title: Muscle185

status: Public on Oct 31 2021

type: SRA

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
raw fastq files from ncRNA sequencing were 5’ trimmed using cutadapt (v3.2) as per manufacturers recommendation using the adapter sequence ‘AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’
Using the built-in function for cutadapt, reads that were of low quality and <17bps were removed from the sequencing data
aligned to sheep reference genome (Oar_rambouillet_v1.0) using STAR (2.6.0c)
counting of reads for each class of ncRNA evaluated in this study was achieved by first subsetting the whole genome annotation files for the reference genome into files that contained only references for a particular ncRNA
aligned reads were then used in featureCounts (1.6.1) with genes as the identifier, with all multimapping reads included in the analysis, along with annotation files specific for each ncRNA to obtain counts
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: normalized counts of long non-coding RNA
Supplementary_files_format_and_content: normalized counts of mircoRNA
Supplementary_files_format_and_content: normalized counts of small nucleolar RNA
Supplementary_files_format_and_content: normalized counts of small nuclear RNA

molecule: total RNA

organism: Ovis aries

source_name: Muscle

extract_protocol:
Total RNA was extracted from the liver and muscle after homogenizing the tissues in Trizol reagent (Life Technologies, Carlsbad, CA) following the manufacturer’s recommendations
Libraries for ncRNA were prepared from total RNA using NEBNext smallRNA kit (New England BioLabs, Ipswich, MA) at the University of Michigan Advanced Genomics Core as per manufacturers recommendations

tag: sheepid

tag: Sex

value: female

tag: treatment

value: prenatal T-treatment

tag: tissue

value: Muscle

tag: molecule subtype

value: smallRNA/noncodingRNA


title: Muscle255


title: Muscle233


title: Muscle48


title: Muscle132

value: control


title: Muscle201


title: Liver233

source_name: Liver

value: Liver


title: Muscle98


title: Liver48


title: Muscle131


title: Liver255


title: Liver185


title: Liver132


title: Liver131


title: Liver201


title: Liver98


title: Rosa26-ECFP omental cells

city: Bunkyo-ku

first: Kyohei

last: Fujita

state: Tokyo

address: 1-5-45, Yushima

country: Japan

institute: Institute of Science Tokyo

data_processing:
For each fastq file, the sequence ID format of each file was converted to the format of Casava 1.8 or later.
The scRNA-seq output data were processed using the Cell Ranger pipeline (10x Genomics, version 4.0.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: omental cells

extract_protocol: Library was prepared for sequencing using standard 10x protocols (Chromium Next GEM Single Cell 3' Reagent Kits v3.1)

value: omenta


title: 1C_N-input_Hs7C

type: genomic

city: Boston

first: Rui

last: Fang

state: MA

address: 221 Longwood Ave. EBRC 222

institute: Brigham and Women's Hospital

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on chip 3 of Affymatrix HumanTiling 2.0 arrays, and were washed and post stained using the Affymetrix 450 Fluidics Station per Affymetrix specifications.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing:
CEL files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.
Regions enriched by TAP N-ChIP were identified using algorithm Model-Based Analysis of Tiling arrays (MAT) (Johnson et al., 2006), and displayed by Integrated Genome Browser (IGB) on genome hg36
ChIP enrichment over input control are displayed in a .BAR file type

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa genomic DNA

label_protocol: ChIP DNA was biotinylated using GeneChip WT double-stranded DNA terminal Labeling Kit

growth_protocol: HeLa cells stably expressing Flag-HA tagged NPAC or Flag-HA tagged LSD2 from pOZ-N vector were grown in DMEM supplemented with 10% FBS

extract_protocol: Chromatin were digested by micrococcal nuclease, and immunoprecipiated by anti-Flag M2 agarose bead, elute with Flag peptide and immunoprecipiated again using anti-HA antibody

treatment_protocol: HeLa cells were subjected to native ChIP, using tandem affinity purification with anti-Flag and anti-HA antibodies

tag: cell line

value: HeLa

tag: genotype

value: WT

tag: chip antibody

value: none (input)


title: colorectal cancer (CRC) tissue circRNA 1

type: RNA

city: Ningbo

first: Jipeng

last: Li

address: 251 East Baizhang Road

country: China

institute: The Affiliated People’s Hospital of Ningbo University

description: circRNA expression data form colorectal cancer 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 by the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. COMBAT was applied to eliminate the batch effect. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: colorectal cancer (CRC) 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: colorectal cancer (CRC) and matched non-tumor tissues.

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

treatment_protocol: Tissues from CRC surgury and promptly frozen in liquid nitrogen.

value: tumor tissue

tag: gender

value: male


title: 3C_N-NP_Hs7C

description: NPAC ChIP tiling array

source_name: Flag-HA ChIP DNA

value: stably expressing Flag-HA tagged NPAC

value: anti-Flag and anti-HA


title: LSD2

value: stably expressing Flag-HA tagged LSD2


title: normal tissue circRNA 1

description: circRNA expression data from normal tissue

source_name: matched non-tumor tissue

value: normal tissue


title: normal tissue circRNA 3


title: colorectal cancer (CRC) tissue circRNA 2


title: normal tissue circRNA 2


title: colorectal cancer (CRC) tissue circRNA 3


title: hNSCs+ Differentiation medium supplemented with Luteolin (1µM) rep3

city: Tsukuba

first: Mariem

last: Achour

state: Ibaraki

address: 1-1-1 Tennodai

institute: Alliance for Research on the Mediterranean and North Africa

description: Gene expression data from 1µM treated control hNSCs after 24 hours

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-U219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software V 4.0 (CHP files ).
RMA

source_name: hNSCs cultured in differentiation cell culture supplemented with Luteolin (1µM) for 24 h, biological rep3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: The human neural stem cells (StemPro™ Neural Stem Cells) which are a cryopreserved Human fetal brain-derived neural stem cells derived from cortex male donor aged of 16 weeks, were purchased from Gibco, USA (Cat. no. A15654).  It was cultured in T25 flasks (BD Falcon) or in 6-well plates (BD Falcon) with KnockOut™ DMEM/F-12 (Gibco, USA, cat.no. 12660012) supplemented with 2% StemPro™ Neural Supplement (Gibco, Cat. no. A1050801), 20 ng/mL of fibroblast growth factor (FGF) basic recombinant human, 20 ng/mL epidermal growth factor (EGF) recombinant human and 2 mM GlutaMAX™-I Supplement (Cat. no. 35050), 6 U/mL heparin (Sigma, Cat. no. H3149), and 200 µM ascorbic acid (Sigma, Cat. no. A8960). For adhesion, Geltrex® (Gibco, Cat. no. A14133) was used to coat the 6-well plate. The hNSCs were cultured at 37ºC in a 95% air / 5% CO2 humidified incubator. The medium was changed every two days.

extract_protocol: The total RNA was extracted from the cells using ISOGEN kit (Nippon Gene Co. Ltd., Japan) following the manufacturer’s instructions, as reported previously by Sasaki et al., 2019. Total RNA was purified using chloroform and Isopropanol (Wako, Japan) and quantified and assessed for quality with a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: To induce differentiation, the same protocol described by Sasaki et al., 2019 was used. Briefly, hNSCs were seeded into 6 wells culture vessels coated with Geltrex® at a density of 2.5 x 104 cells/cm2. After 48 h, growth medium was replaced by differentiation medium: Knockout DMEM/F12 supplemented with 2% StemPro® neural supplement, 2 mM GlutaMAX-I supplement, 6 units/mL heparin and 200µM ascorbic acid supplemented or not with 1µM of Luteolin.

tag: cell type

value: human Neural Stem Cells


title: hNSCs+ Differentiation medium supplemented with Luteolin (1µM) rep1

source_name: hNSCs cultured in differentiation cell culture supplemented with Luteolin (1µM) for 24 h, biological rep1


title: hNSCs+ Differentiation medium supplemented with Luteolin (1µM) rep2

source_name: hNSCs cultured in differentiation cell culture supplemented with Luteolin (1µM) for 24 h, biological rep2


title: hNSCs+ Differentiation medium  rep2

description: Gene expression data from untreated control hNSCs after 24 hours

source_name: hNSCs cultured in differentiation cell culture for 24 h, biological rep2


title: 0886.020.900_D21

city: Silver Spring

first: Ruoting

last: Yang

state: MD

address: 503 Robert Grant Ave

department: CMPN

institute: WRAIR

hyb_protocol: cRNA was hybridized to a human genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.

source_name: Whole Blood

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA) following manufacturer directions

treatment_protocol: treatment protocol is not applicable

tag: time point

tag: age

tag: tbsa

tag: mortality

value: Alive

source_name: Agilent's Universal Human Reference RNA

tag: sample type

value: reference


title: 0886.015.900_hr132


title: hNSCs+ Differentiation medium  rep1

source_name: hNSCs cultured in differentiation cell culture for 24 h, biological rep1


title: 0886.012.900_hr96


title: 0886.003.900_hr4


title: hNSCs+ Differentiation medium  rep3

source_name: hNSCs cultured in differentiation cell culture for 24 h, biological rep3


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title: sample.7b

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

institute: Washington University, St Louis

description: Bulk RNA

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

source_name: Bronchoalveolar lavage

growth_protocol: Juvenile C57BL/6J mice (4-8 weeks old, 20-25g) were obtained from Jackson Laboratories and acclimatized for two weeks before use.  Older (3-16 month old) C57BL/6J mice were sourced either through direct purchase from Jackson Laboratories or as retired breeders obtained from the Washington University School of Medicine Micro-injection Core/Gnotobiotic Facility.  Unless stated, male mice were used for experiments.  Mice were housed in a standard 12-hour light-dark cycle (lights-on at 6:00 AM and lights-off at 6:00 PM local time), with unlimited food and water available.  For certain experiments (FIG), mice were fed either high fat (60%) or low fat (10%) prior to viral infection.  Otherwise they received 20% fat content chow, which is the standard at our animal facility.  All experiments were approved by the Washington University School of Medicine Animal Care and Use Committees.

extract_protocol:
At various time points after infection, lungs were manually excised and immersed in RNAlater solution (Applied Biosystems). Total RNA was isolated from lung homogenates using RNeasy Mini Kits (Qiagen).  Reverse transcription was carried out using the Applied Biosystems High Capacity cDNA Reverse Transcription Kit.  Real Time PCR was performed on the ABI 7500 Fast Real-Time PCR system.
RNA from whole lung homogenates were converted to cDNA libraries for sequencing using the RiboZero Kit (Sigma Aldrich).  Libraries generated from BAL RNA were generated using the SMARTer kit (Clontech).  Sequencing was carried out on a NovaSeq6000 instrument (Illumina).  RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.  Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function (REF).  Performance of the samples was assessed with a spearman correlation matrix and multi-dimensional scaling plots.  Gene/transcript performance was assessed with plots of residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Generalized linear models with robust dispersion estimates were then created to test for gene/transcript level differential expression. Differentially expressed genes and transcripts were then filtered for FDR adjusted p-values less than or equal to 0.05.  To examine age-associated differential gene expression in BAL samples (FIG), Log2 normalized Voom adjusted data was analyzed using one-way ANOVA on ranks.

treatment_protocol: Sendai virus (SeV) was obtained from ATCC (VR-105; Sendai/52). Virus was twice plaque purified, propagated in 10-day-old embryonated chicken eggs, and stored at -70C.  Infectivity of SeV was assayed in VeroE6 cell line as described65.  Influenza A Virus (IAV A/WS/33 H1N1) was obtained from ATCC.  Virus was plaque purified using MDCK (ATCC CCL-34) cells and propagated in 9-day-old embryonated chicken eggs.  SeV at various doses or 5 pfu of H1N1 Influenza A Virus was intra-nasally administered to mice as described29.  Briefly, animals were anesthetized with ketamine/xylazine HCL cocktail and virus at various doses was intra-nasally instilled in 30ml of PBS. Mice were then returned to their cages to recover from anesthesia.

tag: strain

value: lung

value: Basal state

value: 7 months


title: sample.old

description: Bulk RNA

value: > 3 months


title: sample.6wk.pool3

description: Bulk RNA

value: 6 weeks

tag: pool

value: pool 3


title: MGI0061_1_Old_single-cell

description: Single cell RNA seq


title: sample.7c

description: Bulk RNA


title: sample.7mo.pool1

description: Bulk RNA

value: pool 1


title: MGI0061_1_Young_single-cell

description: Single cell RNA seq

value: < 3 months


title: sample.6wk.pool1

description: Bulk RNA

value: Pool 1


title: sample.6wk.pool2

description: Bulk RNA

value: Pool 2


title: 0822.008.900_hr48


title: 0825.013.900_hr108


title: 0822.007.900_hr36


title: 0822.006.900_hr24


title: 0822.004.900_hr8


title: 0822.005.900_hr12


title: 0822.002.900_hr2


title: 0822.003.900_hr4


title: sample.3b

description: Bulk RNA

value: 3 months


title: sample.17.b

description: Bulk RNA

value: 17 months


title: sample.3c

description: Bulk RNA


title: sample.12mo.pool3

description: Bulk RNA

value: 12 months


title: Ischemic Stroke (IS)

city: Shanghai

first: Xiaojing

last: Shi

state: Please Select

address: 1954 Huashan Rd.

institute: Shanghai Jiao Tong University

description:
one sample from murine brain tissue
IS_R20023098-OES20309100-OES20309100

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 (Version 3.1.1).
To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we applied a criterion to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2-fold of standard deviations assuming a Gaussian distribution of each cells’ UMI/gene numbers. Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where 30% of counts belonged to mitochondrial genes. Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count.
Top variable genes across single cells were identified using the method described in Macosko et al. Briefly, the average expression and dispersion were calculated for each gene, genes were subsequently placed into several bins based on the expression.
To remove the batch effects in scRNA-seq data, the mutual nearest neighbors (MNN) presented by Haghverdi et al was performed with the R package batchelor. Cells were clustered based on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in the percentage of expressed cells was used to identify significantly differentially expressed genes (DEGs) between clusters.
We use the R package SingleR for unbiased cell type recognition of scRNA-seq to infer the cell of origin of each of the single cells independently and identify cell types. DEGs were identified using the Seurat package. p value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode counts, gene files, cell barcode files

source_name: Murine brain tissue

extract_protocol:
Single-cell gel beads in emulsions (GEMs) were generated by loading single-cell suspensions onto a Chromium Single-Cell Controller Instrument (10 × Genomics). Approximately 12,000 cells were added to each channel. After that, reverse transcription reactions were engaged to generate barcoded full-length cDNA, and cDNA clean-up was performed with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Next, cDNA was amplified by PCR and the amplified cDNA was fragmented, end-repaired, A-tailed, and ligated to an index adaptor, and then the library was amplified. Every library was sequenced on a HiSeq X Ten platform (Illumina), and 150 bp paired-end reads were generated.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: 10 weeks

tag: condition

value: Ischemic Stroke (IS)

value: brain


title: control

description:
one sample from murine brain tissue
control_R20016596-OES20215100-OES20215100

value: control


title: Striatum, 8684

city: Bar Harbor

first: Vivek

last: Philip

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
gbrs with the following parameters -md  2 -rl  100 -ei  999 -pc  0.0 -te  0.0001 -db  TRUE -dh  TRUE
Genome_build: We create custom genomes of the eight founder strains by introducing strain-specific SNPs and short indels (Mouse Genome Project [Keane et al., 2011] release v5 available at ftp://ftp-mouse. sanger.ac.uk/REL-1505-SNPs_Indels/) to the reference genome (Genome Reference Consortium Mouse Build 38 available at http://ftp.ensembl.org/pub/release-84/ fasta/mus_musculus/dna/) using g2gtools (http://churchill-lab.github.io/ g2gtools)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Striatum

extract_protocol:
To control for circadian effects, the timing of testing and euthanasia were consistently performed between 8-12AM. Surgical instruments cleaned with RNAase away (ThermoFischer Scientific) were used. Whole intact brains were removed, hemisected and incubated in RNAlater (ThermoFischer Scientific) for 8-14 minutes. Under a dissection scope the striatum, hippocampus and prefrontal cortex were removed and soaked for 24 hours at room temperature and then stored at -80 degrees. The striatum was homogenized and total RNA was isolated by a TRIzol Plus kit (Life Technologies) according to the manufacturer’s method including an on-the-column DNase digestion. The quality of the isolated RNA was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and RNA 6000 Nano LabChip assay.  Ribo-depleted RNA was prepared using the RNA RiboErase Stranded cDNA library (Kappa Biosystems). The samples were pair end sequenced on a HiSeq producing paired 100 bp reads at a depth of 50 M read pairs per sample. The External RNA Controls Consortium (ERCC, Ambion) was added to samples to allow for normalization across samples but not used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: F

tag: generation

value: drug naïve straitum


title: 0856.015.900_hr132

value: Alive

value: reference


title: Striatum, 8682

tag: tissue


title: sample.17.a

description: Bulk RNA

value: lung

tag: treatment

value: Basal state


title: sample.12mo.pool2

description: Bulk RNA

value: pool 2


title: Hemorrhagic Stroke (HS)

description:
one sample from murine brain tissue
HS_R20023097-OES20308100-OES20308100

value: Hemorrhagic Stroke (HS)


title: Striatum, 8680


title: Striatum, 8678


title: Striatum, 8679


title: Striatum, 8676


title: Striatum, 8677


title: Striatum, 8675


title: Striatum, 8673


title: Striatum, 8681


title: 0855.011.900_hr84


title: Striatum, 8674


title: Striatum, 8683


title: Striatum, 8667


title: sample.17.c

description: Bulk RNA


title: Striatum, 8671


title: Striatum, 8669


title: Striatum, 8668


title: sample.3a

description: Bulk RNA


title: Striatum, 8665


title: Striatum, 8666


title: Striatum, 8664


title: Striatum, 8662


title: Striatum, 8663


title: Striatum, 8661


title: Striatum, 8670


title: Striatum, 8659


title: Striatum, 8672


title: Striatum, 8658


title: Striatum, 8656


title: Striatum, 8655


title: Striatum, 8657


title: Striatum, 8654


title: Striatum, 8650


title: Striatum, 8653


title: Striatum, 8652


title: MC38gp100-Her2

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

data_processing:
processed with 10X standardard cellranger (3.1.0) pipeline reference (cellranger-mm10-3.0.0) using STAR aligner (version 2.6)
Genome_build: cellranger-mm10-3.0.0 + human herpesvirus 2 strain HG52
Supplementary_files_format_and_content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: tumor

extract_protocol:
Cells were prepared according to 10x Genomics® Single Cell Protocols Cell Preparation Guide, followed by MACS Dead Cell Removal Kit 130-090-101 and RBC removal
Single-cell transcritpome caputred by 10X 3' Reagent Kiits (v3)
After running on 10X Chromium Single Cell Controller, gel beads-in-emulsion (GEMs) were generated. The barcoded and full-length cDNAs were produced after incubation of the GEMs and amplified via PCR.
Library was qualified by Agilent Bioanalyzer 2100 and quantified by real-time PCR on QuantStudio3. Sequenced was done with Illumina NextSeq 550 System using High Output Kit v2.5 (50,000 reads per cell).

treatment_protocol:
FusOn-H3 treated MC38gp100-Her2 tumors were harvested 48 hours post virotherapy and processed to single cell suspensions for scRNA-seq
N/A

value: subcutaneous CT26 tumor

tag: tumor type

value: Cancer and Stromal/vascular


title: H7

treatment_protocol:
FusOn-H3 treated H7 tumors were harvested 48 hours post virotherapy and processed to single cell suspensions for scRNA-seq
N/A

tag: genotype


title: MC38gp100

treatment_protocol:
FusOn-H3 treated MC38gp100 tumors were harvested 48 hours post virotherapy and processed to single cell suspensions for scRNA-seq
N/A


title: H7-Her2

treatment_protocol:
FusOn-H3 treated H7-Her2 tumors were harvested 48 hours post virotherapy and processed to single cell suspensions for scRNA-seq
N/A


title: Striatum, 8646


title: Striatum, 8645


title: Striatum, 8631


title: Striatum, 8647


title: Striatum, 8630


title: Crown Xylem vs. Base Xylem Tree 3 Replicate 1

city: Málaga

first: Francisco

middle: R.

last: Cantón

state: Málaga

address: Campus de Teatinos, s/n

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Tree 3S (2007) technical replicate 1

hyb_protocol: Prehybridization, hybridization, and posthybridization washes were carried out using Pronto!™ Universal Hybridization Kit (Corning) in a HS 400 Pro hybridization station (Tecan Trading AG, Switzerland). Five micrograms of each of the labeled aRNA targets was added to the hybridization solution and denatured at 95°C for 5 min in a thermal block. The slides were hybridized for 16 h at 42°C.

scan_protocol: Scanned with 5 µm resolution on a Q-Scan scanner (Genetix).

data_processing: Spots flagged below 0 using GenePix v6.0 software (Axon Instruments) and those whose signal intensity did not surpass 2X their background signal in both channels were discarded. Background correction was performed with the “normexp” method of the limma library. M value was defined as the base two logarithm of every expression ratio, computed as the ratio between the background-corrected foreground intensities of the Cy5 and Cy3 channels (log 2 Cy5/Cy3). Raw expression data were normalized for all sources of systematic variation with the print-tip loess. using the common assumption of considering the whole microarray expression as invariant. The Biobase v 2.0.1 of the Bioconductor package [Gentleman RC et al. Genome Biol 2004, 5:R80] was installed under R version 2.7.1 for all statistical analysis, mainly the limma v 2.14.5 [Smyth G. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York: Springer; 2005: 397–420] and marray v 1.18.0 (http://www.bioconductor.org/packages/release/bioc/html/marray.html) libraries.

organism: Pinus pinaster

source_name: Total RNA from Crown Xylem of Tree 3

label_protocol: Dye labeled aRNA was synthesized with the Amino allyl MessageAmp II aRNA amplification kit (Ambion Inc., Austin, TX)

growth_protocol: Field-grown adult trees from Sierra Bermeja (Estepona, Spain)

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

treatment_protocol: Crown (CrX) and Base (BX) developing xylems were collected from 28 to 31-year-old straight trees. CrX from the last 5 internodes in the crown, and BX up to 1-meter height from the base of the trunk. After removing bark and phloem, developing xylem was scraped with a sterile blade and immediately frozen in liquid nitrogen. Tissue was kept at -80⁰C until use.

value: 28 years old

value: developing secondary xylem

tag: xylem type

value: crown

tag: harvesting date

source_name: Total RNA from Base Xylem of Tree 3

value: base


title: Striatum, 8660


title: Crown Xylem vs. Base Xylem Tree 2 Replicate 1

description: Tree 2N (2005) technical replicate 1

source_name: Total RNA from Crown Xylem of Tree 2

value: 31 years old

source_name: Total RNA from Base Xylem of Tree 2


title: Striatum, 8632


title: Striatum, 8627

value: M


title: Striatum, 8651


title: Striatum, 8629


title: Striatum, 8649


title: Crown Xylem vs. Base Xylem Tree 1 Replicate 1

description: Tree 1N (2005) technical replicate 1

source_name: Total RNA from Base Xylem of Tree 1

value: 29 years old

source_name: Total RNA from Crown Xylem of Tree 1


title: Crown Xylem vs. Base Xylem Tree 1 Replicate 2

description: Tree 1N (2005) technical replicate 2


title: Striatum, 8626


title: Crown Xylem vs. Base Xylem Tree 2 Replicate 2

description: Tree 2N (2005) technical replicate 2


title: Striatum, 8624


title: ML_10009200086087

city: Trondheim

first: Mari

last: Løset

state: Sør-trøndelag

address: Håkon Jarls gate 11

department: Department of Public Health and Nursing

country: Norway

institute: NTNU

data_processing:
Adpater were removed with cutadapt and reads with quality score lower than 33 were filtered out with fastx_collapser
The reads were mapped to human miRNAs in the miRBase database v22.1 through miraligner tool.
Counts from each sample were combined to form the combined matrix
The count matrices were transformed using the voom algorithm from the limma package of Bioconductor.
MicroRNAs with an average count per million across all samples, of less than one, were filtered out.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with cpm normalized gene counts for 526 expressed miRNAs and every sample

source_name: Skin

extract_protocol:
Participants were adults of European descent. Cases had psoriasis vulgaris and underwent a wash-out period without any topical or systemic-/phototherapy for two and four weeks prior to participation, respectively. Controls did not have psoriasis or any other inflammatory skin disease, nor any first-degree relatives with psoriasis. Participants were excluded if they had used tanning beds four weeks prior to participation. From cases, two 4mm skin biopsies were collected; one PP and one PN. PP was collected from the outer rim of a plaque, in the area which appeared most inflamed macroscopically. From controls, one 4mm skin biopsy NN was collected. When possible, the PN and NN samples were taken from a sun-protected area on the buttock and PN was taken at least 10 cm away from any visible plaque. Biopsies were snap frozen in liquid nitrogen bedside and later stored at -80 °C. Skin biopsies were homogenized using Precellys homogenizer (Bertin Technologies, Rockville, MD USA) and RNA was extracted using mirVana Isolation Kit (Applied Biosystems, Foster City, CA, USA).
Sequencing libraries were prepared using the NEXTflex small RNA-seq kit v3 (Bioo Scientific/PerkinElmer, Austin, TX, USA). Fragments/libraries were run on a Labchip GX (Caliper/PerkinElmer, Hopkinton, MA, USA), for quality control and quantitation. Individual libraries were normalized and pooled. The library pool was later purified with the QIAquick PCR Purification Kit (Qiagen AB, Sweden) and evaluated on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to instructions.
Single-end read sequencing was performed on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA, USA). The reads were mapped to human miRNAs in the miRBase database v22.1 with the miraligner tool.

value: Skin

tag: disease state

value: Control


title: Striatum, 8625

value: drug naïve straitum


title: ML_10009200037845


title: Striatum, 8622


title: Crown Xylem vs. Base Xylem Tree 3 Replicate 2

description: Tree 3S (2007) technical replicate 2


title: Striatum, 8621


title: ML_10009200091839


title: ML_10009200225607


title: Striatum, 8620


title: ML_10009200229539


title: Striatum, 8619


title: Striatum, 8623


title: Striatum, 8615


title: ML_10009200215472


title: ML_10009200212327


title: Striatum, 8614


title: ML_10009200227405


title: Striatum, 8617


title: ML_10009200207372


title: Striatum, 8618


title: ML_10009200217494


title: ML_10009200201978


title: ML_10009200086324


title: ML_10009200211079


title: Striatum, 8613


title: Striatum, 8616


title: ML_10009200203664


title: Striatum, 8609


title: Striatum, 8608


title: ML_10009200184535


title: ML_10009200209407


title: Striatum, 8611


title: Striatum, 8612


title: ML_10009200193297


title: ML_10009200199725


title: ML_10009200221550


title: Striatum, 8610


title: ML_10009200195095


title: Striatum, 8606


title: ML_10009200174413


title: Striatum, 8607


title: Striatum, 8605


title: Striatum, 8603


title: ML_10009200176198


title: Striatum, 8601


title: ML_10009200182849


title: ML_10009200180939


title: Striatum, 8602


title: Striatum, 8597


title: ML_10009200084177


title: ML_10009200095995


title: Striatum, 8604


title: Striatum, 8598


title: ML_10009200172503


title: Striatum, 8600


title: ML_10009200119744


title: ML_10009200080357


title: Striatum, 8599


title: ML_10009200090031


title: ML_10009200063943


title: Striatum, 8596


title: Striatum, 8595


title: Striatum, 8592


title: Striatum, 8593


title: Striatum, 8594


title: ML_10009200047407


title: ML_10009200054832


title: ML_10009200041328


title: Striatum, 8585


title: ML_10009200036149


title: Striatum, 8584


title: Striatum, 8590


title: ML_10009200022431


title: Striatum, 8591


title: ML_10009200031878


title: Striatum, 8581


title: Striatum, 8577


title: Striatum, 8583


title: Striatum, 8582


title: ML_10009200013195


title: ML_10009200024341


title: ML_10009200016702


title: Striatum, 8576


title: ML_10009200014891


title: Striatum, 8574


title: Striatum, 8547

value: F


title: ML_10009200043238


title: ML_10009200007578


title: ML_10009200011410


title: Striatum, 8546


title: ML_10009200004433


title: ML_10009200009376


title: Striatum, 8575


title: Striatum, 8545


title: ML_1715_F

value: Unaffected


title: ML_1675_F


title: Striatum, 8544


title: Striatum, 8543


title: ML_1637_F


title: Striatum, 8541


title: Striatum, 8542


title: Striatum, 8540


title: Striatum, 8537


title: Striatum, 8536


title: ML_1455_F


title: ML_1430_F


title: ML_1490_F


title: Striatum, 8534


title: Striatum, 8535


title: ML_1293_F


title: ML_1400_F


title: ML_1346_F


title: ML_1244_F


title: Striatum, 8533


title: ML_1608_F


title: ML_1613_F


title: Striatum, 8532


title: ML_1242_F


title: ML_1138_F


title: ML_1175_F


title: ML_1092_F


title: Striatum, 8522


title: ML_1082_F


title: Striatum, 8523


title: Striatum, 8521


title: ML_10009200241919


title: Striatum, 8517


title: Striatum, 8520


title: ML_1098_F


title: Striatum, 8518


title: Striatum, 8519


title: ML_10009200235505


title: ML_10009200239885


title: ML_10009200237639


title: Striatum, 8516


title: Striatum, 8505


title: Striatum, 8504


title: ML_10009200231560


title: Striatum, 8506


title: ML_10009200191051


title: ML_10009200219641


title: ML_10009200233582


title: ML_10009200223572


title: Striatum, 8497


title: Striatum, 8502


title: Striatum, 8500


title: Striatum, 8495


title: ML_10009200188704


title: ML_10009200169346


title: ML_10009200186893


title: Striatum, 8496


title: ML_10009200166537


title: ML_10009200179244


title: Striatum, 8498


title: ML_10009200162592


title: ML_10009200164515


title: Striatum, 8503


title: ML_10009200157986


title: Striatum, 8488


title: Striatum, 8501


title: Striatum, 8493


title: Striatum, 8487


title: ML_10009200150909


title: Striatum, 8486


title: ML_10009200148987


title: ML_10009200153593


title: Striatum, 8484


title: Striatum, 8485


title: Striatum, 8474


title: ML_10009200142796


title: Striatum, 8472


title: Striatum, 8473


title: ML_10009200139988


title: Striatum, 8475


title: ML_10009200146965


title: Striatum, 8494


title: ML_10009200160346


title: ML_10009200141910


title: Striatum, 8489


title: Striatum, 8492


title: ML_10009200135147


title: ML_10009200156751


title: Striatum, 8470


title: ML_10009200131900


title: Striatum, 8469


title: ML_10009200126260


title: Striatum, 8468


title: ML_10009200122104


title: Striatum, 8458


title: ML_10009200117722


title: Striatum, 8457


title: Striatum, 8456


title: ML_10009200115700


title: Striatum, 8471


title: ML_10009200113329


title: ML_10009200137966


title: ML_10009200111307


title: Striatum, 8455


title: ML_10009200107139


title: Striatum, 8453


title: Striatum, 8454


title: ML_10009200104106


title: ML_10009200109161


title: ML_10009200098244


title: Striatum, 8185


title: Striatum, 8183


title: Striatum, 8184


title: ML_10009200094200


title: Striatum, 8182


title: Striatum, 8181


title: Striatum, 8168


title: ML_10009200082379


title: ML_10009200089581


title: Striatum, 8167


title: Striatum, 8166


title: ML_10009200076202


title: ML_10009200078224


title: Striatum, 8165


title: Striatum, 8452


title: ML_10009200104890


title: ML_10009200070795


title: ML_10009200100497


title: ML_10009200068774


title: Striatum, 8089


title: ML_10009200051338


title: Striatum, 8088


title: Striatum, 8086


title: Striatum, 8085


title: ML_10009200030182


title: Striatum, 8083


title: ML_10009200026363


title: ML_10009200020857


title: ML_10009200072830


title: ML_10009200003422


title: Striatum, 8081


title: ML_10009200045260


title: Striatum, 8164


title: ML_1715_P

value: Affected


title: Striatum, 8084


title: Striatum, 8090


title: Striatum, 8080


title: Striatum, 8079


title: ML_1613_P


title: Striatum, 8078


title: ML_1637_P


title: Striatum, 8082


title: ML_10009200058316


title: ML_10009200066416


title: ML_1608_P


title: Striatum, 8087


title: Striatum, 8074


title: Striatum, 8077


title: ML_1490_P


title: Striatum, 8073


title: Striatum, 8070


title: ML_1430_P


title: ML_1400_P


title: Striatum, 8069


title: Striatum, 8068


title: Striatum, 8067


title: ML_1346_P


title: Striatum, 8066


title: ML_1175_P


title: ML_1244_P


title: Striatum, 8065


title: Striatum, 8063


title: Striatum, 8064


title: ML_1675_P


title: Striatum, 8060


title: ML_1455_P


title: ML_10009200241794


title: Striatum, 8062


title: Striatum, 8061


title: ML_1092_P


title: Striatum, 8059


title: ML_1082_P


title: ML_1098_P


title: ML_1138_P


title: Striatum, 8058


title: ML_10009200237415


title: Striatum, 8056


title: ML_10009200239661


title: ML_10009200235380


title: Striatum, 8055


title: ML_1293_P


title: ML_10009200231336


title: ML_1242_P


title: Striatum, 8053


title: ML_10009200223348


title: Striatum, 8050


title: Striatum, 8051


title: ML_10009200190837


title: ML_10009200219417


title: Striatum, 8057


title: Striatum, 8048


title: ML_10009200178918


title: ML_10009200169010


title: ML_10009200186557


title: ML_10009200166201


title: ML_10009200160010


title: Striatum, 8043


title: ML_10009200162256


title: ML_10009200157650


title: Striatum, 8047


title: ML_10009200164278


title: ML_10009200157077


title: Striatum, 8042


title: Striatum, 8049


title: Striatum, 8044


title: Striatum, 8040


title: Striatum, 8041


title: ML_10009200150784


title: ML_10009200148651


title: Striatum, 8052


title: Striatum, 8038


title: ML_10009200146629


title: Striatum, 8039


title: Striatum, 8046


title: ML_10009200141673


title: Striatum, 8037


title: ML_10009200139764


title: Striatum, 8036


title: ML_10009200142460


title: ML_10009200137630


title: Striatum, 8032


title: Striatum, 8034


title: Striatum, 8033


title: Striatum, 8031


title: ML_10009200125934


title: ML_10009200117485


title: Striatum, 8028


title: ML_10009200121877


title: ML_10009200131663


title: ML_10009200113092


title: ML_10009200115463


title: Striatum, 8029


title: Striatum, 8027


title: Striatum, 8024


title: Striatum, 8026


title: ML_10009200108835


title: ML_10009200104554


title: Striatum, 8035


title: ML_10009200134821


title: Striatum, 8023


title: ML_10009200097918


title: ML_10009200106925


title: Striatum, 8021


title: Striatum, 8025


title: Striatum, 8019


title: ML_10009200111182


title: ML_10009200100161


title: Patoc3: wild-type strain RNA rep3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
Bowtie version 1.2 with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p35from Subreads package (parameters: -t CDS -g locus_tag -s 1)
Count data were analyzed using R version 3.5.15and the Bioconductor packageDE Seq2 version 1.20.0f. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between P45, hfq1, and Patoc. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Leptospira biflexa serovar Patoc Patoc 1, from MicroScope Platform
Supplementary_files_format_and_content: Matrix from DESeq2

organism: Leptospira biflexa

source_name: wild-type strain

growth_protocol: exponential-phase culture

extract_protocol:
Cells were collected by centrifugation and pelleted cells were resuspended in TRIzol. RNA was then purified according to the manufacturer's instructions (Invitrogen, Saint Aubin, Ile de France, France). DNA was degraded by using a Turbo DNA-free kit according to the manufacturer's instructions (Invitrogen).
From 0.5 μg of total RNA, we depleted ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. On these rRNA-depleted RNAs, the sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher). Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.

treatment_protocol: no treatment of cells

value: wild-type


title: ML_10009200089245


title: Patoc2: wild-type strain RNA rep2


title: Striatum, 8017


title: Striatum, 8022


title: ML_10009200093973


title: Striatum, 8020


title: Striatum, 8030


title: Striatum, 8016


title: Striatum, 8018


title: Striatum, 8014


title: ML_10009200078000


title: P45-3: P45 mutant RNA rep3

source_name: P45 mutant

value: flhG transposon mutant


title: ML_10009200082155


title: Striatum, 8007


title: Striatum, 8009


title: Patoc1: wild-type strain RNA rep1


title: Striatum, 8006


title: Striatum, 8008


title: ML_10009200075975


title: hfq3: hfq mutant RNA rep3

source_name: hfq mutant

value: LEPBIa0945 deletion mutant


title: P45-1: P45 mutant RNA rep1


title: ML_10009200072593


title: ML_10009200066179


title: Striatum, 8002


title: hfq1: hfq mutant RNA rep1


title: ML_10009200070459


title: hfq2: hfq mutant RNA rep2


title: Striatum, 8015


title: 03-145

first: Gwladys

last: Bertin

address: rue de l'observatoire

institute: Institut de Recherche pour le Développement

data_processing:
Mapping with Hisat2 2.2
Aligned reads were assigned to annotated features with Feature-counts 2.0.1
Genome_build: P.falciparum 3D7, PlasmoDB release 49
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene except for variant surface antigens and every sample

molecule: polyA RNA

organism: Plasmodium falciparum

source_name: parasites isolates

extract_protocol:
RNA was extracted as described in Ponts N et al 2012, then digested with DNAse I (Qiagen) and purified using RNEasy MinElute Cleanup kit column (Qiagen). Absence of genomic DNA was assessed by the absence of amplification of p90 gene in qPCR from the direct use of the RNA extract, using Syber Green reagent (Life Technology) on Rotorgene 6000. RNA quality was assessed using Nanodrop (2000c) dosage and Agilent RNA 6000 Pico Kit used with 2100TM Bioanalyzeur (Agilent).
RNA-seq libraries were performed by TruSeq Stranded mRNA protocol (Illumina®, California, U.S.A.)

tag: clinical presentation

value: uncomplicated malaria


title: 03-160


title: Striatum, 8003


title: 03-140


title: Evs 5

city: Napoli

first: Paola

last: De Candia

address: via Pansini 5

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI NAPOLI FEDERICO II - Dipartimento di Medicina molecolare e Biotecnologie mediche

description: Test

data_processing:
Matrix worksheet reports not normalized signal.
Fold Change worksheet is empty because we analyzed only test condition and the fold change evaluation wasn't amonf study purposes.

label: SYBR Green

source_name: Peripheral blood mononuclear cells

label_protocol: A fixed volume of RNA sample was used as input for reverse transcription reaction by miRCURY-LNA RT Kit according to manufacturer’s instruction (Qiagen, U.S.A.). EV-associated miRNAs (n = 752) were profiled by using the complete human miRCURY LNA miRNA panel I+II (V5, Qiagen, U.S.A.).

growth_protocol: CD4+CD25− T cells were purified from peripheral blood mononuclear cells (PBMCs) from buffy coats of human healthy donors by magnetic cell separation with the Dynabeads Regulatory T Cell Kit (Invitrogen), allowing the separation of a 95–99% pure cell population by FACS analysis.

extract_protocol: Total RNA extracted using RNAqueous-4PCR Kit (Ambion, U.S.A.)

treatment_protocol: Cells were then stimulated in vitro for 72 hours in serum-free AIMV Medium AlbuMAX supplement (Gibco) in the presence of anti-CD3 and anti-CD28-coated Dynabeads (0.2 beads per cell) (Invitrogen).

tag: cell type

value: Human Tconv cells


title: ML_10009200044934


title: ML_10009200068550


title: Striatum, 8001


title: Evs 3

description: Test


title: Striatum, 7999


title: 03-153


title: Striatum, 8000


title: Striatum, 7998


title: ML_10009200029745


title: 03-141


title: ML_10009200058079


title: Striatum, 7996


title: ML_10009200051002


title: Striatum, 7997


title: ML_10009200026139


title: 03-137


title: Evs 4

description: Test


title: Evs 1

description: Test


title: 12: Ghurrah Post vaccination (7DPV) PBMC

city: Bareilly

first: Amit

last: Kumar

state: UP

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

data_processing:
Reads with phred score < 30 and adapter sequences were filtered using Trim_galore
Filtered reads were aligned to the Sus scrofa 11.1 transcriptome using Kallisto 0.46.1 and TPM abundances were generated
The TPM abundances generated by kallisto were converted to raw gene counts using tximport R package
Differential expression analysis was carried out through DEseq2
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: text files containing gene expression counts for each sample

organism: Sus scrofa

source_name: PBMC

extract_protocol:
Peripheral blood was collected from jugular vein in Heparin coated vacutainers and immediately processed. PBMC were isolated using density gradient centrifugation using Histopaque. RNA was extracted using TRIzol reagent.
Library preparation was through illumina Truseq RNA Sample Preparation Kit V2 (Poly A Capture)

tag: breed

value: Ghurrah

tag: vaccination

value: Post-CSF vaccination

value: PBMC


title: 11: Ghurrah Post vaccination (7DPV) PBMC


title: Striatum, 7995


title: ML_10009200003297


title: Striatum, 7992


title: Striatum, 7994


title: 468 CELLS-si-NC

city: Jinan

first: Haiting

last: Liu

address: West Wenhua Road 44

institute: Shandong University

data_processing:
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files contains the FPKM values for each sample

source_name: breast cancer cells

growth_protocol: Cells were cultured L15 culture medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THAP7-AS1 was knocked down by transfection with THAP7-AS1 Smart Silencer in 468cells

tag: cell line

tag: morphology

value: epithelioid

value: breast cancer cells

tag: genotype/variation

value: si-NC control


title: ML_10009200020633

value: Skin


title: 03-075


title: 03-110


title: 03-113


title: Striatum, 7993

tag: strain

value: M


title: Evs 2

description: Test


title: 03-060


title: 468 CELLS-si-THAP7-AS1

value: transfection with THAP7-AS1 Smart Silencer

value: THAP7-AS1 knockdown


title: 03-037


title: control3

city: Shenyang

first: Bengang

last: Wang

address: North Nanjing Street 155#

institute: China Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: bile duct

growth_protocol: After collection, the samples were frozen in RNAlater (Life Technologies, Carlsbad, California, USA) storage solution and stored at -80 ℃ for RNA extraction.

extract_protocol:
RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adjacent normal

tag: Sex

value: male

tag: year


title: Striatum, 7991

source_name: Striatum

tag: generation

tag: tissue

value: drug naïve straitum


title: 9: Landrace Post vaccination (7DPV) PBMC

value: Landrace


title: 10: Ghurrah Post vaccination (7DPV) PBMC


title: control2


title: 03-031


title: 03-059


title: 6: Ghurrah Pre vaccination PBMC

value: Pre- CSF vaccination


title: Striatum, 7990


title: Striatum, 7989


title: 5: Ghurrah Pre vaccination PBMC


title: 03-025

value: uncomplicated malaria


title: 8: Landrace Post vaccination (7DPV) PBMC


title: 03-022


title: csae3

value: cholangiocarcinoma


title: Striatum, 7986


title: 02-030

value: cerebral malaria


title: 02-034


title: 7: Landrace Post vaccination (7DPV) PBMC

value: Post-CSF vaccination


title: 4: Ghurrah Pre vaccination PBMC

value: Ghurrah

value: PBMC


title: Striatum, 7988


title: Striatum, 7987


title: control1


title: Striatum, 7984


title: 2: Landrace Pre vaccination PBMC


title: Striatum, 7983


title: 02-027


title: case2


title: IKAROS_CHIP_rep1

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

library_source: genomic

data_processing:
SAM alignments were generated from Illumina Fastq files aligned to human hg38 genome using Novocraft’s novoalign aligner with the following parameters: -o SAM –r Random.
Peak calling was then performed using macs2 (v2.1.1.20160309) using the following settings: -g 2.7e9 –call -summit –f BAMPE –nomodel –B –SPMR –extsize 200.
Generated bedgraph files were then transformed to bw format using UCSC bedGraphToBigWig application (v4)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

growth_protocol: CCRF-CEM cells were cultured in RPMI 1640 medium, 10% fetal bovine serum, 2 mM GlutaMAX-I, 100 U/mL penicillin and 100 μg/mL streptomycin

extract_protocol:
DNA was pruified from sonicated cell lysate (input) or subquentially anti-FLAG antibody precipitation using Zymo ChIP DNA clean & concentrator (Zymo Research)
Libriaries were prepared for sequecing acordding to the instructions of NEBNext ChIP-Seq Library Prep Reagent Set

treatment_protocol: Cells were treated with doxycycline at 1uM for 24 hours

tag: cell lines

tag: chip antibody

value: Flag (Sigma Aldrich, F1804)

tag: treatment

value: treated with Doxycycline for 24 hours


title: IKAROS_CHIP_rep2


title: 3: Landrace Pre vaccination PBMC


title: Striatum, 7985


title: case1


title: GFI1_CHIP_rep2


title: Striatum, 7982


title: 1: Landrace Pre vaccination PBMC


title: 02-025


title: GFI1_CHIP_rep1


title: 02-013


title: S6: NoGC3

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

data_processing:
Raw fastq output was generated from Illumina bcl files using bcl2fastq
Fastqs were aligned to the genome (GRCm39; Gencode M26 annotation) using STAR and read counts were calculated using the Bioconductor function SummarizeOverlaps with default parameters
DESeq2 was used to normalize counts using default parameters
Genome_build: GRCm29
Supplementary_files_format_and_content: Normalized counts using DESeq2

source_name: CD8 T cell

extract_protocol:
Total RNA was extracted from each sorted T cells using a RNeasy micro kit (Qiagen), and each sample was evaluated for the RNA integrity by TapeStation system (Agilent)
cDNA synthesis and enrichment were performed using the SMART v4 protocol (Takara/Clontech), and library preparation was conducted using an Illumina Nextera XT library preparation kit

treatment_protocol: Recipient mice were injected with water soluble form of dexamethasone (5 mg/kg/day i.p.; Sigma-Aldrich) or vehicle (methyl β-cyclodextrin; Sigma-Aldrich) suspended in PBS solution from days -1 to +5 after BMT

value: vehicle

value: CD8 T cell


title: IKAROS_input


title: S5: GC3

value: glucocorticoid


title: S4: GC2


title: Striatum, 7978

value: M


title: Striatum, 7977


title: Striatum, 7980


title: 02-003


title: 02-016


title: S3: NoGC2


title: Striatum, 7981


title: GFI1_input


title: Striatum, 7979


title: S2: NoGC1


title: 02-002


title: HL60_BMI_KO_1

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequence reads were aligned to hg19 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Sambamba 0.5.5.
Deeptools was used to generate RPKM normalized bigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

tag: genotype

value: BMI1 knockout


title: 02-011


title: 02-018


title: 02-017


title: 01-020


title: EZH2i_HL60


title: Striatum, 7976


title: 01-013


title: Striatum, 7974


title: S1: GC1


title: DMSO_HL60

value: DMSO


title: Striatum, 7969

value: drug naïve straitum


title: TnsC_crRNA-4_ChIP-seq_paired_raw

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

data_processing:
ChIP-seq single- and paired-end reads were trimmed and mapped to an E. coli BL21(DE3) reference genome (GenBank accession CP001509.3) using fastp [REF] and Bowtie2 [REF] with default parameters, respectively. Two genomic lacZ/lacI regions and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 335,600-337,101 and 748,601-750,390). Enrichment analysis on pDonor and pQCascade was performed by mapping reads (Bowtie2, default parameters) to the same E. coli BL21(DE3) reference genome concatenated to the respective pQCascade, pTnsABC and pDonor plasmid sequences used in each experiment. For those concatenated reference genome files, sequence elements were separated from one another by inserting 1,000 bp represented as Ns. Mapped reads were sorted and indexed using the SAMtools software package [REF] (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option). Alignments were normalised by RPKM (Reads Per Kilobase per Million mapped reads), as described previously [REF] and converted to 1 bp-bin bigwig files using the deepTools2 [REF] command bamCoverage (--normalizeUsing RPKM -bs 1 parameters). After normalization, genome- and plasmid-mapping reads were visualised in IGV [REF]. The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) [REF] and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously [REF]. Peaks were called on pre-normalised alignments using MACS3 [REF], with the following parameters: [-g 4500000 --nomodel --extsize 400 -q 0.05 -B]. A non-immunoprecipitated control library of Cas8 was used as an input for standardizing all library peak calls (-n option).  Heatmaps of peak calls were first generated by computing a heatmap matrix on the alignments using the deepTools function (computeMatrix reference-point) with default parameters. Subsequently, the deepTools function plotHeatmap was used on the heatmap matrices with the following parameters: [--whatToShow ‘heatmap and colorbar' --sortUsing max]. Venn diagrams were generated using custom R code on MACS3 peak output files. Sequence motifs were identified using MEME (version 4.12.0) with default parameters [REF]. Off-target mismatch analysis on peak calls was performed using a custom Python script. Briefly, a 200-bp sequence around each peak was examined, and the 10-bp sequence most closely matching a 5'-CN-3' PAM and the first 8-nt of the seed sequence, with the 6th bp set as N, was identified. The best-matching sequence was inferred to be the off-target binding site, and the full 34-bp PAM and target sequence was extracted for each peak.
Genome_build: CP001509.3
Supplementary_files_format_and_content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage
Supplementary_files_format_and_content: .bed files were generated using MACS3 and represent peak calls and summit enrichment values
Supplementary_files_format_and_content: .xlsx file contains number of raw and uniquely mapped reads

organism: Escherichia coli

source_name: Solid cell culture

growth_protocol: Transformations were performed using a three-plasmid system, according to the general transposition assay protocol that was previously described (Klompe et al. 2019). In brief, after 16 h incubation at 37 °C on LB-agar plates with antibiotics but no IPTG induction, colonies were scraped and resuspended in 1 ml of fresh LB. The optical density at 600 nm was measured, and approximately 4.0 × 108 cells (equivalent to 1 ml of OD600 = 0.25) were spread onto two LB-agar plates containing antibiotics and supplemented with 0.1 mM IPTG. We chose to culture cells on solid LB-agar to reduce any competition-induced effects of culturing in liquid LB media. Plates were incubated at room temperature (~25 °C) for 44 h, during which time a bacterial lawn formed.

extract_protocol:
IPTG-induced E. coli cells were scraped and spread onto the wall of a 50 ml conical tube in a thin layer, to allow for efficient resuspension and crosslinking in the next step. Crosslinking and immunoprecipitation generally followed previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to a separate tube containing 40 ml of LB medium (~1% final concentration), and the solution was mixed immediately by inverting. This solution was added to the conical tube containing the scraped cells, and the cells were fully resuspended in the LB-formaldehyde solution by vigorous vortexing at room temperature. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD600 was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in either single- or paired-end mode on the Illumina MiniSeq and NextSeq platform. For each ChIP-seq sample, >1,800,000 raw reads (including genomic and plasmid-mapping reads) were obtained.

treatment_protocol: Type I-F3 CRISPR-associated transposon proteins (Cas8/5, Cas7, Cas8, TniQ, TnsC, TnsB, TnsA) from Vibrio cholerase (as described in Klompe et al. 2019 and Vo et al. 2021) were heterologously expressed upon induction with 0.1 mM IPTG

tag: transposon protein

value: TnsC

tag: antibody

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

tag: epitope-tag on sample protein


title: TnsC_deltaTnsAB_crRNA-4_ChIP-seq_paired_raw


title: Striatum, 7968


title: TnsA_crRNA-4_ChIP-seq_paired_raw

value: TnsA


title: 01-006

tag: clinical presentation


title: Striatum, 7967


title: Cas8_crRNA-4_ChIP-seq_paired_raw_rep1


title: Input_Cas8_crRNA-287_ChIP-seq_paired_raw


title: Striatum, 7975


title: Striatum, 7966


title: TnsB_crRNA-4_ChIP-seq_paired_raw

value: TnsB


title: W303_sen1T1623E_R1

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

institute: Institut Jacques Monod-CNRS

data_processing:
Reads were demultiplexed using the the pyBarcodeFilter script from the pyCRACutility suite
Adaptor trimming  with cutadapt 1.15
Quality-trimming with trimmomatic
Mapping with bowtie2
Normalized coverage obtained with the bamCoverage tool of deepTools2 package. Normalization to  counts per 10^7 counts. Reads shorter than 20 nt were filtered out.
Genome_build: R64
Supplementary_files_format_and_content: bigwig files for each sample and for each strand (plus or minus)

organism: Saccharomyces cerevisiae W303

source_name: Yeast cells

growth_protocol: Cells grown on CSM-TRP to OD600= 0.6

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol.
RNA was reverse transcribed using the Reverse transcriptase IV (Invitrogen). The cDNA solution was used to perform multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per ml of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

value: W303-derived strain

value: Rpc160-HTP expressing sen1T1623E


title: Striatum, 7766


title: W303_WT_R2

value: Rpc160-HTP expressing SEN1


title: Striatum, 7765

value: F


title: 01-004

value: cerebral malaria


title: W303_sen1T1623E_R2


title: Striatum, 7764


title: W303_WT_R1


title: HK-2_30µM LPC(18:0)_24H_rep3

city: Nagaizumi-cho

first: Kentaro

last: Yoshioka

state: Shizuoka

address: 465-6, Shimotogari

institute: Kyowa Kirin Co. Ltd.

hyb_protocol: cDNA products were mixed with transcription master mix in the presence of T7 RNA polymerase and Cy3 labelled-CTP and incubated at 40°C for 2 h. Labelled cRNAs were purified and eluted in nuclease-free water. For each hybridization step, Cy3-labelled cRNA was fragmented, and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Human GE v3 8x60K Microarray

scan_protocol: The microarrays were scanned using an Agilent SureScan Microarray Scanner System (G4900DA; Agilent Technologies). Intensity values of each scanned feature were quantified using Agilent feature extraction software version 12.1.1.1, which performs background subtractions.

data_processing: Normalization was performed using Agilent GeneSpring software version 14.9.1 (per chip: normalization to 75th percentile shift). Any array-probe signals that saturated the fluorescence or did not show a significant difference from the background were excluded from the analysis.

label_protocol: Total RNA was amplified and labelled with Cyanine 3 (Cy3) using an Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies), as per the manufacturer's instructions. Briefly, total RNA was reverse-transcribed into double-strand cDNA using a poly dT-T7 promoter primer.

extract_protocol: Total mRNA was isolated using an RNeasy kit (74106; Qiagen, Hilden, Germany).

treatment_protocol: For LPC treatment on HK-2 cells, the cells were pre-incubated in the assay medium, which contained DMEM/F12 with 0.1% fatty acid-free bovine serum albumin (BSA; 017-15141; Wako, Osaka, Japan), overnight at 37 °C in an atmosphere containing 5% CO2. LPC (16:0) or (18:0) (855675C or 855775C; Avanti Polar Lipids, Alabaster, AL, USA) were pre-conjugated to fatty acid-free BSA at 37°C for 5 min. The LPC species or control BSA solutions were added to the cells after 100× dilution in assay medium containing 0.1% dimethyl-sulfoxide (D0798; Tokyo Chemical Industry Co., Ltd., Tokyo, Japan), followed by incubation at 37°C in an atmosphere containing 5% CO2 for the indicated times


title: HK-2_60µM LPC(18:0)_24H_rep2