at the WVU Genomics Core using KAPA mRNA HyperPrep Kit (Roche) using 10 PCR cycles starting with 300-550 ng of RNA. Libraries were ran on the Bioanalyzer with an Agilent HS DNA assay for quality assurance prior to sequencing.

value: Spleen

value: 8 weeks

value: CD3/CD28 stimulated CD4+ T cells

tag: parental treatment

value: Decedent mouse from parents treated with cadmium


title: SIG11_LPS_PSA_3


title: LN-pLPLUC microarray rep 1


title: NBT_S288CdU_SCUra_R12

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 7
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: LN-pLPLUC microarray rep 2


title: Cd6_Stim_JB11

tag: cell type


title: SIG11_LPS_PSA_2


title: NBT_S288CdU_SCUra_R11

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 8
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: Cd6_Unstim_JB8

value: Unstimulated CD4+ T cells


title: SIG11_LPS_6

value: PBS injection


title: N80_SC-Ura_Y8203_R9

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 10
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz

source_name: Random promoter library


title: Cd7_Unstim_JB9


title: SIG11_LPS_PSA_1


title: Ctr7_Stim_JB6

value: Decedent mouse from untreated parents


title: SIG11_LPS_5


title: Ctr6_Stim_JB5


title: N80_SC-Ura_Y8203_R8

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 11
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: LN-R237H microarray rep 2


title: Ctr7_Unstim_JB3


title: NBT_S288CdU_SCUra_R10

description:
Designed promoter library (NBT/designed) in Saccharomyces cerevisiae (S288CdeltaUra3) grown in SD-Ura in log phase, and sorted into expression bin 9
pTpA_random_design_tiling_etc_sequence_IDs.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.all.txt.gz
MolEvol_seq_data_SCUra_only.splitByOrigID.meanEL.min100Reads.txt.gz


title: N80_SC-Ura_Y8203_R7

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 12
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: N80_SC-Ura_Y8203_R6

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 13
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: SIG11_LPS_3


title: Ctr6_Unstim_JB2


title: SIG11_LPS_2


title: SIG11_LPS_4


title: N80_SC-Ura_Y8203_R5

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 14
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: SIG11_PSA_5


title: SIG11_LPS_1


title: SIG11_PSA_6


title: SIG11_PSA_4


title: N80_SC-Ura_Y8203_R4

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 15
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: ko18hb2

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

institute: The University of Queensland

data_processing:
FASTP: fastp -i R1-file.fastq.gz -I R2-file.fastq.gz -o processedfile_R1.fq.gz -O processedfile_R2.fq.gz -w 8 -h paste0(outDir,"QC/","fastp_",metaDF$Sample[i],".html") -j paste0(outDir,"QC/","fastp_",metaDF$Sample[i],".json")
Salmon: salmon quant -i salmonIndex -p 14 --numBootstraps 30 -1 paste0(filesDir,sampleData$ppR1[i]) -2 paste0(filesDir,sampleData$ppR2[i]) -l sampleData$libType[i] -o paste0(outMainDir,sampleData$Sample[i])
tximport: tximport(files, type="salmon", tx2gene = tx2gene, ignoreTxVersion = TRUE, dropInfReps=TRUE, txOut = TRUE)
DESeq2: DESeqDataSetFromTximport(txi, colData = samples, design = ~ Geno * Age * APpos)
count matrix export: write.csv(counts(dds1norm, normalized=TRUE),"DESeqDataSetFromTximport-ddsTxi1-NORMALIZED-geneLevel.csv")
Genome_build: mm10
Supplementary_files_format_and_content: .csv

source_name: dissected embryonic CNS, hindbrain

growth_protocol: Pregnant females under standard mouse housing conditions.

extract_protocol:
CNS dissected, forebrain and spinal cord kept at -80°C until RNA extraction with Qiagen Rneasy kit
NEBNext
RNA-seq Illumina HT2500 ~50M reads SE/PE 50-150bp unstranded

treatment_protocol: Embryos dissected at Embryonic day (E) 13.5 or 15.5.

value: cKO

tag: ap-position

value: HB


title: ko18hb1


title: ko18sc2

source_name: dissected embryonic CNS, spinal cord

value: SC


title: ko18sc1


title: N80_SC-Ura_Y8203_R19

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 0
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: SIG11_PSA_3

value: Brain


title: N80_SC-Ura_Y8203_R2

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 17
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: N80_SC-Ura_Y8203_R18

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 1
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: N80_SC-Ura_Y8203_R3

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 16
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: ko18mb2

source_name: dissected embryonic CNS, midbrain

value: MB


title: N80_SC-Ura_Y8203_R16

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 3
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: N80_SC-Ura_Y8203_R15

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 4
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: SIG11_PSA_1

value: 3 months


title: N80_SC-Ura_Y8203_R17

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 2
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: ko18mb1


title: SIG11_PSA_2

value: PolySia avDP20 injection


title: ko18fb1

source_name: dissected embryonic CNS, forebrain

value: FB


title: wt18sc2

value: ctrl


title: SIG11_PBS_5


title: ko18fb2


title: SIG11_PBS_6


title: N80_SC-Ura_Y8203_R14

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 5
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz

value: SD-Ura


title: SIG11_PBS_4


title: wt18sc1


title: N80_SC-Ura_Y8203_R13

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 6
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: wt18hb2


title: N80_SC-Ura_Y8203_R12

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 7
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: wt18hb1


title: SIG11_PBS_3


title: SIG11_PBS_1


title: N80_SC-Ura_Y8203_R10

description:
Random promoter library (pTpA_1E8) in Saccharomyces cerevisiae (Y8205) grown in SD-Ura in log phase, and sorted into expression bin 9
average_promoter_ELs_per_seq_N80_SD-Ura_Y8205_ALL.shuffled.txt.gz


title: WT LPS_PSA_7

value: wild type

value: LPS injection


title: SIG11_PBS_2


title: wt18mb1