title: ΔelyC rep3_21°C

city: Montreal

first: Fardin

last: Ghobakhlou

state: QC

address: Pavillon Roger-Gaudry, S-640  2900 Boulevard Edouard-Montpetit,  Montréal, QC

department: Microbiology , Infectiology and Immunology

institute: University of Montreal

description:
21c_em9_3
HI.2835.005.Index_15.IK_21C-EM9-3

data_processing:
Poor quality reads were trimmed out with Trimmomatic software. The quality of the reads, before and after trimming, was assessed with FASTQC version 0. 11. 5.
The reads were aligned to the E. coli sub-strain MG1655 reference genome (GCA000801205.1) with Bowtie2 version 2. 2. 9. The reference genome used for the alignment, and the GTF annotation file used for counting the number of reads aligned to each feature, were downloaded from Ensembl (release 27). The aligned data saved as BAM files. The raw alignment read counts for each gene were calculated using featureCounts 1.5.1.
Normalization and differential expression (fold change /Log2 fold change) of genes from the raw alignment counts were determined with a significant p-values (< 0.05) using the DESeq 2. 1. 14.0 in the R program.
Genome_build: GCA000801205.1
Supplementary_files_format_and_content: The output from DESeq2, including the raw counts, normalized relative to the total number of reads. Differentially expressed genes were determined with a p-value (< 0.05), and as part of the multiple comparison testing, significant Benjamini-Hochberg adjusted p-values (p-adj) < 0.05 (5% false discovery rate) were considered. In addition to the counts normalized relative to the library size, the genome-wide occupancy (quantitation) was also computed into density units of fragments per kilobase of exon model per million reads mapped (FPKM).

organism: Escherichia coli

growth_protocol: The pre-cultures were grown in LB medium at 37°C. Triplicate cultures of the wild-type and ∆elyC mutant strains were grown in 250 ml LB 1% NaCl liquid media, 250 rpm, at 21°C and 37°C to early-log phase (OD600 of 0.30 to 0.35). The samples were immediately centrifuged (6000 g) at 4 °C for 5 min.

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (QIAGEN) with the RNAprotect Bacteria reagent (QIAGEN) according to the manufacturer’s protocol. DNA was removed using RNase-Free DNase set from QIAGEN. The RNA was finally resuspended in RNase-Free Water (QIAGEN) and RNA concentration was quantified using the NanoDrop ND-1000 at 260 nm. RNA Ribosome Integrity Numbers (RIN) and purity of the RNA samples were assessed using the Agilent Bioanalyzer 2100 and RNA 6000 Pico Kit. The RIN numbers for all the twelve samples were 9.3 to 10. The rRNA depletion was performed using the Ribo-Zero Magnetic Gold Kit for Gram-negative Bacteria (Illumina).
RNAseq libraries were prepared using KAPA RNA stranded Kit (Roche-Nimblegen). Libraries were assessed and quantified by BioAnalyzer using the High Sensitivity DNA Kit (Agilent). Sequencing was performed on an Illumina HiSeq2000 machine, in 75-nucleotide paired-end mode.

treatment_protocol: The pellets were washed once with cold TES buffer (100 mM NaCl, 1 mM EDTA, 10 mM Tris hydrochloride [pH 7.4]), recentrifuged, and cells snap-frozen in liquid nitrogen and stored at −85 °C.

value: elyC::frt (EM9)

value: Grown at 21°C, harvested at OD600nm 0.3-0.35


title: ΔelyC rep2_37°C

status: Public on Mar 20 2020

type: SRA

country: Canada

description:
37c_em9_2
HI.2835.005.Index_18.IK_37C-EM9-2

library_source: transcriptomic

molecule: total RNA

tag: genotype/variation

tag: treatment

value: Grown at 37°C, harvested at OD600nm 0.3-0.35


title: S2865WT

type: RNA

city: Beijing

first: Jiu

middle: zhi

last: Xu

state: Beijing

address: Yuanmingyuan West Road NO.2

department: College of Biological sciences

country: China

institute: China Agricultural University

description:
S2865WT:gProcessedSignal(raw)
Gene expression of control mouse colon.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 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: Scanned on an Agilent G2565CA scanner.

data_processing:
Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.
gProcessedSignal(raw)

organism: Mus musculus

source_name: Colon, 3.5% DSS in drinking water for 5 days, recover for 1 day

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, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: No treatment.

value: Control

tag: tissue

value: Colon

tag: gender

value: Male


title: 1063G3BMS-Lung

city: Monrovia

first: Claude

middle: J

last: Rogers

state: CA

address: 1225 S. Shamrock Ave.

country: USA

institute: ChromoLogic

data_processing:
Demultiplexing performed in Basespace using FASTQ Generation v1.0.0
Timming performed in Basespace using FASTQ Toolkit v2.2.0 and the following settings: minimal read length = 18; Adaptor sequence to trim from the 3’-end: AACTGTAGGCACCATCAAT; trim bases at the 5’-end with a quality score less than 30; maximum read length = 40; minimum read score = 20
miRNA alignment performed in Basespace using Small RNA v1.0.1 and “Mus musculus/mm10” as species
Sequence runs with less than 100,000 miRNA reads or less than 25% identified mature miRNA content were rejected
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts for the indicated miRNA (rows) and sample (columns) in csv format

source_name: Lung

extract_protocol:
Tissue miRNA was extracted from 20 mg of homogenized tissues in QIAzol (Qiagen) with the miRNEasy Kit (Qiagen).
Libraries for sequencing were prepared using the QIAseq miRNA Library Kit; (Qiagen) with 5.8 µL of miRNA extracts as input, a 1:5 dilution of the 3’-adaptor, a 1:2.5 dilution of the 5’-adaptor, a 1:5 dilution of the RT primer, and 22 amplification cycles. The concentrations of the prepared libraries were determined via Bioanalyzer analysis (2100 Electrophoresis Bioanalyzer, Agilent). Libraries with an adapter dimer peak (~160 nt) at least five times greater than the library peak (~180 nt) were not sequenced.

tag: strain

value: M

tag: irradiated

value: FALSE


title: S2999WT

description:
S2999WT:gProcessedSignal(raw)
Gene expression of control mouse colon.


title: ΔelyC rep1_21°C

description:
21c_em9_1
HI.2835.005.Index_13.IK_21C-EM9-1


title: S2849KO

description:
S2849KO:gProcessedSignal(raw)
Gene expression of Islr knockout mouse colon.

value: Islr knockout


title: S2870WT

description:
S2870WT:gProcessedSignal(raw)
Gene expression of control mouse colon.


title: ΔelyC rep2_21°C

description:
21c_em9_2
HI.2835.005.Index_14.IK_21C-EM9-2


title: S2848KO

description:
S2848KO:gProcessedSignal(raw)
Gene expression of Islr knockout mouse colon.


title: 1062G3BMS-Lung


title: WT rep3_37°C

description:
37c_wt3
HI.2835.005.Index_5.IK_37C-wt3

value: MG1655 (rph1 ilvG rfb-50)


title: WT rep2_37°C

description:
37c_wt2
HI.2835.005.Index_4.IK_37C-wt2


title: ΔelyC rep1_37°C

description:
37c_em9_1
HI.2835.005.Index_16.IK_37C-EM9-1


title: WT rep1_37°C

description:
37c_wt1
HI.2835.005.Index_2.IK_37C-wt1


title: 1061G3BMS-Lung


title: 1052G3AMS-Lung


title: 1056G3AMR-Lung

value: TRUE


title: 1055G3AMR-Lung


title: WT rep3_21°C

description:
21c_wt3
HI.2835.005.Index_12.IK_21C-wt3


title: 1051G3AMS-Lung


title: WT rep1_21°C

description:
21c_wt1
HI.2835.005.Index_6.IK_21C-wt1


title: WT rep2_21°C

description:
21c_wt2
HI.2835.005.Index_7.IK_21C-wt2


title: 1050G3AMS-Lung


title: ΔelyC rep3_37°C

description:
37c_em9_3
HI.2835.005.Index_19.IK_37C-EM9-3


title: 1049G3AMS-Lung


title: 2004G2AMS-PT

source_name: Plasma

extract_protocol:
Circulating miRNA was isolated from 25 µL of plasma using the miRCIRY RNA Isolation Kit (Biofluids; Exiqon).
Libraries for sequencing were prepared using the QIAseq miRNA Library Kit; (Qiagen) with 5.8 µL of miRNA extracts as input, a 1:5 dilution of the 3’-adaptor, a 1:2.5 dilution of the 5’-adaptor, a 1:5 dilution of the RT primer, and 22 amplification cycles. The concentrations of the prepared libraries were determined via Bioanalyzer analysis (2100 Electrophoresis Bioanalyzer, Agilent). Libraries with an adapter dimer peak (~160 nt) at least five times greater than the library peak (~180 nt) were not sequenced.

tag: time point

value: PT


title: 1085G3BFS-Heart

source_name: Heart

value: F


title: 1089G3BFR-Heart


title: Serum Con A EVs

city: Nagoya

first: Reo

last: Kawata

address: 65 Tsurumai-cho, Showa-ku, Nagoya, Japan

department: Drug Safety Sciences

country: Japan

institute: Nagoya university

description:
processed data file: EVs_raw_read_count.xlsx
processed data file: Serum_EVs_Normalized_read_counts.xlsx

data_processing:
The FASTQ files generated by the Illumina MiSeq System were analyzed with CLC Genomics Workbench (Qiagen). Adaptor sequences were trimmed, and sequences with a length less than 15 or more than 35 bp were discarded before counting. The trimmed data were mapped to the mouse mature miRNA-seq in miRBase ver. 22.1, allowing two-base mismatches. In exosomal small RNA analysis, the trimmed data were also mapped to mature ath- miRNA-seq with perfect matches. miRNAs with a total read count of the samples less than 10 were filtered out. In RAW264.7 small RNA analysis, normalization and statistical analysis were performed by the edgeR package using TCC-GUI (Su et al. 2019) and the differentially expressed miRNA genes (DEGs) compared with each control group were identified with a q value < 0.1 and fold change (FC) > 2 or < 0.5. In exosomal small RNA analysis, the read counts were normalized by divided by the read counts of spike in control miRNA and DEGs compared with each control group were identified with FC > 2 or < 0.5.
Genome_build: miRBase ver. 22.1
Supplementary_files_format_and_content: *.xlsx: Excel files containing raw and normalized read counts in individual files.

source_name: Serum extracellular vesicles

growth_protocol:
RAW264.7 cells, a mouse macrophage cell line, was obtained from RIKEN BioResource Research Center (Ibaraki, Japan). The cells were maintained in Dulbecco’s Modified Eagle Medium (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% fetal bovine serum (Sigma-Aldrich), 2 mM glutamine and 3.5 g/L glucose (Fujifilm Wako Pure Chemical Corporation) at 37°C in 5% CO2 atmosphere.
Female BALB/c mice (7-8 weeks old) were obtained from Japan SLC (Hamamatsu, Japan). The animals were housed under a 12-hour light/dark cycle in a controlled environment (maintained at 23 ± 2°C with a relative humidity of 55 ± 10%) in the institutional animal facility with ad libitum access to food and water, and they were acclimated to our facility before the experiments. All procedures performed on the animals were approved by the Animal Care Committee of Nagoya University Graduate School of Medicine and were carried out in accordance with the guidelines established by the Institute for Laboratory Animal Research of the Medical School of Nagoya University, Japan.

extract_protocol:
For RAW264.7 RNA extraction, total RNA was extracted using a miRNeasy Mini Kit according to the manufacturer’s protocol. For exosomal RNA extraction, Arabidopsis thaliana (ath)-miR159a-3p, a spike in control, was added to the EVs lysate in QIAzol Lysis Reagent, and total RNA was extracted using a miRNeasy Serum/Plasma Kit according to the manufacturer’s protocol.
The quantity and quality of the RNA samples were checked with an Agilent BioAnalyzer (Agilent Technologies) using an RNA6000 Pico Kit (Agilent Technologies). cDNA libraries for miRNA-seq were synthesized with a NEBNext Multiplex Small RNA Library Prep Set for Illumina and quantified with a Qubit 2.0 fluorometer (Life Technologies) using a Qubit dsDNA HS Assay Kit (Life Technologies) according to the manufacturer’s protocol. miRNA-seq was performed with an Illumina MiSeq System using MiSeq Reagent Kit v3. For improved cluster formation, denatured PhiX Control v3 was added to the cDNA libraries. Sequencing was performed with 51 bp single-end reads.

treatment_protocol:
For RAW264.7 extracellular vesicles (RAW EVs) isolation, RAW264.7 cells were seeded at a density of 3 × 10e6 cells/plates in 100 mm culture dishes and preincubated for 24 h. After 24 h incubation with 25 ug/mL Con A or Saline in EVs-free culture medium, the culture supernatants were collected and centrifuged at 2,000 g at 4°C for 10 min. The supernatants were filtered through a 0.2 um syringe filter followed by centrifugation at 175,000 g at 4°C for 4 h. The EVs pellets were resuspended in PBS and centrifuged again at 175,000 g at 4°C for 4 h. The supernatant was discarded, and then, the following reagents were added to the pellet: PBS for in vitro EVs treatment experiment or QIAzol Lysis Reagent for RNA extraction.
For Serum EVs isolation, mice (8-9 weeks old) were intravenously administered a single dose of 15 mg/kg Con A dissolved in saline (5 mL/kg). Blood samples were obtained from the caudal vena cava under isoflurane anesthesia 9 h after administration of Con A. The obtained blood was collected to serum separator tube and incubated over 15 min at room temperature to allow clotting. The clotted blood was centrifuged at 1,600 g at 4°C for 10 min to obtain serum. The obtained serum was centrifuged at 16,500 g at 4°C for 20 min, and the supernatant (pretreated serum) was stored at −80°C until its use. The pretreated serum was centrifuged at 208,000 g at 4°C for 70 min. The EVs pellet was resuspended in PBS and centrifuged again at 208,000 g at 4°C for 70 min. The supernatant was discarded, and then, the following reagents were added to the pellet: PBS for in vitro EVs treatment experiment or QIAzol Lysis Reagent for RNA extraction.
For the EVs treatment, RAW264.7 cells were seeded at a density of 1.5 × 10e5 cells/well in 24-well plates and preincubated for 24 h. After 8 h incubation with 6E+09 particles/mL EVs in EVs-free medium, the cells were treated with Con A or Saline. After further incubation for 16 h, the cells were harvested with QIAzol Lysis Reagent for RNA extraction.

tag: cell type

value: Serum extracellular vesicles

value: BALB/c

value: Female

tag: age

value: 8-9 weeks

value: Concanavalin A


title: 1087G3BFS-Heart


title: RAW Saline EVs

description:
processed data file: EVs_raw_read_count.xlsx
processed data file: RAW_EVs_Normalized_read_counts.xlsx

source_name: RAW264.7 extracellular vesicles

value: Macrophage cell line extracellular vesicles

value: Saline


title: Serum Saline EVs


title: RAW Con A EVs/Con A #1

description:
processed data file: RAW264.7_processed data file: RAW_read_count.xlsx
processed data file: ALL_RAW264.7_samples_Normalized_read_counts.xlsx
processed data file: RAW_Con_A_EVs_Con_A_vs_PBS_Con_A_Normalized_read_counts.xlsx

source_name: RAW264.7 cells

tag: cell line

value: Macrophage cell line

value: RAW Con A EVs/Concanavalin A


title: RAW Con A EVs/Con A #2

value: Male


title: RAW Con A EVs/Con A #3


title: 1076G3AFS-Heart


title: 1075G3AFS-Heart


title: 1074G3AFS-Heart


title: RAW Saline EVs/Con A #3

description:
processed data file: RAW264.7_processed data file: RAW_read_count.xlsx
processed data file: ALL_RAW264.7_samples_Normalized_read_counts.xlsx

value: RAW Saline EVs/Concanavalin A


title: RAW Saline EVs/Con A #2


title: 1073G3AFS-Heart

value: FALSE


title: 2094G4BFR-Heart


title: 2092G4BFR-Heart


title: Serum Con A EVs/Con A #2

description:
processed data file: RAW264.7_processed data file: RAW_read_count.xlsx
processed data file: ALL_RAW264.7_samples_Normalized_read_counts.xlsx
processed data file: Serum_Con_A_EVs_Con_A_vs_PBS_Con_A_Normalized_read_counts.xlsx

value: Serum Con A EVs/Concanavalin A


title: RAW Saline EVs/Con A #1


title: 2091G4BFR-Heart


title: RAW Con A EVs


title: 2089G4BFR-Heart


title: PBS/Con A #2

description:
processed data file: RAW264.7_processed data file: RAW_read_count.xlsx
processed data file: ALL_RAW264.7_samples_Normalized_read_counts.xlsx
processed data file: Serum_Con_A_EVs_Con_A_vs_PBS_Con_A_Normalized_read_counts.xlsx
processed data file: RAW_Con_A_EVs_Con_A_vs_PBS_Con_A_Normalized_read_counts.xlsx

value: PBS/Concanavalin A


title: PBS/Con A #3


title: 2088G4BFS-Heart


title: Serum Con A EVs/Con A #1


title: 1086G3BFS-Heart


title: PBS/Con A #1


title: 2085G4BFS-Heart


title: 2082G4AFR-Heart

value: TRUE


title: 2076G4AFS-Heart


title: 2077G4AFR-Heart


title: 2081G4AFR-Heart


title: 2075G4AFS-Heart


title: 2073G4AFS-Heart


title: Input

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

library_source: genomic

data_processing:
basecall CASAVA 1.8
demultiplexing with bcl2fastq v.2
low quality bases and adapter removal made with bbduk
reads were aligned to mouse genome in pair end with bwa mem
duplicates were marked with sambamba markdup -p -t 10
mapped reads were quantified by tranforming in BigWig with Deeptools bamCoverage 2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files obtained from aligned reads and quantified by a binsize of 10bp with Deeptools bamCoverage

molecule: genomic DNA

source_name: NMuMG cells

extract_protocol:
as reported in Chu et al. (Mol.Cell 44, 667–678, 2011)
ChIP Elute Kit and DNA SMART ChIP-Seq Kit—Illumina® sequencing library preparation from low-input DNA templates

treatment_protocol: no treatment

value: NMuMG


title: 2074G4AFS-Heart

value: F


title: Odd set


title: Even set


title: 1069G3BMR-Heart

value: M


title: 1065G3BMR-Heart


title: 2086G4BFS-Heart


title: BE2C THZ1 treatment

city: Sydney

first: matthew

middle: kwok kei

last: wong

state: New South Wales

address: Lowy cancer centre, University of New South Wales

department: histone modification group

country: Australia

institute: Children's Cancer Institute

description: BE(2)-C MYCN -amplified neuroblastoma cells

hyb_protocol: 2.3 ug of fragmented, labeled cDNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_0007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing: The microarray data were analyzed in R (http://www.r-project.org/) with bioconductor packages (http://www.bioconductor.org/), and normalised with GenePattern software (Version 3.9.0 Broad Institute) and LimmaGP modules (version 20.0).

label: Biotin

organism: Homo sapiens

source_name: BE(2)-C cells, treated with THZ1

label_protocol: We used the Affymerix GeneChip WT Plus Reagent Kit: Manual Target Preparation for GeneChip Whole Transcript Expression Arrays (Affymetrix_WT_Plus_User_Guide). 100 ng of total RNA was used for input.

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: BE2C neuroblastoma cells were treated  with either vehicle control, 32nM THZ1, 250nM ponatinib, 1000nM lapatinib, THZ1+ponatinib or THZ1 + lapatinib for 6 hours.

value: Subclone of the SK-N-BE(2) neuroblastoma cell line. Derived from the metastatic site (bone marrow) in a two-year-old Caucasian male with malignant neuroblastoma.


title: BE2C THZ1 ponatinib combo treatment

source_name: BE(2)-C cells, treated with THZ1 and ponatinib combination


title: BE2C ponatinib treatment

source_name: BE(2)-C cells, treated with ponatinib


title: 1062G3BMS-Heart


title: 1063G3BMS-Heart


title: 1061G3BMS-Heart


title: BE2C vehicle control treatment

source_name: BE(2)-C cells, treated with vehicle control


title: BE2C lapatinib treatment

source_name: BE(2)-C cells, treated with lapatinib


title: 1056G3AMR-Heart


title: bulk RNA_sgSmg7 cells Rep2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
Genes expression :Raw reads were first trimmed using Trimmomatic (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs (less than 3) were trimmed, and a 4-bp sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Only reads with more than 50-bp were kept. The resulting reads were mapped to the mm10 genome using STAR 33 (v.2.5.2b) with the following parameters: --outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --quantMode TranscriptomeSAM GeneCounts. The generated gene expression count files generated by STAR were then used for estimating gene expression.
Repeats expression :Multi-mapped reads and reads mapping to intronic or intergenic regions were extracted and then mapped to the repeats pseudo-genome. First, the TagReadWithGeneExon command of the dropseq tools was used to tag the reads into utr, coding, intergenic and intronic reads using the bam tag “XF”. Multi-mapped reads, intergenic and intronic reads were extracted and mapped to the repeats pseudo-genome using STAR. The STAR read counts were used as an estimate of repeats expression.
Analysis: For each sample, the genes and repeats expression matrices were merged together and then the “Trimmed Mean of M-values” normalization (TMM) method from the R/Bioconductor package edgeR package was used to calculate the normalized expression
Genome_build: mm10
Supplementary_files_format_and_content: tab

growth_protocol: ES-E14TG2a cells were cultured with medium consisted of DMEM (Gibco, Cat. # 11995) with 15% FBS (Sigma, Cat. #F6178), 1000 U/ml mouse leukemia inhibitory factor (Millipore, Cat. #ESG1107), 0.1 mM non-essential amino acids (Gibco, Cat. # 11140), 0.1mM β-mercaptoethanol (Gibco, Cat. #  21986023), 1 mM Glutamine-max (Gibco, Cat. # 25030), 1 mM sodium pyruvate (Gibco, Cat. # 11360)) and penicillin/streptomycin (100 U/ml) (Gibco, Cat, #15140).

extract_protocol:
Cellular RNA and DNA was harvested using Qiagen Allprep RNA/DNA mini kit (Qiagen, Cat 80204).
The bulk RNA-seq library was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Cat E7420S).

treatment_protocol: Doxycycline is added to induce Dux transgene.

tag: manipulation

tag: dux induction

value: Yes

tag: line


title: bulk RNA_D4 2C- cells Rep1


title: bulk RNA_sgGFP cells Rep2

value: sgGFP


title: bulk RNA_sgGFP cells Rep1


title: bulk RNA_D4 2C- cells Rep2


title: 1055G3AMR-Heart


title: BE2C THZ1 lapatinib combo treatment

source_name: BE(2)-C cells, treated with THZ1 and lapatinib combination


title: 1051G3AMS-Heart


title: 10x 24H collected cells from 2C+ cells

data_processing:
Quantification: Quantification was done in two steps: 1) For gene expression, we directly quantified using cellranger (v.13.1). The “cellranger  mkfastq” command was used to demultiplex the different samples and the “cellranger count” command was used to generate the gene-per-cell expression matrices for each sample by aligning the reads to the mm10 genome and quantifying expression of the Ensembl genes (GRCm38.93).
To quantify the expression of repeats we used the same pseudogenome reference created for RNA-seq analysis (Fu et al,2019). First, the “cellranger mkref” command was to create a custom 10x pseudogenome reference. Next, using a custom python script we extracted all the reads that do not map to any known gene (reads not having the GX or the AN tag). Then, “cellranger count” command was used to generate the repeat-per-cell expression matrices for each sample. The raw cell counts of repeats and genes were merged together.
to distinguish between valid cells and empty-droplets we used the emptyDrops function from the DropletUtils R/Bioconductor package
the scran package was then used to normalize the counts. First, the quickCluster method with parameter min.size=50 was called to cluster similar cells based on their rank correlations, then, we computed the size factors using the computeSumFactors function and finally we normalized the counts by calling the normalize function from the scater package
Analysis: Seurat R package (v3) was then used to load and pool all the dataset together. We filtered out cells with <800 detected transcripts and cells in which the mitochondrial transcriptome occupies >10% of the total transcripts. Genes expressed in less than 3 cells were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: tab

extract_protocol:
Cellular RNA and DNA was harvested using Qiagen Allprep RNA/DNA mini kit (Qiagen, Cat 80204).
The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer. 2C-like cells were sorted and keep cultured for 24 hours before harvested for single-cell RNA-seq.

treatment_protocol: Doxycycline is added to induce Dux transgene. 10.1126/science.1247005".


title: 1052G3AMS-Heart


title: bulk RNA_sgSmg7 cells Rep1


title: 1064G3BMS-Heart


title: bulk RNA_D2 2C+ cells Rep1


title: bulk RNA_D2 2C+ cells Rep2


title: 1049G3AMS-Heart


title: 1050G3AMS-Heart


title: bulk RNA_D2 2C- cells Rep2


title: Serum Con A EVs/Con A #3

value: BALB/c


title: bulk RNA_D2 2C- cells Rep1


title: bell_CLIP-seq_rep2

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

data_processing:
A preprocessing of the CLIP libraries involving adapter removal, filtering of reads according to their quality (MAPQ score>15) and collapsing of reads with exact matching sequences were performed using bioinformatics tools that based on Galaxy framework (Afgan et al., 2018).
The reads surviving preprocessing stage were mapped on the last assembly of Drosophila melanogaster genome dm6 (UCSC Genome Browser, https://genome.ucsc.edu/) using Bowtie 2 (Langmead et al., 2009). Reads were mapped allowing unique hits and up to 2 mismatches.
Peak calling to determine specific signals over background reads were performed using Piranha program (Uren et al., 2012) by zero-truncated negative binomial likelihoods method. The whole Drosophila genome was split into 30 nt intervals (bins) and coverage in these windows was counted for maximum coverage greater than or equal to the 0.87 cut-off (selection conditions p>0.87, bin=30 nt).
Pearson’s correlation analysis for comparison of CLIP1 and CLIP2 libraries was performed using Libre office software.
Genome_build: dm6
Supplementary_files_format_and_content: Peak_calling_piranha.xlsx

organism: Drosophila melanogaster

source_name: testes

extract_protocol:
Freshly dissected testes of 0-3 day yw males (500 pairs per one library) were cross-linked on ice with UV radiation (254 nm) three times at 600 mJ/cm2 in the presence of 200 mkl cold PBS (in 1 cm2 glass dish). Testes were transferred in 1.7-ml polypropylene microcentrifuge tubes and pelleted at 300g at 4°C. Supernatant solution over the organs was carefully removed by a tip and cross-linked material was stored at -70°C until further use. Cells lysates were obtained using pre-chilled Dounce homogenizer on ice in a cold lysis buffer containing (50 mM Tris-HCl, pH 8.0, 200 mM NaCl, 2 mM MgCl2, 1 mM DTT, 0.5% Nonidet P-40 (NP-40), in the presence of protease and phosphatase inhibitors (Sigma) in DEPC-treated water and Ribolock (Thermo Fisher Scientific)) by two series from 15 strokes of B pestle with 1-2 min incubation between series. The lysates were transferred in 1.7-ml polypropylene microcentrifuge tubes and were treated by RQ1 RNase-Free DNase (Promega) 40U/ml during 10 min at 37°C with vortexing. To generate RNA fragments of appropriate length we treated our lysates by RNAse A 7 min at 37°C. Immediately after that the lysates were supplemented by Ribolock (Thermo Fisher Scientific). The lysates were centrifuged at 13,200 rpm at 4°C for 20 min. Supernatants were transferred in new tubes and diluted to protein concentration of 8-10 mg/ml with lysis buffer containing (50 mM Tris-HCl, pH 8.0, 200 mM NaCl, 2 mM MgCl2, 1 mM DTT, 0.5% Nonidet P-40, protease and phosphatase inhibitors (Sigma), Ribolock (Thermo Fisher Scientific). We used 150 mkl mixed 50%-slurry of anti-mouse IgG beads (Invitrogen) for each tube of cross-linked lysate. Beads were previously washed two times with 500 µl cold phosphate-buffered saline (PBS) supplied by Tween 20 (1 × PBS, 0.1% Tween 20 (PBST)) and incubated with 8 mkl anti-Belle antibodies (described in Kotov et al., 2016) for CLIP library preparations or 8 mkl normal mouse serum for negative control in 200 mkl PBST during 20 min at room temperature on the rotator. Antibody-coated beads were washed and pre-equilibrated with lysis buffer. Then clariﬁed lysates were added to the experimental and control tubes. After incubation during 40 min at RT on the rotator washing was performed four times with 1 ml washing buffer NT2 (50 mM Tris–HCl, pH 8.0; 300 mM NaCl; 1 mM MgCl2; 1 mM DTT; 0.05% NP-40) and once with 200 mkl (without Ribolock). The beads were pre-equilibrated with buffer for T4 RNA ligase 2 truncated (NEB). Dephosphorylating of RNA 3’-ends were performed on-bead by Calf Intestinal Alkaline Phosphatase (Roche) 1U/mkl during 10 min at 37°C with frequent agitation. After that the beads were washed by 1 ml NT2 buffer with Ribolock two times. Previously pre-adenylated 3’-adapter (5’DNA Adenylated kit (NEB) was used for preparation) was ligated with RNAs on-bead by T4 RNA ligase2 (NEB) 400 U in 30 mkl of ligation reaction 2 h at 25°C on the thermal mixer. The beads were washed three times by 1 ml NT2 buffer with Ribolock. 5’-end RNA labeling was done by treating samples with 4 µl PNK enzyme (10 U/mkl; NEB), 1× PNK B buffer (NEB) and 2 µl γ32P-ATP (10 mCi/ml) 10 min at 37°C with mixing at 1000 rpm 15 s after each 3 min period of incubation. After that 10 µl cold 1 mM ATP was added to the beads and incubation was continued for 5 min. Beads were washed three times with NT2 buffer. Belle-RNA complexes were eluted with 30 µl 2x sample buffer supplemented by 200 mM DTT 5 min at 70°C, and complexes were resolved in 8% Bis-Tris gels using MOPS-based running buffer (50 mM MOPS, 50 mM Tris base, 1 mM EDTA, 0.1% SDS, DEPC-treated water). Complexes were transferred from gel into nitrocellulose membrane (S&S BA-85). The membrane was exposed to storage phosphor screen for 1–2 h. Storage phosphor screen was scanned using Typhoon imager (GE Healthcare), and image was obtained. Fragments of membrane containing the main radioactive signals higher 85 kDa were cut, fragmented with a clean scalpel blade, transferred in tubes and incubated with 100 mkl proteinase K solution (4 mg/ml proteinase K dissolved in buffer PK (100 mM Tris-HCl, pH 7.5, 10 mM EDTA and 50 mM NaCl) for 20 min at 37°C with agitation at 1000 rpm. After that 100 mkl PK/7M-urea buffer were added to each tube and they were incubated more 20 min at 37°C at 1000 rpm. Then 200 mkl Trisol LS (Invitrogene) for RNA isolation and 200 mkl chloroform were added to each tube and they were mixed strongly 30 s. After incubation 5 min at 4°C tubes were centrifuged at 13 000 g and 4°C for 10 min. Upper phases were transferred in new microcentrifuge tubes and pelleted in a presence of 300 mM sodium acetate, 1 mkl glycoblue (from stock 15 mg/ml, Thermo Fisher Scientific) and 2.5x volume of EtOH overnight at -20°C.
Ligation of 5’-adapter RA5 was performed using 1 mkl T4 RNA ligase (NEB) in manufacturer’s buffer supplemented by 1mM ATP solution 2h at 37°C with subsequent precipitation. Complementary DNA (cDNA) libraries were prepared after reverse transcription (SuperScript™ III Reverse Transcriptase kit (Thermo Scientific Fisher)) and subsequent PCR tests for optimal amplification with forward RP1 primer and reverse Illumina index primer and HS-Taq DNA pol (Thermo Fisher Scientific).

value: testes


title: bell_CLIP-seq_rep1


title: bulk RNA_D1 2C+ cells Rep2


title: stainless

city: Annandale

first: Aaron

middle: Alexander

last: Jones

state: NJ

address: 1545 Route 22 East

institute: ExxonMobil Research and Engineering

data_processing:
Raw cDNA reads were aligned end-to-end using Bowtie 2 version 2.2.9 against the reference genome of H. congolense WG6 (GenBank: GCA_900111505.1; WGS: FOHM01) with parameters (-D 20 -R 3 -N 0 -L 20 -I S,1,0.50) equivalent to the very sensitive pre-set and allowing for concordant alignment of paired-end with larger gaps.
Cuffquant (version 2.2.1), with option --multi-read-correct, was used to obtain the read counts (FPKM) for each replicate.
Cufflinks (Version 2.2.1) with options --multi-read-correct and --frag-bias-correct was used to combine and normalize the read counts (geometric) and evaluate the differentially expressed genes.
A BLASTp search of all H. congolense coding sequences was conducted against all known sporulation genes and were considered as Homologous Protein sequences when they had an E-value <1x10-3, an identity >30%, and a bit score >50 (Pearson).
Genome_build: GCA_900111505.1
Supplementary_files_format_and_content: Tab-delimited text file including FPKM values for each sample_mean, fold change comparisons between each sample,  the annotations, and uniprot hits.

organism: Halanaerobium congolense

source_name: Biofilm on stainless steel surface

growth_protocol: Grown in an anaerobic CDC biofilm reactor at 20C in once-flow-through configuration at 1 ml/min flow of 15% NaCl mineral media with 20mM  glucose and 20mM sodium thiosulfate

extract_protocol:
whole biofilm coupons transferred to RNA later (Ambion) frozen at -80C, shipped to Geneqiz LLC (South Plainfiled, NJ, USA where RNA was isolated, cDNA libraries were constructed, purified, and sequenced on Illumina HiSeq 2500 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 8 weeks (Sampling Timepoint)

tag: surface type

value: Manufactured (stainless)

tag: sample type

value: Biofilm


title: 10x 2C+ 0H collected cells


title: polycarbonate-2

source_name: Biofilm on polycarbonate surface duplicate

value: Manufactured (polycarbonate)


title: bulk RNA_D1 2C+ cells Rep1


title: polycarbonate-1

source_name: Biofilm on polycarbonate surface


title: Y8

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Sample collection: GFP+MHCIICD11c+CD11b+Lineage-CD172a+CD24- cDC2 cells were flow sorted into lysis buffer for transcriptomic analysis

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Nextera transposase adapter sequence. They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.45.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
A log2RPM count quantitation was carried in SeqMonk (v1.45.0) using the RNA-Seq pipeline. The file is tab delimited and contains the following columns: (1) Gene (2) Chromosome; (3) Start; (4) End; (5) Strand (12-..) log2 RPM for each sample
Genome_build: GRCm38

source_name: Isolated from inguinal lymph node

extract_protocol:
mRNA was isolated from sorted GFP+MHCIICD11c+CD11b+Lineage-CD172a+CD24- cDC2 cells  using the SMART-SeqV4 Ultra-low input RNA kit (Takara-Clontech) and sorting 800 cells directly into lysis buffer.
cDNA libraries were subsequently generated using the Nextera XT DNA kit (Illumina).

tag: Sex

value: male

value: Isolated from inguinal lymph node

tag: markers


title: limestone-2

source_name: Biofilm on limestone surface duplicate

value: Natural (limestone)


title: limestone-1

source_name: Biofilm on limestone surface


title: glass-2

source_name: Biofilm on glass surface duplicate

value: Manufactured (glass)


title: Y7


title: glass-1

source_name: Biofilm on glass surface


title: Y6


title: feldspar-2

source_name: Biofilm on feldspar surface duplicate

value: Natural (feldspar)


title: Y5


title: basalt-1

source_name: Biofilm on basalt surface

value: Natural (basalt)


title: Y3


title: apatite-2

source_name: Biofilm on apatite surface duplicate

value: Natural (apatite)


title: p63 knockout Cdx2 transgene Mouse esophagus replicate 2

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

description: Biological replicate 2 of 3 p63 knockout Cdx2 transgene Mouse esophagus

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA

data_processing: Agilent Feature Extraction Software 9.1

source_name: Esophageal epithelium p63-/-;Cdx2 mouse

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color( Agilent p/n 5188-5340) according to the provided protocol.

growth_protocol: The mice were bred in-house to generate offsprings of proper genotypes.

extract_protocol: Total RNA was extracted from mouse esophageal tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen; Valencia, CA).

treatment_protocol: Mice were PCR-genotyped according to protocols provided by the original developers.

tag: genotype

value: p63-/-;Cdx2 mouse

tag: background strain

value: esophagus

value: epithelium

source_name: Agilent's Universal Mouse Reference RNA

tag: rna source

value: 11 mouse cell lines

value: Cultured cells


title: p63 knockout Cdx2 transgene Mouse esophagus replicate 1

description: Biological replicate 1 of 3 p63 knockout Cdx2 transgene Mouse esophagus

tag: tissue


title: p63 knockout Mouse esophagus replicate 2

description: Biological replicate 2 of 3 p63 knockout Mouse esophagus

source_name: Esophageal epithelium p63-/- mouse

value: p63-/- mouse


title: apatite-1

source_name: Biofilm on apatite surface

tag: strain

value: 8 weeks (Sampling Timepoint)


title: Y2


title: Wild type Mouse (Negative control) esophagus replicate 3

description: Biological replicate 3 of 4 wild type esophagus

source_name: Esophageal epithelium of C57BL/6J mouse

value: WT mouse


title: Pten(null)-Lkb1(wt)_PADC_2

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: RMA processing

source_name: Prostate tumor tissue from a Ptenpc-/- Lkb1pc+/+ mouse

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Total RNA was extracted from FFPE tissue using RNAstorm FFPE RNA extraction kit (Cell Data Sciences) according to the manufacturer's instructions.

value: Ptenpc-/- Lkb1pc+/+

tag: tumor type

value: Prostate tumor tissue

value: Prostate tumor tissue (FFPE)


title: 06_cbf1_CLIP_ctrl

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description: non-crosslinked sample

data_processing:
Quality and adapter trimming was performed using Cutadapt 1.17 (cutoff Phred score of 20 in NextSeq mode).
Reads >11 nt were aligned using READemption 0.4.5 and segemehl 0.2.0 (accuracy cutoff of 80%).
Normalization was performed by filtering positions with read counts <6 standard deviations from 0. The distribution ratios between the paired XL and ctrl samples presented a clear bimodal distribution representing the background and crosslink-enriched positions, which were separated by k-means clustering. Size factors were calculated from the background positions present across all replicates against a geometric mean pseudo-reference, as introduced in DESeq.
Peak calling was performed using PEAKachu 0.1.0 setting the maximum fragment size to 50 and using the previously calculated size factors.
Genome_build: NC_003028.3
Supplementary_files_format_and_content: wig files contain normalized coverage information from the CLIP-seq experiment

organism: Streptococcus pneumoniae

source_name: RNA fragments bound to Cbf1

extract_protocol:
Cells were either irradiated (XL) by UV light or not (ctrl). Following immunoprecipitation and trimming of the RNA bound to Cbf1, the RNA was radioactively labeled and the RNA-Cbf1 complexes were transferred to a membrane by western blotting. The RNA was then extracted from the membrane by digestion of the protein.
After ligation of 3' and 5' adapters, cDNA preparation was performed and the resulting cDNA was amplified by PCR. Fragments between 140-250 bp were size-selected from a gel and again amplified by PCR to obtain the final library.

tag: growth phase

value: Mid-exponential (OD 0.5)


title: O7

value: male

tag: cell type

value: Isolated from inguinal lymph node


title: 05_cbf1_CLIP_ctrl

description: non-crosslinked sample


title: p63 knockout Mouse esophagus replicate 1

description: Biological replicate 1 of 3 p63 knockout Mouse esophagus

tag: age


title: p63 knockout Mouse esophagus replicate 3

description: Biological replicate 3 of 3 p63 knockout Mouse esophagus


title: 04_cbf1_CLIP_ctrl

description: non-crosslinked sample


title: feldspar-1

source_name: Biofilm on feldspar surface

value: Natural (feldspar)

value: Biofilm


title: Pten(null)-Lkb1(wt)_PADC_4


title: basalt-2

source_name: Biofilm on basalt surface duplicate

value: Natural (basalt)


title: Wild type Mouse (Negative control) esophagus replicate 2

description: Biological replicate 2 of 4 wild type esophagus


title: 03_cbf1_CLIP_XL

description: crosslinked sample


title: O6

source_name: Isolated from inguinal lymph node


title: Pten(null)-Lkb1(wt)_PADC_5


title: Wild type Mouse (Negative control) esophagus replicate 4

description: Biological replicate 4 of 4 wild type esophagus


title: 01_cbf1_CLIP_XL

description: crosslinked sample


title: O5


title: Pten(null)-Lkb1(wt)_PADC_3


title: 2087G4BFS-Heart

source_name: Heart

tag: gender

value: F

tag: irradiated

value: FALSE


title: Pten(null)-Lkb1(wt)_PADC_1


title: Wild type Mouse (Negative control) esophagus replicate 1

description: Biological replicate 1 of 4 wild type esophagus

value: esophagus

value: epithelium


title: Pten(het)-Lkb1(null)_Late carcinoma_4

source_name: Late prostate tumor tissue from a Ptenpc+/- Lkb1pc-/- mouse

value: Ptenpc+/- Lkb1pc-/-

value: Late prostate tumor tissue


title: Pten(het)-Lkb1(null)_Late carcinoma_3


title: O4


title: Pten(het)-Lkb1(null)_Late carcinoma_2


title: Fraction_20

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.10 with Python 3.5.2 . Command line parameters: -q 20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Sequenced reads were mapped to NC_003028.3 Streptococcus pneumoniae TIGR4 genome using segemehl  version 0.2.0-418 with Python version: 3.6.5.  READemption tool version: 0.4.3 was used for this purpose. Command line parameter:  reademption  align -r  -a 95  -l 20 --fastq
Coverage files were generated using READemption tool version: 0.4.3. Command line parameter:  reademption  coverage
Genome_build: NC_003028.3
Supplementary_files_format_and_content: wig

source_name: Clarified whole cell lysate

extract_protocol:
Clarified lysates were centrifuged on a glycerol gradient, which was subsequently fractionated and the RNA extracted by P/C/I extraction. Input control was isolated using TRIzol reagent.
RNA was fragmented, and the 3' TruSeq adapter ligated to the 3' end. Following cDNA synthesis, the 5' TruSeq adapter was ligated to the 3' end and the resulting cDNA amplified by PCR.

value: wild type


title: Fraction_17


title: Fraction_18


title: Fraction_21P

description: Pellet of gradient


title: Fraction_16


title: Pten(het)-Lkb1(null)_Late carcinoma_1


title: O2


title: Fraction_15


title: 02_cbf1_CLIP_XL

description: crosslinked sample


title: Fraction_13


title: Fraction_11


title: Fraction_09


title: Fraction_10


title: Fraction_08


title: O3


title: Fraction_07


title: hIslets_IV_Artemether

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Human pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 4

data_processing:
Drop-seq data were processed using the Drop-seq Tools v1.12 software (Macosko lab). Briefly, each transcriptome Read2 was tagged with the cell barcode (bases 1 to 12) and unique molecular identifier (UMI) barcode (bases 13 to 20) obtained from Read1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.4.0 the mouse reference genome (Ensembl GRCh38 release). Cell barcodes were corrected for possible bead synthesis errors, allowing the removal of up to four bases using the DetectBeadSynthesisErrors tool from the Drop-seq Tools v1.12 software. Reads aligning to exons were tagged with the respective gene name, and counts of UMI-deduplicated reads per gene within each cell were used to build a digital gene expression matrix comprising all cells with transcript counts.
Genome_build: Human: GRCh38/h38
Supplementary_files_format_and_content: Reads.csv; Read counts
Supplementary_files_format_and_content: Metadata.tsv; Cell annotation

source_name: Pancreatic Islet cells

growth_protocol: Human islets were extracted cadaveric donors and shipped using the Islet Integrated Distribution Program (IIDP) Human islets were cultured in CMRL media supplemented with 10% FBS and 1X Glutamax, and mantained in culture at 37 C in a 5% CO2 humidified atmosphere.

extract_protocol:
Islet dissociation was performed by incubating the islets in accutase for 20 min at room temperature. Reaction was stopped by adding CMRL media with 10% FBS. The dissociated islets were filtered through a 40 µm filter to obtain a single-cell suspension.
Single-cell RNA-seq was performed using Drop-seq

treatment_protocol: Islets were treated with 10muM Artemether and DMSO as control for 72 hours.

tag: treatment

value: Artemether (10muM)

tag: time point

tag: replicate


title: hIslets_IV_DMSO

description: Human pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 4

value: DMSO (Control)


title: Fraction_06


title: Fraction_04


title: Fraction_05


title: Pten(het)-Lkb1(null)_Early carcinoma_2

source_name: Early prostate tumor tissue from a Ptenpc+/- Lkb1pc-/- mouse

value: Early prostate tumor tissue


title: Pten(het)-Lkb1(null)_Early carcinoma_4

value: Prostate tumor tissue (FFPE)


title: Fraction_14

value: Mid-exponential (OD 0.5)


title: Fraction_02


title: Fraction_01


title: Fraction_03


title: Fraction_12


title: Pten(het)-Lkb1(null)_Early carcinoma_1


title: Advillin_NG_ip_2

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: Actively translated mRNA

data_processing:
Library strategy: Ribo-Seq
Genome build: Ensembl Mus musculus release 91: GRCm38.p5 (GCA_000001635.7)

source_name: Immunoprecipitated ribosome-bound mRNA from the left and right nodose ganglion of Advillin:RiboTag mice

extract_protocol: The nodose ganglion, dorsal root ganglion, and celiac superior mesenteric ganglion were dissected into PBS with cycloheximide (0.2 mg/mL) (PBS/CHX). The RiboTag immunoprecipitation protocol (http://depts.washington.edu/mcklab/RiboTagIPprotocol2014.pdf)  was then followed with the following modifications: All samples were homogenized by hand with a dounce homogenizer in 2.5 mL supplemented homogenization buffer (changes per 2.5 mL: 50 µl Protease Inhibitor, 75 µl heparin (100 mg/mL stock), 25 µl SUPERase In RNase Inhibitor). Samples were then centrifuged for 10 minutes at 10,000 G, after which 800 µl of supernatant was removed and 5µL of anti-HA antibody (Abcam, ab9110) was added. For input samples, 40uL of supernatant was removed and 60uL of PicoPure lysis buffer was added. These input samples were then put at -80°C. Immunoprecipitated samples were kept rotating at 4°C with antibody for 1 hour. 200 µl of Thermo Protein magnetic A/G beads were washed with homogenization buffer, added to the sample, and kept rotating for 30 minutes at 4°C. The beads were washed four times with high-salt buffer and samples were eluted with 100 µl of PicoPure lysis buffer.  RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

value: Left and right nodose ganglion


title: Pten(het)-Lkb1(null)_Early carcinoma_3


title: Advillin_NG_ip_1

description: Actively translated mRNA


title: Fraction_00L

description: Input control


title: SNS_NG_ip_4

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from the left and right nodose ganglion of SNS:RiboTag mice


title: Nav1.8_NG_ip_2

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from the left and right nodose ganglion of Nav1.8:RiboTag mice


title: SNS_NG_ip_3

description: Actively translated mRNA


title: Nav1.8_NG_ip_1

description: Actively translated mRNA


title: Mut2_3

city: Bielefeld

first: Andreas

last: Albersmeier

address: Universitätsstr. 27

institute: Bielefeld University

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_Mut0_vs_Mut2.txt
DESeq2_results_WT2_vs_Mut2.txt

data_processing:
Bcl2fastq v1.8.4
Bowtie2
Visualization and Read count in ReadXplorer
DESeq2
Genome_build: NC_007181.1
Supplementary_files_format_and_content: Raw reads in table containing all samples; DESeq2 result tables for different comparisons; both result forms contain start/stop position of the gene

organism: Sulfolobus acidocaldarius

source_name: cell culture

growth_protocol: S. acidocaldarius strains MW001pyrEF+ (WT) and tfb3::pyrEF (Mut) were grown aerobically at 75°C in basal Brock media pH 3.5, supplemented with 0.1% (w/v) NZ-amine and 0.2% (w/v) dextrin

extract_protocol:
RNA isolation using TriZOL according to Hottes et al. 2004 (Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media)
Depletion of rRNA was performed using the Ribo-Zero rRNA Removal Kit (Bacteria) according to the manufacturerer's protocol with the following modifications: 1µg RNA and 90µl beads were used, 4µl of the ribbosomal removal solution were added to the mix, which had a final volume of 20µl. Libraries were prepared according to Illumina's instructions for TruSeq mRNA stranded samples, starting with resuspension of RNA in 17.5µl Fragment/Prime/Finish Mix after Ethanol precipitation. Libraries were sequenced on a HiSeq1500 in RAPID mode according to manufacturerer's protocol

treatment_protocol: For UV treatment, 10 ml of cultures of MW001pyrEF+ and tfb3::pyrEF (OD600 = 0.2-0.3) were transferred to a Petri dish and UV light exposure was carried out at 100 J/m2. After that, cultures were incubated at 75°C for 90 min

tag: timepoint

value: 90 minutes after UV-treatment

value: MW001 tbf3::pyrEF

value: tfb3 insertion mutant

value: biological replicate 3


title: SNS_NG_ip_2

description: Actively translated mRNA


title: CGSMG_Snap25_ip_GF_3

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from the celiac superior mesenteric ganglion of germ free Snap25:RiboTag mice

value: Celiac superior mesenteric ganglion


title: SNS_NG_ip_1

description: Actively translated mRNA


title: Mut1_2

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_Mut0_vs_Mut1.txt
DESeq2_results_WT1_vs_Mut1.txt

value: 45 minutes after UV-treatment

value: biological replicate 2


title: Mut1_1

value: biological replicate 1


title: CGSMG_Snap25_ip_GF_1

description: Actively translated mRNA


title: CGSMG_Snap25_ip_GF_2

description: Actively translated mRNA


title: Mut0_3

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_Mut0_vs_Mut1.txt
DESeq2_results_Mut0_vs_Mut2.txt
DESeq2_results_WT0_vs_Mut0.txt

value: before UV-treatment


title: Mut1_3


title: Plasma_MCI_005

city: Shanghai

first: Haining

last: He

address: 600 South Wan Ping Road

department: Department of Geriatric Psychiatry

institute: Shanghai Mental Health Center

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual. (1) The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. (2) Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). (3) Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: plasma

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: (1) 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. (2) The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. (3) Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: [sample collection protocol]  Blood samples of all participants were collected after fasting for 12 hours. Then plasma was separated by centrifugation at 3,000 rpm for 20 minutes at 4C.

value: Male

tag: educational year

tag: moca

tag: diagnosis

value: Mild cognitive impairment due to Alzheimer's disease

value: plasma


title: Plasma_MCI_003


title: Plasma_MCI_006


title: Plasma_MCI_007

value: Female


title: Plasma_NC_3437

value: Normal Aging


title: Mut2_2

tag: genotype


title: Plasma_MCI_002


title: Mut0_2


title: CGSMG_Snap25_ip_SPF_2

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from the celiac superior mesenteric ganglion of specific pathogen free Snap25:RiboTag mice


title: Mut2_1


title: Mut0_1


title: CGSMG_Snap25_ip_SPF_3

description: Actively translated mRNA


title: WT2_3

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_WT0_vs_WT2.txt
DESeq2_results_WT2_vs_Mut2.txt

value: WT


title: CGSMG_Snap25_ip_SPF_1

description: Actively translated mRNA


title: Plasma_NC_5952


title: WT2_2


title: DN-sorted CD8+#3 [001-012]

city: Amsterdam

first: Monika

middle: C

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood foundation

description:
rRNA depletion; DN3 (001-012)
HHMLTBBXX_103001-001-012_GCGTTAGA_L008
HHNGYBBXX_103001-001-012_GCGTTAGA_L001

data_processing:
Fastq quality was assessed with FastQC version 0.11.7
Reads were aligned with STAR version 2.5.0a on the human genome hg38-release 92 from ENSEMBL. STAR was also used to count reads per genes.
Read counts were complied in one table with R + RStudio.
Genome_build: Ensembl human genome hg38-release 92
Supplementary_files_format_and_content: Raw reads are in fastq format. Read counts are raw read counts.

source_name: DN-sorted CD8+

growth_protocol: T cells were activated with 10ng/mL PMA/1µM Ionomycin (Sigma-Aldrich) for 4h in the presence of 1:1000 monensin (eBioscience). Cells were stained in sterile PBS for 30min at 4°C with anti-CD8α (RPA-T8, BD) and Near-IR live-dead marker (ThermoFisher).

extract_protocol:
RNA was isolated with the RNAeasy-FFPE kit (Quiagen) according to the manufacturer’s protocol, omitting the steps directed at deparaffinization. RNA was resuspended in RNAse-free water.
Sequencing was performed with FFPE-library preparation (GenomeScan, Leiden, the Netherlands), including Ribosomal RNA depletion with NEB Next rRNA depletion kit (NEB# E6310). Sequencing was performed on Illumina HiSeq 4000, with an average depth of 21 million paired-end 150nt (PE150) reads.

treatment_protocol: Intracellular cytokine staining (ICCS) was performed with CytoFix-CytoPerm kit (BD) according to the manufacturer’s protocol, adjusted as follows: Prior to use, CytoFIX was pre-incubated on ice for 2min with 40IU/mL murine RNAse inhibitors (M0314, NEB). After 15min of incubation at 4°C, cells were washed 1x with 1x CytoPerm that was pre-incubated with 40IU/mL RNAse inhibitors Cells were then incubated in 1xCytoPerm (+ RNAse inhibitor) for 15 min at 4°C. Cells were washed and re-suspended in Sorting buffer (2xSSC: 300mM NaCl, 30mM sodium citrate, 80U/mL RNAse inhibitor). Antibodies directed against IL-2 (MQ1-17H12) and IFN-g (4S.B3) were incubated overnight in Sorting buffer at 4°C. Cells were washed once and re-suspended in Sorting buffer prior to FACS-sorting. IFNg/IL2-producers sorted cells were pelleted and frozen at -80°C until further use.

value: 40 pooled human CD8+ donors

value: CD8+ Lymphocytes

tag: cell subtype

value: IL2- IFNG- sorted activated CD8+


title: DP-sorted CD8+#3 [001-011]

description:
rRNA depletion; DP3 (001-011)
HHMLTBBXX_103001-001-011_GTCCTAAG_L008
HHNGYBBXX_103001-001-011_GTCCTAAG_L001

source_name: DP-sorted CD8+

tag: tissue

value: IL2+ IFNG+sorted activated CD8+


title: Plasma_NC_9012


title: Plasma_NC_3436


title: Plasma_NC_4066


title: IFNG-sorted CD8+#3 [001-010]

description:
rRNA depletion; IFNG3 (001-010)
HHMLTBBXX_103001-001-010_CTCAGAAG_L008
HHNGYBBXX_103001-001-010_CTCAGAAG_L001

source_name: IFNG-sorted CD8+

value: IL2- FNG+ sorted activated CD8+


title: WT2_1

value: 90 minutes after UV-treatment

tag: strain


title: IL2-sorted CD8+#3 [001-009]

description:
rRNA depletion; IL23 (001-009)
HHMLTBBXX_103001-001-009_GCAATTCC_L008
HHNGYBBXX_103001-001-009_GCAATTCC_L001

source_name: IL2-sorted CD8+

value: IL2+ IFNG- sorted activated CD8+


title: WT1_3

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_WT0_vs_WT1.txt
DESeq2_results_WT1_vs_Mut1.txt

value: 45 minutes after UV-treatment

value: biological replicate 3


title: DN-sorted CD8+#2 [001-008]

description:
rRNA depletion; DN2 (001-008)
HHMLTBBXX_103001-001-008_TCTACGCA_L008
HHNGYBBXX_103001-001-008_TCTACGCA_L001


title: WT1_2

value: biological replicate 2


title: WT1_1

value: biological replicate 1


title: DP-sorted CD8+#2 [001-007]

description:
rRNA depletion; DP2 (001-007)
HHMLTBBXX_103001-001-007_GAGAGTAC_L008
HHNGYBBXX_103001-001-007_GAGAGTAC_L001


title: WT0_3

description:
processed data files:
Raw_reads_all_samples.txt
DESeq2_results_WT0_vs_WT1.txt
DESeq2_results_WT0_vs_WT2.txt
DESeq2_results_WT0_vs_Mut0.txt

value: before UV-treatment


title: IL2-sorted CD8+#2 [001-005]

description:
rRNA depletion; IL22 (001-005)
HHMLTBBXX_103001-001-005_TCGGATTC_L008
HHNGYBBXX_103001-001-005_TCGGATTC_L001


title: DRG_Snap25_ip_GF_3

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from thoracic 9 dorsal root ganglion of germ free Snap25:RiboTag mice

value: Dorsal root ganglion thoracic 9


title: IFNG-sorted CD8+#2 [001-006]

description:
rRNA depletion; IFNG2 (001-006)
HHMLTBBXX_103001-001-006_CTGTACCA_L008
HHNGYBBXX_103001-001-006_CTGTACCA_L001


title: DN-sorted CD8+#1 [001-004]

description:
rRNA depletion; DN1 (001-004)
HHMLTBBXX_103001-001-004_GGAAGAGA_L008
HHNGYBBXX_103001-001-004_GGAAGAGA_L001


title: WT0_2


title: WT0_1


title: Fraction_19

value: Mid-exponential (OD 0.5)

value: wild type


title: DRG_Snap25_ip_GF_1

description: Actively translated mRNA


title: DP-sorted CD8+#1 [001-003]

description:
rRNA depletion; DP1  (001-003)
HHMLTBBXX_103001-001-003_CGAATTGC_L008
HHNGYBBXX_103001-001-003_CGAATTGC_L001


title: IFNG-sorted CD8+#1 [001-002]

description:
rRNA depletion; IFNG1  (001-002)
HHMLTBBXX_103001-001-002_GAACGAAG_L008
HHNGYBBXX_103001-001-002_GAACGAAG_L001


title: DRG_Snap25_ip_SPF_2

description: Actively translated mRNA

source_name: Immunoprecipitated ribosome-bound mRNA from thoracic 9 dorsal root ganglion of specific pathogen free Snap25:RiboTag mice


title: DRG_Snap25_ip_GF_2

description: Actively translated mRNA


title: DRG_Snap25_ip_SPF_1

description: Actively translated mRNA


title: PBS_IEC-3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and were pre-processed with trimmomatic (v0.28) to remove low quality base calls, reads with an 'N' base call and adapter sequences
reads wre mapped to the reference genome (mm10) with the the hisat2 aligner (v2.1.0) and using splice site information from the ensembl 95 version of the structural annotation (parameters for hisat2: --known-splicesite-infile Mouse_E95.splices --rna-strandness R -p 4)
read counts per gene were determined with the featurecounts software (v1.6.1; "-Q 10 --primary -T 3")
differential gene expression was determined with de DESeq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited tekst file containing raw abundance measurements (output from featureCounts)

source_name: intestinal epithelial cells

extract_protocol:
Total RNA was extracted with the Aurum total RNA mini kit (732-6820, Biorad) according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 450 µg LPS or PBS for 6 hours


title: N_OsbHLH044_crl1OE ; biological repetition 2 [67.5.13.4_rep2]

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

description: Gene expression data from stem base

hyb_protocol: Following fragmentation and biotin end labeling, 4 ug of cDNA were hybridized for 20 hr at 48°C on the Affymetrix® Rice Gene 1.1ST Jp Array. Strip arrays were washed and stained on the fluidic station of the Affymetrix GeneAtlas system using Hybridization Wash & Stain kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: Data were generated with Affymetrix Epression Console v 1.4.1 and RMA algorithm.

label: biotin

organism: Oryza sativa Japonica Group

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.5.13.4, repetition 2

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

growth_protocol: Oryza sativa L. cv. Taichung 65 crl1 mutant (Inukai et al., 2005)  overexpressing the bHLH044 gene (OsbHLH044_crl1OE) lines and nul segregant sister lines without t-DNA (N_OsbHLH044_crl1OE_67.5.13.4) were used used. Seeds of transgenic lines were hulled and disinfected by incubation for 3 min in ethanol 70%, then 90 min in 3.8% sodium hypochlorite solution containing 1% (v/v) of Tween80 and finally quadruple rinsed in milli-Q water. Disinfected hulled seeds were sown in petri dishes (ref. 82.1473.001, Starstedt, Nümbrecht, Germany) containing a filter pad (ref. 1001-090, Whatman paper, GE Healthcare, Buckinghamshire, UK) wet with 15 mL MS/2 medium, including Gamborg B5 vitamin (Duchefa M0231, Duchefa Biochemie B.V., Haarlem, The Nederlands) and placed in culture chambers at 27°C, 70% relative humidity, and 14 hours daylight regime. After 5 days, the plantlets were transferred into 250 mL wide-collar Erlenmeyer flasks containing 30 mL MS/2 medium, including Gamborg B5 vitamin (Duchefa M0231, Duchefa Biochemie B.V., Haarlem, The Nederlands) for 24 h. The experiment was repeated independently three times with two independant couple of OsbHLH044 overexpression lines and its null segregant sister lines. For each biological replicate, ten to fifteen stem bases were collected and immediately frozen in liquid nitrogen. After grounding 8~12 stem bases in liquid nitrogen using a TissueLyser II tissue disruption system (Qiagen, Venlo, the Netherlands) with 3 mm steel beads for 15 sec at 30 Hz, RNA were extracted using the Plant RNeasy Kit (Qiagen 74904, Qiagen, Venlo, the Netherlands) in presence of DNAse I treatment (Qiagen 79254 , Qiagen, Venlo, the Netherlands) using a purification column according manufacturer’s instructions. RNA were quantified at 260 nm with a ND-1000 spectrophotometer (Thermo-Fisher, Waltham, MA, USA).

extract_protocol: 8~12 stem bases of each transgenic lines were grounded in liquid nitrogen to perform RNA extractions, that correspond to one independent repetition of the experiment. In total 3 x (8~12) stem bases were processed that corespond to three intependant repetition of the experiment. RNA were extracted using the Plant RNeasy Kit (Qiagen 74904, Qiagen, Venlo, the Netherlands).

treatment_protocol: Stem bases were harvested and immediately frozen in liquid nitrogen.

value: stem base


title: N_OsbHLH044_crl1OE ; biological repetition 3 [67.5.13.4_rep3]

description: Gene expression data from stem base

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.5.13.4, repetition 3


title: PBS_IEC-2


title: OsbHLH044_crl1OE ; biological repetition 1 [67.5.9.12_rep1]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.5.9.12, repetition 1


title: OsbHLH044_crl1OE ; biological repetition 3 [67.1.11.7_rep3]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.1.11.7, repetition 3


title: OsbHLH044_crl1OE ; biological repetition 3 [67.5.9.12_rep3]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.5.9.12, repetition 3


title: OsbHLH044_crl1OE ; biological repetition 2 [67.5.9.12_rep2]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.5.9.12, repetition 2


title: pin1∆ rep3

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v2.28) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/OLD/20150909/Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; DESeq2 file for comparison of pin1∆ mutant with WT

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: S. pombe

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: N_OsbHLH044_crl1OE ; biological repetition 1 [67.5.13.4_rep1]

description: Gene expression data from stem base

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.5.13.4, repetition 1


title: pin1∆ rep2


title: IL2-sorted CD8+#1 [001-001]

description:
rRNA depletion; IL21 (001-001)
HHMLTBBXX_103001-001-001_TTGCGAGA_L008
HHNGYBBXX_103001-001-001_TTGCGAGA_L001

value: 40 pooled human CD8+ donors

tag: cell type

value: CD8+ Lymphocytes


title: pin1∆ rep1


title: PBS_IEC-1

tag: age


title: LPS_IEC-3


title: OsbHLH044_crl1OE ; biological repetition 2 [67.1.11.7_rep2]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.1.11.7, repetition 2


title: LPS_IEC-2


title: Glucose rep3

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114 ST and 87 AVE

department: Medical Microbiology and Immunology

institute: University of Alberta

data_processing:
Base calls performed using Cyberduck(FTP).
FASTQC was used to evaluate the quality of raw paired-end sequencing reads.
Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic.
Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0).
The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR.
In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample, and differentially expressed genes

source_name: Whole fly

growth_protocol: Flies were raised on standard cornmeal at 25˚C before eclosion.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. 5 whole flies were used per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Adult male flies were raised on either unmodified or glucose-enriched (50 g/L) holidic food for 20 days at 25˚C.

value: whole fly

tag: food

value: glucose-enriched holidic


title: Glucose rep2


title: ISLR_2

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: xls file includes TPM values for each Sample.

source_name: HEK293FT cells

growth_protocol: Cells were incubated with DMEM medium with 10% FBS in CO2 incubators at 37℃.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treat with ISLR secreted supernatant or empty vector control supernatant for 72 hours

value: embryonal kidney cells

tag: agent

value: ISLR

tag: cell line


title: ISLR_3


title: LPS_IEC-1


title: N_OsbHLH044_crl1OE ; biological repetition 3 [67.1.1.5_rep3]

description: Gene expression data from stem base

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.1.1.5, repetition 3


title: ISLR_1


title: Glucose rep1


title: NC_3

value: empty vector control


title: OsbHLH044_crl1OE ; biological repetition 1 [67.1.11.7_rep1]

description: Gene expression data from stem base

source_name: Rice stem base from overexpressing bHLH044 lines, line OsbHLH044_crl1OE_67.1.11.7, repetition 1


title: NC_2


title: Unmodified rep3

value: unmodified holidic


title: Unmodified rep2


title: Unmodified rep1


title: Specimen-T4

status: Public on Mar 19 2020

city: Hengyang

first: Zhifeng

last: Liu

state: Hunan

address: 69# Chuanshan Road, Shigu District Hengyang, Hunan

institute: The First Affiliated Hospital of University of South China

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)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: circRNA abundance measurements

source_name: Nasopharynx

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand

tag: gender

value: Female

value: Nasopharyngeal carcinoma

tag: tnm stage


title: Specimen-T2

value: Male


title: Specimen-T1


title: NC_1


title: Specimen-N2

value: Nasopharyngitis tissue


title: Specimen-N4


title: Specimen-T3


title: Specimen-N1


title: Tbx6 30d

city: Tokyo

first: SHO

last: HAGINIWA

address: 5 Shinanomachi, Shinjuku-ku

department: Cardiology

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: Raw data were processed with Affymetrix Expression Console software version 1.4 for normalization.

source_name: introduction of Tbx6 into neonatal heart after 30 days

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual,  Affymetrix).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Eight-week-old male and female ICR (Jcl:ICR) mice were purchased from CLEA Japan (Tokyo, Japan). For subcutaneous injection, neonatal mice (P1) were anesthetized with isoflurane, and 5 μl of vector preparation (5x1010 viral genome particles per animal) or PBS was injected under the dorsal skin. The hearts were collected 7 and 30 days after injection.

extract_protocol: RNA was extracted from Heart　that introduction of PBS into neonatal heart after 7days, introduction of Tbx6 into neonatal heart after 7days, introduction of PBS into neonatal heart after 30days,and introduction of Tbx6 into neonatal heart after 30days  using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012) quantified using a NanoDrop-2000c spectrophotometer. Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: heart

tag: treatment

value: ICR (Jcl:ICR)


title: PBS 30d

source_name: introduction of PBS into neonatal heart after 30 days


title: N_OsbHLH044_crl1OE ; biological repetition 2 [67.1.1.5_rep2]

description: Gene expression data from stem base

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.1.1.5, repetition 2

value: stem base


title: hIslets_III_DMSO2_36hr

description: Human pancreatic islet cells, treated with DMSO (Control) for 36hr, replicate: 3

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.1.0).
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: Human: GRCh38/h38, Mouse: mm10
Supplementary_files_format_and_content: Matrices: corrected transcript per million (TPM) matrices. Data in mtx format, row names (genes), and column names (barcodes)
Supplementary_files_format_and_content: CellAnnotation_final.tsv; Annotation of cell types to barcodes

source_name: Pancreatic Islet cells

growth_protocol: Human islets were extracted cadaveric donors and shipped using the Islet Integrated Distribution Program (IIDP) Mouse islets were extracted and shipped from the Collombat laboratory. Both human and mouse islets were cultured in CMRL media supplemented with 10% FBS and 1X Glutamax, and mantained in culture at 37 C in a 5% CO2 humidified atmosphere.

extract_protocol:
Islet dissociation was performed by incubating the islets in accutase for 20 min at room temperature. Reaction was stopped by adding CMRL media with 10% FBS. The dissociated islets were filtered through a 40 µm filter to obtain a single-cell suspension.
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Islets were treated with 10muM Artemether, 100 muM GABA, 10 muM FoxO inhibitor and DMSO as control for 36 and 72 hours.

value: Pancreatic Islet cells

value: DMSO (Control)

tag: treatment time

tag: replicate


title: hIslets_III_DMSO1_72hr

description: Human pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 3


title: hIslets_III_DMSO2_72hr


title: hIslets_III_DMSO3_72hr


title: hIslets_III_DMSO1_36hr


title: Tbx6 7d

source_name: introduction of Tbx6 into neonatal heart after 7 days


title: hIslets_III_A3_72hr

description: Human pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 3

value: Artemether (10muM)


title: hIslets_III_A2_72hr


title: hIslets_III_A1_72hr


title: Specimen-N3


title: hIslets_III_A1_36hr

description: Human pancreatic islet cells, treated with Artemether (10muM) for 36hr, replicate: 3


title: hIslets_II_GABA

description: Human pancreatic islet cells, treated with GABA(100muM) for 72hr, replicate: 2


title: hIslets_II_A2

description: Human pancreatic islet cells, treated with Artemether (Sigma, 10muM) for 72hr, replicate: 2

value: Artemether (Sigma, 10muM)


title: hIslets_II_DMSO

description: Human pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 2


title: hIslets_I_FoxO

description: Human pancreatic islet cells, treated with FOXO inhibitor(10muM) for 72hr, replicate: 1

value: FOXO inhibitor(10muM)


title: hIslets_I_GABA

description: Human pancreatic islet cells, treated with GABA (100muM) for 72hr, replicate: 1

value: GABA (100muM)


title: PBS 7d

source_name: introduction of PBS into neonatal heart after 7 days


title: patient_diagnosis

type: genomic

city: Lublin

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

description: sample collected at the time of diagnosis

hyb_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

data_processing:
To calculate the copy number of altered regions, the data were normalized to baseline reference intensities using NA 32.3 FFPE v.2 reference model (Affymetrix). The hidden Markov model available within the software package was used to determine the copy number states (CN) and their breakpoints. Thresholds of log 2 ratio ≥0.58 and ≤1 were used to categorize altered regions as CN variation (CNV) gains (amplifications) and copy number losses (deletions), respectively. To prevent the detection of false-positive CNVs arising due to microarray unspecific signals, only regions that involved at least 50 consecutive probes were considered in the analysis of gains or losses in this study. Amplificationsand deletions were analyzed separately. To exclude aberrations representing common normal CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). To identify the genes involved in the CNVs further, the UCSC database ( http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org) were used.
Gene annotation and gene overlap were determined using the human genome build 19 and NetAffx (http://www.affymetrix.com).The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukaemia-associated region/gene-specific CNAs (leukaemia genes_all_20150505; Fullerton Overlap Map_hg19).

source_name: bone marrow

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

extract_protocol: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

value: bone marrow

value: female


title: hIslets_II_A1

description: Human pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 2


title: hIslets_I_DMSO

description: Human pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 1


title: N_OsbHLH044_crl1OE ; biological repetition 1 [67.1.1.5_rep1]

description: Gene expression data from stem base

source_name: Rice stem base from nul segregant sister lines of overexpressing bHLH044 lines, line N_OsbHLH044_crl1OE_67.1.1.5, repetition 1

tag: genotype


title: hIslets_III_A2_36hr


title: hIslets_II_FoxO

description: Human pancreatic islet cells, treated with FOXO inhibitor(10muM) for 72hr, replicate: 2


title: patient_relapse

description: sample collected at the time of relapse

scan_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

treatment_protocol: After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.


title: hIslets_I_A10

description: Human pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 1


title: X9166_Cer_BPD.FLY_P5_5

first: Richard

last: Gilbertson

address: Robinson way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

data_processing:
SE 50bp end reads aligned to GRCm38 with HISAT2 (default parameters)
Reads counted on annotated features with sub-reads featureCounts
Supplementary_files_format_and_content: raw counts

source_name: primary cerebella

extract_protocol:
Cerebella and Tumor samples were removed  flash frozen on dry ice. RNA was extraceted using Trizol reagent. Qiagen RNeasy Plus universal kit (Cat. # 73404) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sampletype

value: BPtchD-FLY

value: Cerebellum

tag: model

value: Shh


title: X7782_Cer_BPD.FLY_P5_3

tag: tissue


title: DMP022G20_Tum_BDCP.FLY_Implants_1

value: BDCP-FLY

value: TumorWntFLY

value: Implants

value: Wnt


title: DMP021R13_Tum_BCP_Implants_4

value: BCP

value: TumorWntNormal


title: DMP021R14_Tum_BCP_Implants_5


title: X51760_Cer_BPD.FLFL_P30_3

value: BPtchD-FLFL


title: X7604_Cer_BPD.FLFL_P13_4


title: X7311_Cer_BPD.FLFL_P13_5


title: X8458_Cer_BPD.FLFL_P5_3


title: DMP017B3_Tum_BDCP.FLY_Implants_5


title: X47062_Cer_BPD.FLY_P13_5


title: DMP015G19_Tum_BDCP.FLY_Implants_4


title: X47508_Tum_BPD.FLY_P30_3

value: TumorShhFLY


title: X46821_Cer_BP_P14_4

value: BPtch


title: X46316_Tum_BPD.FLPlus_P30_5

value: BPtchD-FLPlus

value: TumorShhFLPLUS


title: X46805_Cer_BPD.FLY_P13_3


title: X46798_Cer_BPD.FLPlus_P13_2


title: X4108P10_Cer_BPD.FLPlus_E16d5_1


title: X44305_Cer_BP_P5_1


title: DMP017B12_Tum_BDCP.FLY_Implants_2


title: X41010P1_Cer_BPD.FLPlus_E16d5_2


title: X7783_Cer_BPD.FLY_P5_4


title: X40007_Cer_BP_P13_5


title: X9165_Cer_BPD.FLFL_P5_4


title: X38385_Cer_BPD.FLY_P5_1


title: X38384_Cer_BPD.FLPlus_P5_1


title: X46311_Cer_BPD.FLPlus_P30_3


title: X38371_Cer_BP_P5_4


title: X32755_Cer_BP_P30_2


title: X34751_Cer_BPD.FLY_P30_4


title: X37858_Tum_BPD.FLY_P30_5


title: DMP022B1_Tum_BDCP.FLY_Implants_3


title: X31373_Cer_BPD.FLFL_P30_2


title: X31371_Tum_BP_P30_2

value: TumorShhNormal


title: X41010P5_Cer_BPD.FLPlus_E16d5_3


title: X31373P3_Cer_BPD.FLY_E16d5_2


title: X18773_Cer_BP_P30_1


title: X31373P2_Cer_BPD.FLY_E16d5_1


title: X34750_Tum_BP_P30_5


title: X38372_Cer_BP_P5_5


title: X18775_Cer_BP_P30_3


title: X21037_Tum_BPD.FLPlus_P30_3


title: X34748_Cer_BPD.FLPlus_P30_5


title: X18773P7_Cer_BP_E16d5_5


title: X18773P2_Cer_BP_E16d5_2


title: X18773P1_Cer_BP_E16d5_1


title: X14983_Cer_BPD.FLFL_P5_5


title: DMP22TQ20_Tum_BDCP.FLY_Implants_2


title: X13695_Cer_BPD.FLPlus_P5_4


title: X17489_Tum_BPD.FLPlus_P30_2


title: X14982_Cer_BPD.FLPlus_P5_5


title: DMP022G19_Tum_BDCP.FLY_Implants_3


title: X31373P9_Cer_BPD.FLFL_E16d5_4


title: X37858_Cer_BPD.FLY_P30_5


title: X31373P1_Cer_BPD.FLFL_E16d5_1


title: DMP022B2_Tum_BDCP.FLY_Implants_4


title: DMP022B3_Tum_BDCP.FLY_Implants_5


title: DMP021R12_Tum_BCP_Implants_3


title: DMP017B9_Tum_BDCP.FLY_Implants_1


title: DMP021R10_Tum_BCP_Implants_2


title: X47508_Cer_BPD.FLY_P30_1


title: X46804_Cer_BPD.FLY_P13_2


title: X47059_Tum_BPD.FLY_P30_2


title: X46809_Cer_BPD.FLY_P13_4


title: X9170_Cer_BP_P5_3


title: X46807_Cer_BP_P13_1


title: X46820_Cer_BP_P14_3


title: X47061_Cer_BPD.FLFL_P13_2


title: X7784_Cer_BPD.FLFL_P5_2


title: X457_Tum_BPD.FLY_P30_1


title: X44304_Cer_BPD.FLY_P5_2


title: X9168_Cer_BP_P5_2


title: X44302_Cer_BPD.FLPlus_P5_2


title: X4108P4_Cer_BPD.FLY_E16d5_5


title: X41010P2_Cer_BPD.FLFL_E16d5_5


title: X7781_Cer_BPD.FLFL_P5_1


title: X37044_Cer_BPD.FLFL_P30_1


title: X35318_Cer_BPD.FLY_P30_3


title: DMP021R9_Tum_BCP_Implants_1


title: X40008_Cer_BPD.FLY_P13_1


title: X40006_Cer_BPD.FLPlus_P13_1


title: X34752_Tum_BP_P30_3


title: X34749_Tum_BPD.FLY_P30_4


title: X31373P6_Cer_BPD.FLFL_E16d5_2


title: X8306_Cer_BP_P13_2


title: X31373P10_Cer_BPD.FLY_E16d5_4


title: X34752_Cer_BP_P30_4


title: X31373P7_Cer_BPD.FLFL_E16d5_3


title: X31374_Tum_BPD.FLPlus_P30_4


title: X31373P4_Cer_BPD.FLY_E16d5_3


title: X17490_Tum_BPD.FLPlus_P30_1


title: X18773P5_Cer_BP_E16d5_4


title: X31369_Cer_BPD.FLY_P30_2


title: X18775_Tum_BP_P30_1


title: X31371_Cer_BP_P30_5


title: X15787_Cer_BPD.FLFL_P13_1


title: X15588_Cer_BPD.FLPlus_P13_5


title: X15585_Cer_BPD.FLPlus_P13_3


title: X18773P3_Cer_BP_E16d5_3


title: X13504_Cer_BPD.FLPlus_P30_2


title: X13693_Cer_BPD.FLPlus_P5_3


title: X11693_Cer_BPD.FLPlus_P30_1


title: X15586_Cer_BPD.FLPlus_P13_4


title: X8726

value: BD-FLY


title: X9061

value: BDCP-FLFL


title: X9064

value: BDCP-FLPlus


title: X9065

value: Cerebellum


title: X8652

value: BD-FL-FL


title: X1381_Cer_BPD.FLFL_P13_3

value: Shh


title: X8309


title: X8302


title: X17488_Cer_BPD.FLPlus_P30_4


title: X8161

value: WT


title: X51393


title: X51378P8


title: X51378P7


title: X8299

value: BD-FLPlus


title: X5090


title: X51378P4


title: X50187


title: X50184P6

value: BDCP-FLY

value: Wnt


title: X8657


title: X48603P5


title: X50139


title: X21039_Tum_BP_P30_4


title: X51394


title: X48275P7


title: X48275P4


title: X47471


title: X47126P9


title: X47126P3

value: BCP


title: X43792


title: X4463


title: X50184P3


title: X47282


title: X47122


title: X37703


title: X35943


title: X48603P11


title: X32709


title: X38232


title: X32706


title: X27119


title: X27714


title: X26858


title: X25420


title: X24991


title: X50184P5


title: X24990


title: X47620A


title: X24993


title: X23603


title: X23605


title: X27716


title: X23156


title: X23157


title: X23239


title: X22827


title: X22579


title: X22369


title: X23155


title: X312P7


title: X21965


title: X22311


title: X21964


title: X21767


title: X25447


title: X20530


title: X19121


title: X20527


title: X19119


title: X19122


title: X14829


title: X18045


title: X18


title: X15091


title: X12564P8


title: X11714P8


title: X8639


title: X8727


title: X10464


title: X48275P5


title: X8306


title: X5260


title: X8297


title: X51826P8


title: X8638


title: X8298


title: X8307


title: X51378P6


title: X51828


title: X5258


title: X5089


title: X51029P2


title: X50184P7


title: X18556


title: Fmr1-KO 3

city: Worcester

first: Elisa

last: Donnard

state: MA

address: 368 Plantation St

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: Single-cell RNA-Seq

data_processing:
Sequencing reads were processed as previously described (Derr et al., 2016) and the pipeline is available through GitHub (github.com/garber-lab/inDrop_Processing). Briefly, fastq files were generated with bcl2fastq using parameters --use-bases-mask y58n*,y*,I*,y16n* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 --barcode-mismatches 1. Valid reads were extracted using the barcode information in R1 files (V2 bead version samples) or R3 files (V3.8 bead version samples). Read files R2 (V2 bead version samples) or R1 (V3.8 bead version samples) were aligned to the mm10 genome using TopHat v2.0.14 with default parameters and the reference transcriptome RefSeq v69.
Alignment files were filtered to contain only reads from cell barcodes with at least 1,000 aligned reads and were submitted through ESAT (github.com/garber-lab/ESAT) for gene-level quantification of unique molecule identifiers (UMIs) with parameters -wLen 100 -wOlap 50 -wExt 1000 -sigTest .01 -multimap ignore -scPrep. Finally, we identify and correct UMIs that are likely a result of sequencing errors, by merging the UMIs observed only once that display hamming distance of 1 from a UMI detected by two or more aligned reads.
Barcodes representing empty droplets were removed by filtering for a minimum of 700 UMIs observed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of unique molecular identifier (UMI) counts per gene for each cell
Supplementary_files_format_and_content: Metadata for each cell barcode in the quantification matrix file

source_name: Cortex

extract_protocol:
Dissociated cortical cells were resuspended in PBS, filtered through a 70 micron cell strainer followed by a 40 micron tip strainer, and counted with a Countess instrument (Life Technologies). The cells were further diluted to the final concentration (80,000 cells/mL) with OptiPrep (Sigma) and PBS, and the final concentration of OptiPrep was 15% vol/vol. A total of 2,000 to 5,000 cortical cells were collected per mouse using an InDrop setup.
Libraries were barcoded independently for aliquots containing ~1,200 cells, and constructed following the InDrop protocol (Klein et al., 2015; Zilionis et al., 2017).

treatment_protocol: P5 mice were euthanized by decapitation and the brain was rapidly removed and placed in cold dissection buffer (1x HBSS). The brain was rapidly dissected to collect the cerebral cortex (both hemispheres) and the tissue was dissociated using the Papain dissociation system (Worthington Biochemical) following the manufacturer’s protocol with a 30 minute incubation.

value: Cortex

tag: strain

value: FVB.129P2-Pde6b+ Tyrc-ch Fmr1tm1Cgr/J

value: Postnatal day 5 (P5)

tag: indrop bead version


title: X51378P2

city: Cambridge


title: X8301


title: WT 2

description: Single-cell RNA-Seq

value: FVB.129P2-Pde6b+ Tyrc-ch/AntJ

tag: developmental stage


title: X15092


title: WT 1

description: Single-cell RNA-Seq


title: X48277P6


title: X51029


title: X5093


title: Fmr1-KO 2

description: Single-cell RNA-Seq


title: Fmr1-KO 1

description: Single-cell RNA-Seq


title: WT 3

description: Single-cell RNA-Seq


title: X50184P2


title: X50184P1