title: TOP2A ChIPSeq

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
Tags were aligned to mouse genome (mm9) using Bowtie (version 1.2.0).
Peaks were called using HOMER and filtering by Fold change enrichment over input of 10-fold and standard quality parameters.
For genome tracks, we used bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPKM normalization.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files (bigWig)

source_name: Thymocytes

extract_protocol:
To prepare chromatin, mouse thymus was extracted from 4-6-week old mice, washed twice with cold PBS and mechanically disaggregated into single cells in 1ml EDTA buffer (100 mM NaCl, 1 mM KH2PO4, 3 mM KCl, 10 mM Na2HPO4, 1 mM EDTA). Thymocytes were then washed twice and resuspended again in EDTA buffer. Cells were fixed by adding formaldehyde to a final concentration of 1% and incubated at 37ºC for 10 min.
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

tag: cell type

value: Thymocytes isolated from mouse thymus

tag: chip antibody

value: TOP2A (Abcam - ab52934)


title: RNA_ileal_tissue_Sample68_rep2

status: Public on Dec 23 2019

type: RNA

city: Los Angeles

first: Alka

last: Potdar

state: CA

address: 110 George Burns Rd

department: Medicine/GI

country: USA

institute: Cedars-Sinai Medical Center

description: Gene expression from RNA from ileal tissue of Sample68_rep2

hyb_protocol: Hybridization was performed in duplicate for each sample. Hybridization to Whole Human Genome 4x44k Microarrays (Agilent) was performed by the Genome Technology Access Center (GTAC) at Washington University – St. Louis.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). The feature extraction file was exported as a .txt file.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cy5 labeling was performed with the ULST Fluorescent Labeling kit (Kreatech). Technical duplicate hybridizations (HYB-A and HYB-B) were performed for each sample.

extract_protocol: Two fresh, unstained 5-µm FFPE tissue sections on glass microscope slides were obtained. Slides were not baked after cutting. For each sample, the two tissue sections were scraped off of the slides using a clean razor and placed in 1.5 mL Eppendorf tubes. The tubes were briefly centrifuged to place the sample towards the bottoms or sides of the tube. RNA extraction and DNase treatment was performed using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s instructions, using the Xylene protocol for the paraffin removal step and 30 µL RNase-free H2O for the elution step. RNA was initially quantified by NanoDrop. Subsequent total RNA quantification and quality assessment was performed by Bioanalyzer 2100 (Agilent Technologies). Samples were excluded from the study if >20% of the RNA fragments were >200 base pairs in length, as determined with the Bioanalyzer software.

treatment_protocol: Whole-thickness ileal tissue was scraped from the FFPE tissue sections followed by RNA extraction using the RNeasy FFPE kit (Qiagen) according to the manufacturer's instructions.

tag: ^sample

tag: batch

tag: tissue

value: uninvolved small bowel (SB) ileal tissue

tag: gender

value: male

tag: age


title: Mouse0MIWI-KO-rep1

type: SRA

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

library_source: transcriptomic

data_processing:
The 3′ adaptor sequence from the reads were removed and those reads whose PHRED score <5 was further filtered. The reads passed the quality check were mapped to human genome (hg19) and or mouse genome (mm10) using piPipes allowing 1 mismatch.
For RNA-seq, CAGE and PAS-seq, we first removed rRNA reads using bowtie 2.2.5 with default parameters48 and then the unaligned reads were further mapped to human genome (hg19) using STAR 2.3 (Ref. 52). Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and normalized bigWig files are generated by custom scripts.
Raw reads were mapped to genome using Bowtie 2.2.5 with parameter —very-sensitive. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8. We, then, normalized genome coverage files in bigWig format that were calculated using homemade script. Data are presented in bigWig file of unique mapping reads as read depth per million reads (rpm). We used Model-based analysis of ChIP-seq (MACS 1.1.2; Ref. 58) with parameter -q 0.01 to detect A-MYB peaks that were significantly enriched over input (1,296 genomic regions; false discovery rate [FDR] < 0.05).
Genome_build: hg19; mm10
Supplementary_files_format_and_content: bigWig; narrowPeak; rpm.txt (text)

organism: Mus musculus

source_name: Testis

extract_protocol:
Total RNA was extracted from the mouse FACS-sorted germ cells using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
In brief, total RNA was run on 15% urea polyacrylamide gel electrophoresis (PAGE) to select small RNAs ranging from 18–34 nt. To prevent microRNAs and siRNAs entering to the library, sRNAs were oxidized with sodium periodate (NaIO4) prior to 3′ adaptor ligation. We then ligated the 3′ adaptor (5′-rApp NNN TGG AAT TCT CGG GTG CCA AGG /ddC/-3′ or 5′-rApp TGG AAT TCT CGG GTG CCA AGG /ddC/-3′; Supplementary file 1) in the presence of 50% (w/v) PEG8000 (Rigaku, 1008063). After 3′ ligation, ligated sRNAs were run on 15% PAGE to eliminate the non-ligated 3′ adaptor; ligated sRNAs that were 42 to 60 nt with 3′ adaptor were purified. Thereafter, 5′ adaptor was ligated.

value: Testis

tag: developmental stage

value: Adult


title: Mouse-MIWI-HET-rep2


title: Mouse-MIWI-HET-rep1


title: RNA_ileal_tissue_Sample62_rep1

description: Gene expression from RNA from ileal tissue of Sample62_rep1

value: female


title: Mouse-AMYB-minus-minus-smallRNAseq-rep2


title: Mouse0MIWI-KO-rep2


title: KO_137_KO_PEG

city: Trondheim

first: Reidar

last: Fossmark

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Base calling were done on the NextSeq 500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.17 (Illumina, Inc. San Diego, CA, USA).
Transcript counts were estimated from unfiltered fastq files using Kallisto version 0.42.4 with an index built on the Ensembl GRCm38 cdna sequences. The Kallisto results were imported into the sleuth R-package for further statistical analysis and raw transcript counts were exported to a tab separated file by the command sleuth_to_matrix and options which_df=”obs_raw” and which_units=”est_counts” .
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated file with estimated transcript counts from Kallisto/Sleuth. Transcripts in rows and samples in columns.

source_name: HKATPase KO_peg_gastric corpus

extract_protocol:
A sample of the gastric corpus was colleceted, and RNA was extracted using RNeasy Mini kit (Qiagen).
RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina).
Libraries were normalized and pooled to 2.0 pM and subjected to clustering on two NextSeq 500 high output flowcells. Finally single read sequencing was performed for 75 cycles on a NextSeq 500 instrument

tag: strain background

value: BalbC

tag: genotype/variation

value: HKATPase KO

value: 13 months

tag: treatment

value: peg

value: gastric corpus


title: RNA_ileal_tissue_Sample60_rep1

description: Gene expression from RNA from ileal tissue of Sample60_rep1


title: RNA_ileal_tissue_Sample59_rep2

description: Gene expression from RNA from ileal tissue of Sample59_rep2


title: RNA_ileal_tissue_Sample59_rep1

description: Gene expression from RNA from ileal tissue of Sample59_rep1


title: WT_120_WT_PEG

source_name: wild type_peg_gastric corpus

value: wild type


title: RNA_ileal_tissue_Sample58_rep2

description: Gene expression from RNA from ileal tissue of Sample58_rep2


title: RNA_ileal_tissue_Sample66_rep1

description: Gene expression from RNA from ileal tissue of Sample66_rep1


title: RNA_ileal_tissue_Sample58_rep1

description: Gene expression from RNA from ileal tissue of Sample58_rep1


title: TOP2B Novus ChIPSeq

library_source: genomic

data_processing:
Tags were aligned to mouse genome (mm9) using Bowtie (version 1.2.0).
Peaks were called using HOMER and filtering by Fold change enrichment over input of 10-fold and standard quality parameters.
For genome tracks, we used bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPKM normalization.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files (bigWig) and peak files (bed)

molecule: genomic DNA

tag: strain

value: TOP2B (Novus Biologicals - NB100-40842)


title: TOP2B SC ChIPSeq

value: TOP2B (SantaCruz – sc13059)


title: IgG ChIPSeq

value: IgG (Sigma - I8140)


title: RNA_ileal_tissue_Sample57_rep2

description: Gene expression from RNA from ileal tissue of Sample57_rep2


title: RNA_ileal_tissue_Sample63_rep2

description: Gene expression from RNA from ileal tissue of Sample63_rep2


title: RNA_ileal_tissue_Sample57_rep1

description: Gene expression from RNA from ileal tissue of Sample57_rep1


title: Human-ChIPseq-H3K4me3_ChIP-A17

extract_protocol:
Total DNA was extracted from frozen tissues.
Briefly, frozen tissues were cut into small pieces on dry ice and transferred to 1.7 ml tubes containing cold PBS. Samples were then cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. Thereafter, fixed tissues were crushed in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a “B” pestle of Dounce homogenizer (Kimble-Chase, Vineland, USA). Furthermore, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220) to shear the chromatin into 150 to 200 bp. Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5.5 µg of anti-A‑MYB (Sigma, HPA008791) and 4.5 µg of anti-H3K4me3 (Abcam, ab8580). Following the immunoprecipitation of the chromatin with the antibody of interest, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8) and prepared ChIP-seq libraries for anti-AMYB, anti-H3K4me3 and input DNA as previously described.


title: Human-ChIPseq-H3K4me3_input-A17


title: RNA_ileal_tissue_Sample61_rep1

description: Gene expression from RNA from ileal tissue of Sample61_rep1


title: Human-ChIPseq-H3K4me3_input-A15


title: RNA_ileal_tissue_Sample56_rep2

description: Gene expression from RNA from ileal tissue of Sample56_rep2


title: RNA_ileal_tissue_Sample56_rep1

description: Gene expression from RNA from ileal tissue of Sample56_rep1


title: RNA_ileal_tissue_Sample60_rep2

description: Gene expression from RNA from ileal tissue of Sample60_rep2


title: Mouse-AMYB-minus-minus-smallRNAseq-rep1


title: Human-ChIPseq-H3K4me3_ChIP-A15


title: Human-ChIPseq-H3K4me3_input-A1


title: RNA_ileal_tissue_Sample54_rep1

description: Gene expression from RNA from ileal tissue of Sample54_rep1


title: RNA_ileal_tissue_Sample54_rep2

description: Gene expression from RNA from ileal tissue of Sample54_rep2


title: RNA_ileal_tissue_Sample55_rep2

description: Gene expression from RNA from ileal tissue of Sample55_rep2


title: Human-ChIPseq-H3K4me3_ChIP-A1


title: Human-ChIPseq-input-S1

source_name: Kidney

value: Kidney


title: RNA_ileal_tissue_Sample53_rep1

description: Gene expression from RNA from ileal tissue of Sample53_rep1


title: RNA_ileal_tissue_Sample53_rep2

description: Gene expression from RNA from ileal tissue of Sample53_rep2


title: Human-ChIPseq-H3K4me3_ChIP-S1


title: Human-ChIPseq-AMYB_ChIP-S1

value: anti-A-MYB


title: RNA_ileal_tissue_Sample52_rep1

description: Gene expression from RNA from ileal tissue of Sample52_rep1


title: Human-ChIPseq-AMYB_ChIP-A17


title: RNA_ileal_tissue_Sample51_rep2

description: Gene expression from RNA from ileal tissue of Sample51_rep2


title: Human-ChIPseq-AMYB_input-A10


title: Human-ChIPseq-AMYB_input-A16


title: Human-ChIPseq-AMYB_ChIP-A16


title: Human-ChIPseq-AMYB_ChIP-A10


title: RNA_ileal_tissue_Sample51_rep1

description: Gene expression from RNA from ileal tissue of Sample51_rep1


title: RNA_ileal_tissue_Sample50_rep1

description: Gene expression from RNA from ileal tissue of Sample50_rep1


title: RNA_ileal_tissue_Sample49_rep2

description: Gene expression from RNA from ileal tissue of Sample49_rep2


title: RNA_ileal_tissue_Sample50_rep2

description: Gene expression from RNA from ileal tissue of Sample50_rep2


title: RNA_ileal_tissue_Sample55_rep1

description: Gene expression from RNA from ileal tissue of Sample55_rep1


title: Human-ChIPseq-AMYB_ChIP-A8


title: Human-ChIPseq-AMYB_input-A8


title: RNA_ileal_tissue_Sample49_rep1

description: Gene expression from RNA from ileal tissue of Sample49_rep1


title: Human-ChIPseq-AMYB_input-A17


title: RNA_ileal_tissue_Sample48_rep2

description: Gene expression from RNA from ileal tissue of Sample48_rep2


title: Human-ChIPseq-AMYB_input-A1


title: RNA_ileal_tissue_Sample52_rep2

description: Gene expression from RNA from ileal tissue of Sample52_rep2


title: RNA_ileal_tissue_Sample48_rep1

description: Gene expression from RNA from ileal tissue of Sample48_rep1


title: Human-ChIPseq-AMYB_ChIP-A1


title: RNA_ileal_tissue_Sample47_rep2

description: Gene expression from RNA from ileal tissue of Sample47_rep2


title: RNA_ileal_tissue_Sample47_rep1

description: Gene expression from RNA from ileal tissue of Sample47_rep1


title: Human-PASseq-J1

extract_protocol:
Total RNA was extracted from the human frozen testis tissues using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
Briefly, we extracted poly(A)+ RNA from the total RNA using Dynabeads mRNA purification beads (Ambion, 61006). Poly(A)+ RNA was then fragmented at 70°C for 7 min by chemical hydrolysis yielding 60 to 80 nt fragments. Fragmented RNA was further reverse transcribed using barcoded oligo(dT) oligonucleotides containing sites for forward and reverse Illumina sequencing primers that were separated by a hexa-ethyleneglycol spacer (Sp18). The oligonucleotides contained unique molecular index (UMI), enabling the PCR duplicate removal, preceded by 5′p-GG for efficient cDNA circularization. cDNA was further circularized using Circligase ssDNA ligase (Illumina, CL4111K) at 60°C for 4 h. Following cDNA circularization, fourteen cycles of PCR amplification was performed using KAPA HiFi library amplification kit (Kapa Biosystems, KK2611).


title: PMAko1

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
total RNA
DiffCtl_vs_DiffC9-ExpDiff.csv
UndiffC9_vs_DiffC9-ExpDiff.csv

data_processing:
RNAseq analysis
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
hg38
comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: U937 cells

growth_protocol: U937 cells were cultured in RPMI-1640 medium (Gibco) with 10% heat-inactivated FBS (Gibco), 1% penicillin-streptomycin, and Glutamax (2 mM). Cells were passaged every 2-3 days in a controlled humidified incubator at 37 °C, with 5% CO2.

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: To differentiate cells

value: PMA treated C9KO


title: PMAcon3

description:
total RNA
DiffCtl_vs_DiffC9-ExpDiff.csv
UndiffCtl_vs_DiffCtl-ExpDiff.csv

value: PMA treated WT


title: PMAko2


title: PMAko3


title: RNA_ileal_tissue_Sample45_rep2

description: Gene expression from RNA from ileal tissue of Sample45_rep2

value: uninvolved small bowel (SB) ileal tissue


title: RNA_ileal_tissue_Sample46_rep1

description: Gene expression from RNA from ileal tissue of Sample46_rep1

value: male


title: RNA_ileal_tissue_Sample46_rep2

description: Gene expression from RNA from ileal tissue of Sample46_rep2


title: RNA_ileal_tissue_Sample45_rep1

description: Gene expression from RNA from ileal tissue of Sample45_rep1


title: PMAcon1


title: PMAcon2


title: Human-PASseq-A15

value: Testis

value: Adult


title: Human-PASseq-A2


title: RNA_ileal_tissue_Sample44_rep2

description: Gene expression from RNA from ileal tissue of Sample44_rep2

value: female


title: RNA_ileal_tissue_Sample44_rep1

description: Gene expression from RNA from ileal tissue of Sample44_rep1


title: ko3

description:
total RNA
UndiffCtl_vs_UndiffC9-ExpDiff.csv
UndiffC9_vs_DiffC9-ExpDiff.csv


title: Human-CAGEseq-J1-rep2

extract_protocol:
Total RNA was extracted from the human frozen testis tissues using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
Briefly, following the rRNA removal, poly(A)+ RNA was extracted from the total RNA using Dynabeads mRNA purification beads (Ambion, 61006). RNA samples were heated to 68°C for 5 min and chilled on ice immediately. To prevent the 5′-end phosphorylated RNA entering to the library, we treated RNA samples with ten units of Antarctic Phosphatase (NEB, M0289) at 37°C for 1h. After heat inactivating Antarctic Phosphatase at 70°C for 5 min, we extracted RNA by phenol:chloroform:isoamyl alcohol (25:24:1; pH 6.7). Thereafter, 5′-end cap was removed from the RNA samples using twenty units of Tobacco Decapping Enzyme (Enzymax, LLC, 87) in the presence of 1 mM MnCl2 at 37°C for 2 h followed by phenol:chloroform:isoamyl alcohol extraction. After 5′ ligation, we performed reverse transcription using random oligo primer containing 3′ adaptor sequence. We then performed two cycle of PCR and purified the PCR products 200 to 400 bp. After that we perform ten more cycle of final PCR.

value: Juvenile


title: RNA_ileal_tissue_Sample43_rep2

description: Gene expression from RNA from ileal tissue of Sample43_rep2


title: RNA_ileal_tissue_Sample42_rep2

description: Gene expression from RNA from ileal tissue of Sample42_rep2


title: RNA_ileal_tissue_Sample43_rep1

description: Gene expression from RNA from ileal tissue of Sample43_rep1


title: ko2


title: Human-CAGEseq-J1-rep1


title: RNA_ileal_tissue_Sample42_rep1

description: Gene expression from RNA from ileal tissue of Sample42_rep1


title: RNA_ileal_tissue_Sample41_rep1

description: Gene expression from RNA from ileal tissue of Sample41_rep1


title: ko1


title: Human-CAGEseq-A15


title: Human-CAGEseq-A2


title: RNA_ileal_tissue_Sample41_rep2

description: Gene expression from RNA from ileal tissue of Sample41_rep2


title: RNA_ileal_tissue_Sample40_rep2

description: Gene expression from RNA from ileal tissue of Sample40_rep2


title: RNA_ileal_tissue_Sample39_rep2

description: Gene expression from RNA from ileal tissue of Sample39_rep2


title: RNA_ileal_tissue_Sample40_rep1

description: Gene expression from RNA from ileal tissue of Sample40_rep1


title: con1

description:
total RNA
UndiffCtl_vs_UndiffC9-ExpDiff.csv
UndiffCtl_vs_DiffCtl-ExpDiff.csv

value: WT


title: Human-CAGEseq-A1


title: con2


title: Human-PASseq-A1


title: RNA_ileal_tissue_Sample39_rep1

description: Gene expression from RNA from ileal tissue of Sample39_rep1


title: RNA_ileal_tissue_Sample36_rep2

description: Gene expression from RNA from ileal tissue of Sample36_rep2


title: Human-smallRNAseq-J3

description:
LCH-008-Ox-ID5
processed data file: merged.rpm

extract_protocol:
Total RNA was extracted from the human frozen testis tissues using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
In brief, total RNA was run on 15% urea polyacrylamide gel electrophoresis (PAGE) to select small RNAs ranging from 18–34 nt. To prevent microRNAs and siRNAs entering to the library, sRNAs were oxidized with sodium periodate (NaIO4) prior to 3′ adaptor ligation. We then ligated the 3′ adaptor (5′-rApp NNN TGG AAT TCT CGG GTG CCA AGG /ddC/-3′ or 5′-rApp TGG AAT TCT CGG GTG CCA AGG /ddC/-3′; Supplementary file 1) in the presence of 50% (w/v) PEG8000 (Rigaku, 1008063). After 3′ ligation, ligated sRNAs were run on 15% PAGE to eliminate the non-ligated 3′ adaptor; ligated sRNAs that were 42 to 60 nt with 3′ adaptor were purified. Thereafter, 5′ adaptor was ligated.


title: RNA_ileal_tissue_Sample37_rep2

description: Gene expression from RNA from ileal tissue of Sample37_rep2


title: RNA_ileal_tissue_Sample37_rep1

description: Gene expression from RNA from ileal tissue of Sample37_rep1


title: Human-smallRNAseq-J1-rep2

description:
N1643-5YO-Rep2-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample38_rep2

description: Gene expression from RNA from ileal tissue of Sample38_rep2


title: RNA_ileal_tissue_Sample35_rep2

description: Gene expression from RNA from ileal tissue of Sample35_rep2


title: RNA_ileal_tissue_Sample35_rep1

description: Gene expression from RNA from ileal tissue of Sample35_rep1


title: Human-smallRNAseq-J1-rep1

description:
N1643-5YO-Rep1-Ox
processed data file: merged.rpm


title: con3


title: RNA_ileal_tissue_Sample34_rep2

description: Gene expression from RNA from ileal tissue of Sample34_rep2


title: RNA_ileal_tissue_Sample34_rep1

description: Gene expression from RNA from ileal tissue of Sample34_rep1


title: RNA_ileal_tissue_Sample38_rep1

description: Gene expression from RNA from ileal tissue of Sample38_rep1


title: RNA_ileal_tissue_Sample33_rep2

description: Gene expression from RNA from ileal tissue of Sample33_rep2


title: RNA_ileal_tissue_Sample33_rep1

description: Gene expression from RNA from ileal tissue of Sample33_rep1


title: Human-smallRNAseq-A13

description:
S8+
processed data file: merged.rpm


title: Human-smallRNAseq-A14

description:
s904-Ox-ID3
processed data file: merged.rpm


title: Human-smallRNAseq-J2

description:
TTC-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample32_rep1

description: Gene expression from RNA from ileal tissue of Sample32_rep1


title: RNA_ileal_tissue_Sample31_rep2

description: Gene expression from RNA from ileal tissue of Sample31_rep2


title: RNA_ileal_tissue_Sample32_rep2

description: Gene expression from RNA from ileal tissue of Sample32_rep2


title: RNA_ileal_tissue_Sample31_rep1

description: Gene expression from RNA from ileal tissue of Sample31_rep1


title: RNA_ileal_tissue_Sample30_rep2

description: Gene expression from RNA from ileal tissue of Sample30_rep2


title: RNA_ileal_tissue_Sample36_rep1

description: Gene expression from RNA from ileal tissue of Sample36_rep1


title: Human-smallRNAseq-A10

description:
6615NT_Ox
processed data file: merged.rpm


title: Human-smallRNAseq-A11

description:
N7377-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample30_rep1

description: Gene expression from RNA from ileal tissue of Sample30_rep1


title: RNA_ileal_tissue_Sample29_rep2

description: Gene expression from RNA from ileal tissue of Sample29_rep2


title: RNA_ileal_tissue_Sample29_rep1

description: Gene expression from RNA from ileal tissue of Sample29_rep1


title: PEPT1-KO iPS-IEC

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

description:
PEPT1-KO iPS-IEC
AR3144_02

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: YOW-iPS, intestinal epithelial-like cells, iPSC-derived, PEPT1-KO

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human iPS cells were seeded at an appropriate cell density (5×10^4 cells/cm^2) in an uncoated manner using 0.1 μg/cm^2 iMatrix-511 (Nippi) with StemFit AK02N medium (Ajinomoto). Human iPS cells were subcultured every 6 days.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: In vitro differentiation; Human iPS cells were differentiated into IEC according to our previous report with some modifications (Negoro et al., 2018). To perform the definitive endoderm differentiation, human iPS cells were dissociated into single cells by using TrypLE Select Enzyme and plated onto growth factor reduced BD Matrigel Basement Membrane Matrix (BD Biosciences). These cells were cultured with StemFit AK02N medium until they reached approximately 80% confluence, and then culture with RPMI1640 medium (Sigma-Aldrich) containing 100 ng/ml Activin A (R&D Systems), 1×GlutaMAX (Thermo Fisher Scientific), penicillin-streptomycin (P/S; Nacalai Tesque), 1×B27 Supplement Minus Vitamin A (Thermo Fisher Scientific), and 1 μM CHIR99021 (FUJIFILM Wako) for 1 day, and then cultured with RPMI1640 medium containing 100 ng/ml Activin A, 1×GlutaMAX, P/S, and 1×B27 Supplement Minus Vitamin A for 2 days. For the induction of intestinal progenitor cells, the definitive endoderm cells were cultured for 4 days in the intestinal differentiation medium consists of DMEM-High Glucose medium (FUJIFILM Wako) containing 10% knockout serum replacement (KSR; Thermo Fisher Scientific), 1% non-essential amino acid Solution (NEAA; Thermo Fisher Scientific), penicillin-streptomycin, 1×GlutaMAX, and 20 nM LY2090314 (MedChem Express). Then, for the induction of intestinal epithelial-like cells, the intestinal progenitor cells were cultured for 20 days in WNT3A-, R-spondin 3-, and Noggin-expressing cell (ATCC; CRL3276)-conditioned intestinal differentiation medium containing 3 nM LY2090314, 10 μM SB202190 (FUJIFILM Wako), 1 μM dexamethasone (DEX; FUJIFILM Wako), 50 ng/ml epidermal growth factor (EGF; R&D Systems), and 20 ng/ml insulin-like growth factor-1 (IGF-1; R&D Systems).

value: iPS-IEC

tag: genotype

value: SLC15A1/PEPT1 knockout


title: heat shock 5009 strain gpessi_20080903_kl_20082008_5009B_heat3

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum 5009 mutant grown aerobically temperature stress

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria cDNA were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed using the mas5 algorithm described in the Affymetrix statistical algorithms description document (http://www.affymetrix.com). Signal values from the arrays were then analyzed using Genespring GX 7.3 (Agilent Technologies,CA, USA). Only those genes which are “present” (i.e., expressed, based on the detection P-value ≤ 0.06) in 80% of all replicates were further considered. For experiments comparing different conditions, each chip was normalized to the median. Values below 0.01 were set to 0.01. For statistical comparisons, the  student t-test with a P-value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2, when comparing different conditions amongst culture-grown bacteria.

label: biotin

organism: Bradyrhizobium japonicum

source_name: B. japonicum 5009 grown aerobically

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix).   The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase (OD600 of 0.4-0.5). For harvesting, cultures were rapidly transferred to cold tubes containing one tenth of the culture volume of “stop solution” (10% Tris-HCl-buffered phenol [pH 8] in ethanol), centrifuged for 5 min (10,800 × g; 4°C), the supernatant was decanted, and cells were frozen in liquid nitrogen and stored at −80°C.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 4-to–20% acrylamide gradient gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada). Labeling was performed according to the protocol for free-living bacteria.

value: B. japonicum 5009

tag: growth condition

value: 15 min 43 °C

tag: growth medium

value: AG

tag: treatment group

value: heat shock


title: heat shock 09-32 strain henneckeguests_20080613_kl_20080613_5009_heat_3

description: B. japonicum 09-32 mutant grown aerobically temperature stress

source_name: B. japonicum 09-32 grown aerobically

value: B. japonicum 09-32


title: heat shock 09-32 strain henneckeguests_20080613_kl_20080613_5009_heat_2


title: heat shock 5009 strain gpessi_20080903_kl_20082008_5009B_heat2


title: heat shock 5009 strain gpessi_20080903_kl_20082008_5009B_heat1


title: RNA_ileal_tissue_Sample27_rep2

description: Gene expression from RNA from ileal tissue of Sample27_rep2


title: RNA_ileal_tissue_Sample28_rep2

description: Gene expression from RNA from ileal tissue of Sample28_rep2


title: RNA_ileal_tissue_Sample28_rep1

description: Gene expression from RNA from ileal tissue of Sample28_rep1


title: Human-smallRNAseq-A8

description:
P75-Ox-ID1
processed data file: merged.rpm


title: WT iPS-IEC

description:
WT iPS-IEC
AR3144_01

source_name: YOW-iPS, intestinal epithelial-like cells, iPSC-derived, WT

value: SLC15A1/PEPT1 wild type


title: Human-smallRNAseq-A7

description:
S6+
processed data file: merged.rpm


title: Human-smallRNAseq-A12

description:
Ambion-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample26_rep2

description: Gene expression from RNA from ileal tissue of Sample26_rep2


title: RNA_ileal_tissue_Sample27_rep1

description: Gene expression from RNA from ileal tissue of Sample27_rep1


title: heat shock 5032 strain henneckeguests_20080613_kl_20080613_5032_heat_2

description: B. japonicum 5032 mutant grown aerobically temperature stress

source_name: B. japonicum 5032 grown aerobically

value: B. japonicum 5032


title: heat shock 09-32 strain henneckeguests_20080613_kl_20080613_5009_heat_4


title: Human-smallRNAseq-A6

description:
8377NT_Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample26_rep1

description: Gene expression from RNA from ileal tissue of Sample26_rep1


title: RNA_ileal_tissue_Sample25_rep2

description: Gene expression from RNA from ileal tissue of Sample25_rep2


title: Human-smallRNAseq-A9

description:
8289NT_Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample25_rep1

description: Gene expression from RNA from ileal tissue of Sample25_rep1


title: RNA_ileal_tissue_Sample24_rep2

description: Gene expression from RNA from ileal tissue of Sample24_rep2


title: heat shock 5032 strain henneckeguests_20080613_kl_20080613_5032_heat_4


title: Human-smallRNAseq-A5

description:
8357NT_Ox
processed data file: merged.rpm


title: Human-smallRNAseq-A4

description:
9268NT_Ox
processed data file: merged.rpm


title: heat shock 5032 strain henneckeguests_20080613_kl_20080613_5032_heat_3


title: pH 8 klang_D8

description: B. japonicum grown aerobically pH 8

source_name: B. japonicum grown aerobically

value: wild-type

value: 4 h 28 °C pH 8

value: pH 8


title: RNA_ileal_tissue_Sample23_rep2

description: Gene expression from RNA from ileal tissue of Sample23_rep2

value: uninvolved small bowel (SB) ileal tissue


title: RNA_ileal_tissue_Sample24_rep1

description: Gene expression from RNA from ileal tissue of Sample24_rep1

value: male


title: RNA_ileal_tissue_Sample22_rep1

description: Gene expression from RNA from ileal tissue of Sample22_rep1


title: RNA_ileal_tissue_Sample23_rep1

description: Gene expression from RNA from ileal tissue of Sample23_rep1

value: female


title: RNA_ileal_tissue_Sample22_rep2

description: Gene expression from RNA from ileal tissue of Sample22_rep2


title: Human-smallRNAseq-A3

description:
S7+
processed data file: merged.rpm

value: Testis

value: Adult


title: Human-smallRNAseq-A2

description:
N8150-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample21_rep2

description: Gene expression from RNA from ileal tissue of Sample21_rep2


title: pH 8 klang_C8

description: B. japonicum grown aerobically pH 8


title: pH 8 klang_B8

description: B. japonicum grown aerobically pH 8


title: Human-smallRNAseq-A1

description:
N7358-Ox
processed data file: merged.rpm


title: RNA_ileal_tissue_Sample21_rep1

description: Gene expression from RNA from ileal tissue of Sample21_rep1


title: Human-RNAseq-J3

extract_protocol:
Total RNA was extracted from the human frozen testis tissues using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
Briefly, 186 short antisense (AS) DNA oligos (50–80 nt) that are complementary to rRNAs were designed and pooled (0.05µM/each). 1 µl of pooled rRNA AS oligos were added to 1 µg of total RNA and hybridized to rRNAs in the presence of 100 mM Tris-HCl (pH 7.4) and 200 mM NaCl at 95°C and cooled to 22°C (−0.1°C/sec). Additional incubation at 22°C was performed for 5 min. Thereafter, the DNA:RNA hybrids were digested with ten units of Thermostable RNase h (Epicentre, H39500) in the presence of 50 mM Tris-HCl (pH 7.4), 0.1M NaCl, and 20 mM MgCl2 at 45°C for 30 min. After RNase h digestion, samples were treated with DNase using four units of Turbo DNase (Thermo Fisher, AM2238) at 37°C for 20 min and purified with RNA Clean & Concentrator-5 (Zymo Research, R1015) to enrich RNA >200 nt and remove tRNAs.

value: Juvenile


title: RNA_ileal_tissue_Sample20_rep2

description: Gene expression from RNA from ileal tissue of Sample20_rep2


title: Human-RNAseq-J2


title: RNA_ileal_tissue_Sample20_rep1

description: Gene expression from RNA from ileal tissue of Sample20_rep1


title: RNA_ileal_tissue_Sample19_rep2

description: Gene expression from RNA from ileal tissue of Sample19_rep2


title: Human-RNAseq-J1-rep2


title: pH 4 klang_Q4

description: B. japonicum grown aerobically pH 4

value: 4 h 28 °C pH 4

value: pH 4


title: pH 4 klang_P4

description: B. japonicum grown aerobically pH 4


title: salt stress Ir070807_nacl_kathrin

description: B. japonicum grown aerobically salt stress

value: 4 h 28 °C 80 mM NaCl

value: 80 mM NaCl


title: RNA_ileal_tissue_Sample19_rep1

description: Gene expression from RNA from ileal tissue of Sample19_rep1


title: RNA_ileal_tissue_Sample18_rep1

description: Gene expression from RNA from ileal tissue of Sample18_rep1


title: RNA_ileal_tissue_Sample18_rep2

description: Gene expression from RNA from ileal tissue of Sample18_rep2


title: Human-RNAseq-A13


title: Human-RNAseq-A11


title: RNA_ileal_tissue_Sample16_rep2

description: Gene expression from RNA from ileal tissue of Sample16_rep2


title: Human-RNAseq-A14


title: RNA_ileal_tissue_Sample17_rep1

description: Gene expression from RNA from ileal tissue of Sample17_rep1


title: RNA_ileal_tissue_Sample17_rep2

description: Gene expression from RNA from ileal tissue of Sample17_rep2


title: Human-RNAseq-A10


title: Human-RNAseq-A9


title: Human-RNAseq-J1-rep1


title: RNA_ileal_tissue_Sample16_rep1

description: Gene expression from RNA from ileal tissue of Sample16_rep1


title: Human-RNAseq-A12


title: salt stress klang_NaCl4

value: AG


title: RNA_ileal_tissue_Sample15_rep2

description: Gene expression from RNA from ileal tissue of Sample15_rep2


title: salt stress klang_NaCl3


title: pH 4 klang_O4

description: B. japonicum grown aerobically pH 4


title: basis stress mg270605_wtp8-

description: B. japonicum grown aerobically basis

value: 4 h 28 °C

value: basis


title: salt stress klang_NaCl2


title: temperature stress gpessi_20080903_kl_20082008_wt_heatstress

description: B. japonicum grown aerobically temperature stress

value: temperature stress


title: temperature stress klang_W35.2

value: wild-type


title: temperature stress klang_X35.2


title: basis stress mg270605_wtp7-

description: B. japonicum grown aerobically basis


title: Human-RNAseq-A7


title: RNA_ileal_tissue_Sample15_rep1

description: Gene expression from RNA from ileal tissue of Sample15_rep1


title: RNA_ileal_tissue_Sample14_rep2

description: Gene expression from RNA from ileal tissue of Sample14_rep2


title: RNA_ileal_tissue_Sample14_rep1

description: Gene expression from RNA from ileal tissue of Sample14_rep1


title: Human-RNAseq-A5


title: Human-RNAseq-A4


title: basis stress mg_220506_wt_n8-

description: B. japonicum grown aerobically basis


title: RNA_ileal_tissue_Sample13_rep2

description: Gene expression from RNA from ileal tissue of Sample13_rep2


title: RNA_ileal_tissue_Sample13_rep1

description: Gene expression from RNA from ileal tissue of Sample13_rep1


title: basis stress klang_wtA-

description: B. japonicum grown aerobically basis


title: Human-RNAseq-A2


title: RNA_ileal_tissue_Sample12_rep2

description: Gene expression from RNA from ileal tissue of Sample12_rep2


title: basis stress mg270605_wtn7-

description: B. japonicum grown aerobically basis


title: Human-RNAseq-A1


title: heat shock klang_R15_43

description: B. japonicum grown aerobically heat shock

value: 15 min 43 °C

value: heat shock


title: Human-RNAseq-A6


title: RNA_ileal_tissue_Sample12_rep1

description: Gene expression from RNA from ileal tissue of Sample12_rep1

value: uninvolved small bowel (SB) ileal tissue


title: RNA_ileal_tissue_Sample11_rep2

description: Gene expression from RNA from ileal tissue of Sample11_rep2

value: male


title: heat shock klang_N15_43


title: P4

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

country: China

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie (Langmead,Ben, 2010).
MicroRNA counts were calculated using featureCounts (Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of microRNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) and then purified by QIAquick® PCR Purification Kit (Qiagen, Hilden, Germany), and put to size selection by using gel Prep. The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

tag: subject status

value: psoriasis patient

value: blood

value: peripheral blood mononuclear cells (PBMC)


title: P3

tag: cell type


title: RNA_ileal_tissue_Sample11_rep1

description: Gene expression from RNA from ileal tissue of Sample11_rep1


title: P2


title: P1


title: RNA_ileal_tissue_Sample10_rep1

description: Gene expression from RNA from ileal tissue of Sample10_rep1

value: female


title: Human-RNAseq-A3

value: Testis

value: Adult


title: RNA_ileal_tissue_Sample9_rep2

description: Gene expression from RNA from ileal tissue of Sample9_rep2


title: HC5

value: healty control


title: heat shock basis klang_R15_28

description: B. japonicum grown aerobically basis for heat shock

value: 15 min 28 °C

value: basis for heat shock


title: heat shock klang_I15_43

value: AG


title: CGH Tdp2-/-Atm-/- Exp6

type: genomic

hyb_protocol: Hybridization was performed during 40 hours at 67ºC. Agilent Mouse Genome CGH Microarray, 2x105K (DesignID=014699) was then used.

scan_protocol: GenePix pro 7.0 of GenePix 4100A Microarrays Scanner (Molecular Devices, LLC).

data_processing: The R package snapCGH  was used for background subtraction and normalization.

label_protocol: 1g of DNA was labeled following the standard Agilent protocol: “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. Enzymatic Labeling for blood, cells, or tissues” (Version 7.4, August 2015)”. Cy3 and Cy5 were used for control and thymocyte samples, respectively.

extract_protocol: DNeasy Blood and Tissue Kit (Qiagen) following recommendations of the manufacturer

value: Thymocytes

value: Kidney


title: CGH Tdp2+/+Atm-/- Exp1

source_name: Brain/Kidney

value: Brain/Kidney


title: CGH Tdp2+/+Atm-/- Exp2


title: CGH Tdp2+/+Atm-/- Exp3


title: heat shock basis klang_T15_28

value: wild-type


title: HC4


title: heat shock basis klang_N15_28


title: CGH Tdp2-/-Atm-/- Exp3


title: CGH Tdp2-/-Atm-/- Exp4


title: RNA_ileal_tissue_Sample9_rep1

description: Gene expression from RNA from ileal tissue of Sample9_rep1


title: CGH Tdp2-/-Atm-/- Exp5


title: CGH Tdp2-/-Atm-/- Exp2


title: RNA_ileal_tissue_Sample8_rep2

description: Gene expression from RNA from ileal tissue of Sample8_rep2


title: 148KO D3 rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: 148KO D3_monocyte-derived dendritic cells

growth_protocol: Cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37°C and 5% CO2 or collected directly for subsequent experiments. To obtain moDCs, mouse monocytes were isolated from BM with the Mouse Monocyte Isolation Kit (BM) according to the technical manual (Miltenyi, Germany). Cells were cultured with 100ng/mL GM-CSF (Peprotech) and 50ng/mL IL-4 (Peprotech) for 7 days and then sorted by Flow cytometry (FACSAriaTM III, BD).

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Mouse monocyte derived dendritic cells were primed with interferon α for 24 hours, and then cultured with R837, together with or without spermidine for 18 hours.

value: Bone marrow

value: monocyte-derived dendritic cells

value: GMCSF+IL4 day 3


title: 148KO D3 rep3


title: 148KO D3 rep1


title: RNA_ileal_tissue_Sample10_rep2

description: Gene expression from RNA from ileal tissue of Sample10_rep2

value: uninvolved small bowel (SB) ileal tissue


title: HC2

value: male

value: blood


title: WT D3 rep3

source_name: WT D3_monocyte-derived dendritic cells

value: wild type


title: RNA_ileal_tissue_Sample7_rep2

description: Gene expression from RNA from ileal tissue of Sample7_rep2


title: RNA_ileal_tissue_Sample7_rep1

description: Gene expression from RNA from ileal tissue of Sample7_rep1


title: CGH Tdp2-/-Atm-/- Exp1


title: heat shock klang_O15_43

value: 15 min 43 °C

value: heat shock


title: Chlorprothixene treated Kasumi-1 cells, 24 hours

first: Ji

last: Zhang

state: Select a State or Province

address: 197 Ruijin 2nd Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-Seq reads were mapped to human reference genome (hg19) using hisat2 with default parameters
FPKM value for each gene was calculated by StringTie
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

source_name: Kasumi-1 cell line

growth_protocol: NB4 and Kasumi-1 cells were grown in 1640 medium with 10% FBS.

extract_protocol:
Cellular RNA was isolated by RNeasy Mini Kit (Qiagen, Germantown, MD, USA) using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.
RNA sequencing libraries were prepared according to the IlluminaTruseq TM  RNA sample prep Kit

value: Chlorprothixene 40 uM 24 hours

tag: cell line


title: HC3

value: healty control

value: peripheral blood mononuclear cells (PBMC)


title: RNA_ileal_tissue_Sample6_rep2

description: Gene expression from RNA from ileal tissue of Sample6_rep2

tag: ^sample

value: female


title: Chlorprothixene treated Kasumi-1 cells, 12 hours

value: Chlorprothixene 40 uM 12 hours


title: RNA_ileal_tissue_Sample8_rep1

description: Gene expression from RNA from ileal tissue of Sample8_rep1

tag: batch


title: WT D3 rep2

tag: tissue


title: RNA_ileal_tissue_Sample6_rep1

description: Gene expression from RNA from ileal tissue of Sample6_rep1

tag: gender


title: RNA_ileal_tissue_Sample5_rep2

description: Gene expression from RNA from ileal tissue of Sample5_rep2

tag: age


title: WT D3 rep1


title: Un-treated Kasumi-1 cells


title: 148KO D0 rep3

source_name: 148KO D0_monocyte-derived dendritic cells

value: GMCSF+IL4 day 0


title: Chlorprothixene treated Kasumi-1 cells, 6 hours

value: Chlorprothixene 40 uM 6 hours


title: RNA_ileal_tissue_Sample5_rep1

description: Gene expression from RNA from ileal tissue of Sample5_rep1


title: 148KO D0 rep2


title: Chlorprothixene treated NB4 cells, 24 hours

source_name: NB4 cell line


title: 148KO D0 rep1


title: RNA_ileal_tissue_Sample4_rep2

description: Gene expression from RNA from ileal tissue of Sample4_rep2


title: HC1


title: RNA_ileal_tissue_Sample3_rep2

description: Gene expression from RNA from ileal tissue of Sample3_rep2


title: Chlorprothixene treated NB4 cells, 6 hours


title: Un-treated NB4 cells


title: RNA_ileal_tissue_Sample4_rep1

description: Gene expression from RNA from ileal tissue of Sample4_rep1


title: WT D0 rep3

source_name: WT D0_monocyte-derived dendritic cells


title: WT D0 rep2


title: WT D0 rep1


title: RNA_ileal_tissue_Sample3_rep1

description: Gene expression from RNA from ileal tissue of Sample3_rep1


title: Control_Genomic_Input_3

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Unprecipitated Genomic Input DNA
Counts of reads within each peak investigated

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
Nascent RNA-seq reads were aligned to the RN6 transcriptome using STAR
Nascent RNA-seq counts were generated using HTSeq-count
ChIP-seq reads and Unprecipitated Input reads were aligned to the RN6 genome assembly using BWA
Peak calling was performed with MACS2
Peaks were filtered using the IDR pipeline from the Encode Project with an IDR cutoff of 0.01.
Number of reads in peaks were counted using HTSeq-count.
Genome_build: RN6
Supplementary_files_format_and_content: Peak calling was performed with MACS2, Count files were generated using HTSeq-count.
Supplementary_files_format_and_content: BigWig Read-Count Normalized Files. Merged bigWig files contain the average of all individual samples.

organism: Rattus norvegicus

source_name: Unprecipitated Input Controls

extract_protocol:
Nascent RNA: Addition of biotinylated Uracil to cell culture followed by biotinylation pulldown of Nascent RNA plus Qiagen miRNAeasy
ChIP-Seq: Active Motif ChIP-it
NEBNext adapter ligation or SMARTer smRNA-seq adapter ligation kit

treatment_protocol: 50 micromolar cAMP followed by 30 minutes or 3.5 hours of washout

value: Primary Schwann Cells

value: Control


title: Chlorprothixene treated NB4 cells, 12 hours


title: RNA_ileal_tissue_Sample2_rep2

description: Gene expression from RNA from ileal tissue of Sample2_rep2


title: Control-t3_rep2

description:
DNA - integrated sgRNA sequence
3day growth, replicate 2
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt

data_processing:
CRISPR screen analysis
illumina basecalling
casTLE normalization and analyzis
MAGeCK normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_CRISPR.sh
comma separated value text files with normalized abundance measurements and differential representation (output from casTLE and MAGeCK)

growth_protocol: Control and C9KO cells infected with the genome-wide sgRNA library were grown in separate spinner flasks. Cells were maintained for 10 days at 1000× coverage (~1000 cells containing each sgRNA) at a concentration of 500,000 cells/mL,

extract_protocol:
Genomic DNA was extracted for all screen populations separately according to the protocol included with QIAGEN Blood Maxi Kit.
sgRNA sequences were amplified and prepared for deep-sequencing by two sequential PCR reactions as described previously (Morgens et al., 2016).

treatment_protocol: ~450 million control and ~450 million C9KO cells were differentiated with 50nM PMA in 300 ml of 50nM PMA-treated U937 growth media in three 15 cm tissue culture dishes. After three days, the supernatant was removed and pelleted to isolate any non-adherent cells while the adherent cells were trypsinized. Both cell populations were pooled together and replated in fresh media lacking PMA for two additional days. On the fifth day, genomic DNA was extracted.

value: WT


title: RNA_ileal_tissue_Sample2_rep1

description: Gene expression from RNA from ileal tissue of Sample2_rep1

extract_protocol: Two fresh, unstained 5-µm FFPE tissue sections on glass microscope slides were obtained. Slides were not baked after cutting. For each sample, the two tissue sections were scraped off of the slides using a clean razor and placed in 1.5 mL Eppendorf tubes. The tubes were briefly centrifuged to place the sample towards the bottoms or sides of the tube. RNA extraction and DNase treatment was performed using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s instructions, using the Xylene protocol for the paraffin removal step and 30 µL RNase-free H2O for the elution step. RNA was initially quantified by NanoDrop. Subsequent total RNA quantification and quality assessment was performed by Bioanalyzer 2100 (Agilent Technologies). Samples were excluded from the study if >20% of the RNA fragments were >200 base pairs in length, as determined with the Bioanalyzer software.


title: RNA_ileal_tissue_Sample1_rep2

description: Gene expression from RNA from ileal tissue of Sample1_rep2


title: Control_Genomic_Input_2


title: Control_Genomic_Input_1


title: Control-t3_rep1

description:
DNA - integrated sgRNA sequence
3day growth, replicate 1
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: RNA_ileal_tissue_Sample1_rep1

description: Gene expression from RNA from ileal tissue of Sample1_rep1


title: Control-t12_rep2

description:
DNA - integrated sgRNA sequence
12day growth, replicate 2
combo_Control-t12_rep1_vs_C9KO-t12_rep1_VS_Control-t12_rep2_vs_C9KO-t12_rep2.csv
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: 3.5hr_Genomic_Input_3

value: 30 minute cAMP at 100 micromolar followed by 3.5 hour washout


title: Macaque-ChIPseq-input

organism: Macaca mulatta

source_name: Testis

value: Testis

tag: developmental stage

value: Adult

tag: chip antibody


title: Control-t12_rep1

description:
DNA - integrated sgRNA sequence
12day growth, replicate 1
combo_Control-t12_rep1_vs_C9KO-t12_rep1_VS_Control-t12_rep2_vs_C9KO-t12_rep2.csv
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: Macaque-ChIPseq-AMYB_ChIP

value: anti-A-MYB


title: Control-PMA-t3_rep2

description:
DNA - integrated sgRNA sequence
3day growth, replicate 2
Control-PMA-t12_rep1,Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep1,C9KO-PMA-t12_rep2.gene_summary.txt

value: PMA treated WT


title: 30min_Genomic_Input_3

description:
Unprecipitated Genomic Input DNA
Counts of reads within each peak investigated
Run 2 Single-read fastq file

value: 30 minute cAMP at 100 micromolar followed by 30 minute washout


title: 3.5hr_Genomic_Input_1


title: 30min_Genomic_Input_2


title: swim3_2017July

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

data_processing:
Base calling and demultiplexing was done using Illumina’s HiSeq 2500 built-in software
FastQC v0.11.7 was run to check quality of reads
Alignment was done using STAR v2.6.1a, with default alignment parameters to PA14 genome UCBPP-PA14_109
Transcript counts were generated using HTSeq-count v0.9.1, with the options -s reverse -a 10 -f bam -r pos -m intersection-nonempty -t CDS
MultiQC v1.6.dev0 was used to compile a report for the above data processing steps
Genome_build: ASM1462v1
Supplementary_files_format_and_content: Tab-delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa

source_name: PA14 cells

growth_protocol: Swarming and swimming agar plates

extract_protocol:
RNA isolation was perfomed using the Rneasy Mini Kit (QIAGEN) and eluted RNA was purified using the TURBO DNA-free kit (Thermo-Fisher). Samples were depleted of rRNA using the RiboZero Bacteria Kit (Illumina)
cDNA libraries were constructed using KAPA Stranded Total RNA Kit (Kapa Biosystems)

tag: condition

value: control


title: M-MDSCs_normal_8mon_rep3

city: shanghai

first: yujuan

last: shen

address: Rui jin Er road

institute: National Institute of Parasitic Diseases

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Eg(-)M-MDSC-3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: M-MDSCs, 8mon, normal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified with a RNeasy Mini Kit (Qiagen, p/n 74104) and quantified using NanoDrop ND-2000 (Thermo Fisher Scientific). RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Splenic M-MDSCs were isolated immediately after the BALB/c mice sacrificed under sterile conditions at 8 months after Echinococcus granulosus protoscoleces infection. Single-cell suspensions were enriched with magnetic cell sorting (MACS; Miltenyi Biotec) according to the manufacturer’s protocol.

value: BALB/c

value: spleen

value: M-MDSCs

tag: infection

tag: time


title: M-MDSCs_Eg-infected_8mon_rep3

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Eg(+)M-MDSC-3

source_name: M-MDSCs, 8mon, Eg-infected

tag: strain

value: Echinococcus granulosus

value: 8 months after infection


title: M-MDSCs_Eg-infected_8mon_rep2

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Eg(+)M-MDSC-2


title: Control-PMA-t12_rep2

description:
DNA - integrated sgRNA sequence
12day growth, replicate 2
combo_Control-PMA-t12_rep1_vs_C9KO-PMA-t12_rep1_VS_Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep2.csv
Control-PMA-t12_rep1,Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep1,C9KO-PMA-t12_rep2.gene_summary.txt

source_name: U937 cells

tag: treatment


title: M-MDSCs_normal_8mon_rep2

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Eg(-)M-MDSC-2


title: M-MDSCs_normal_8mon_rep1

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Eg(-)M-MDSC-1


title: M-MDSCs_Eg-infected_8mon_rep1

description:
Microarray Analysis of LncRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Eg(+)M-MDSC-1


title: swim2_2017July


title: 30min_Genomic_Input_1

description:
Unprecipitated Genomic Input DNA
Counts of reads within each peak investigated


title: 3.5hr_Genomic_Input_2


title: Control-PMA-t12_rep1

description:
DNA - integrated sgRNA sequence
12day growth, replicate 1
combo_Control-PMA-t12_rep1_vs_C9KO-PMA-t12_rep1_VS_Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep2.csv
Control-PMA-t12_rep1,Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep1,C9KO-PMA-t12_rep2.gene_summary.txt


title: Control_H3K4me3_3

description:
Anti-H3K4me3 Immunoprecipitated
Counts of reads within each peak investigated

source_name: H3K4me3 ChIP

tag: antibody


title: C9KO-t3_rep2

description:
DNA - integrated sgRNA sequence
3day growth, replicate 2
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: CD62L low CD4+ T cells from non-responder of patient 1; ICI-21

city: Koto-ku,

first: Masashi

last: Kitazawa

state: Tokyo

institute: National of Institute of Advanced Industrial Science and Technology (AIST)

hyb_protocol: Following fragmentation, 1.8 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console™ Software 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CD62L low CD4+ T cells_non-responder

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip™ WT PLUS Reagent Kit Manual, Affymetrix).

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

tag: subject id

tag: response to nivolumab treatment

value: non-responder

tag: cell

value: CD62L low CD4+ T cells


title: CD62L low CD4+ T cells from non-responder of patient 2; ICI-52


title: Control_H3K4me3_2

tag: cell type

value: Primary Schwann Cells


title: Control-PMA-t3_rep1

description:
DNA - integrated sgRNA sequence
3day growth, replicate 1
Control-PMA-t12_rep1,Control-PMA-t12_rep2_vs_C9KO-PMA-t12_rep1,C9KO-PMA-t12_rep2.gene_summary.txt


title: CD62L low CD4+ T cells from intermediate responder of patient 2; ICI-56

source_name: CD62L low CD4+ T cells_intermediate responder

value: intermediate responder


title: swim1_2017July


title: C9KO-t12_rep2


title: swarm3_2017July

value: swarming


title: CD62L low CD4+ T cells from good responder of patient 2; ICI-44

source_name: CD62L low CD4+ T cells_good responder

value: good responder


title: 3.5hr_H3K4me3_3

value: 30 minute cAMP at 100 micromolar followed by 3.5 hour washout


title: 3.5hr_H3K4me3_2


title: C9KO-PMA-t3_rep2

value: PMA treated C9KO


title: swarm2_2017July


title: swim3_2016Nov


title: CD62L low CD4+ T cells from good responder of patient 1; ICI-39


title: 3.5hr_H3K4me3_1


title: swim2_2016Nov


title: C9KO-t3_rep1

description:
DNA - integrated sgRNA sequence
3day growth, replicate 1
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: swim1_2016Nov


title: CD62L low CD4+ T cells from intermediate responder of patient 1; ICI-17


title: swarm2_2016Nov


title: C9KO-PMA-t12_rep2


title: C9KO-PMA-t3_rep1


title: 30min_H3K4me3_2


title: Human-RNAseq-A8

value: Testis

value: Adult


title: swarm1_2016Nov


title: Control_H3K4me3_1

value: Control


title: 30min_H3K4me3_3

description:
Anti-H3K4me3 Immunoprecipitated
Counts of reads within each peak investigated
Run 2 Single-read fastq file

value: 30 minute cAMP at 100 micromolar followed by 30 minute washout


title: CD62L high CD4+ T cells from non-responder of patient 1; ICI-21

source_name: CD62L high CD4+ T cells_non-responder

value: CD62L high CD4+ T cells


title: CD62L high CD4+ T cells from intermediate responder of patient 2; ICI-56

source_name: CD62L high CD4+ T cells_intermediate responder


title: CD62L high CD4+ T cells from intermediate responder of patient 1; ICI-17


title: C9KO-PMA-t12_rep1


title: 30min_H3K4me3_1


title: C9KO-t12_rep1

description:
DNA - integrated sgRNA sequence
12day growth, replicate 1
combo_Control-t12_rep1_vs_C9KO-t12_rep1_VS_Control-t12_rep2_vs_C9KO-t12_rep2.csv
Control-t12_rep1,Control-t12_rep2_vs_C9KO-t12_rep1,C9KO-t12_rep2.gene_summary.txt


title: CD62L high CD4+ T cells from good responder of patient 1; ICI-39

source_name: CD62L high CD4+ T cells_good responder


title: CD62L high CD4+ T cells from good responder of patient 2; ICI-44


title: shTARBP2-Input-r1

status: Public on Dec 22 2019

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
Reads were first subjected to adapter removal and quality trimming using cutadapt (-q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15).
Bowtie2 (v.2.3;  --sensitive-local -N 1) was used to map the reads to the human genome (build hg19).
MDA-LM2 m6A sites from Alarcon et al (Cell, 2015) were used as feature to count reads in both MeRIP and input samples. EdgeR was used to compare changes in MeRIP/input upon TARBP2 silencing.
Genome_build: hg19
Supplementary_files_format_and_content: peaks_combined.bed and count-table

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep.

extract_protocol:
RNA samples were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on HiSeq 2500.

treatment_protocol: Cells were lysed using LB1 buffer, the nuclear fraction was then lysed with M-PER (Thermo Scientific) buffer and diluted 10-fold in dilution buffer before the immunoprecipitation. Rabbit α-m6A antibody (Synaptic Systems) and rabbit IgG control bound to protein A Dynabeads were used for the immunoprecipitations. The immunoprecipitated RNA was eluted with N6-methyladenosine (Sigma-Aldrich), ethanol precipitated and resuspended in water.

tag: shRNA

tag: fraction

value: Input


title: shControl-MeRIP-r1

value: shControl

value: MeRIP


title: shTARBP2-MeRIP-r1


title: shTARBP2-MeRIP-r2


title: shControl-MeRIP-r2


title: CD62L high CD4+ T cells from non-responder of patient 2; ICI-52


title: shTARBP2-Input-r2


title: MH-seq replicate 2

city: East lansing

first: Jiming

last: Jiang

state: Michigan

address: 612 Wilson Rd

institute: Michigan State University

data_processing:
Quality filtering and adapter trimming were done using Cutadapt.
Short reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MNase hypersensitive sites (MHS) were identified using Jazz software (https://github.com/zhangtaolab/Jazz/).
Genome_build: TAIR10
Supplementary_files_format_and_content: bed file were generated using Jazz software. bigWig file were generated using deepTools.

organism: Arabidopsis thaliana

source_name: seeding

growth_protocol: Sterilized seeds of A. thaliana ecotype Columbia (Col-0) were germinated in half-strength MS medium and grown under 16 h light/8 h dark cycle at 23°C for two weeks.

extract_protocol:
Two-week-old seedling tissues were collected and immediately fixed with 1% of final concentration of formaldehyde under vacuum for 10 min at room temperature, then followed by 5min neutralization by adding 0.125 M as the final concentration of glycine. Approximately 2.0 g of fixed seedling tissues was ground into a fine powder in liquid nitrogen and nuclei prepared following published protocols [73]. The final purified pellet of nuclei was suspended in 2.6 ml MNase digestion buffer (MNB, 10% sucrose, 50mM Tris-HCl, pH 7.5, 4mM MgCl2 and 1mM CaCl2). The suspended nuclei were divided into 5 of 1.5 ml Eppendorf tubes (500 µl per aliquot) after aliquoting 100 µl of nuclei as an undigested control.
Chromatin is digested by MNase and small fragments less than 100bp were collected. Illumina library following standard Illumina library preparation procedures.

tag: ecotype

value: Columbia (Col-0)

value: two weeks

tag: tissue

value: seedling


title: siControl

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Reads mapping to features residing within introns (e.g. miRNAs, snoRNA, and other RNAs) were removed bedtools (intersectBed).
MISO was then used to quantify changes in intron retention for introns that are bound by TARBP2. In comparison, a set of randomly selected introns without TARBP2 binding were investogated as controls.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

treatment_protocol: 10,000 cells were seeded and were transfected the next day with siRNAs via Lipofectaime 2000 (Invitrogen).

value: siControl


title: MH-seq

tag: age


title: siTARBP2


title: siControl_rep1

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Reads mapping to features residing within introns (e.g. miRNAs, snoRNA, and other RNAs) were removed bedtools (intersectBed).
MISO was then used to quantify changes in intron retention for introns that are bound by SRSF1. In comparison, a set of randomly selected introns without TARBP2 binding were investogated as controls.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

tag: replicate

tag: sirna


title: siControl_rep2


title: shControl-Input-r1


title: siSRSF1_rep2


title: Melanoma cells culture with Siglec1 expressing HEK293T cells 3

city: Goyang-si

first: Rohit

last: Singh

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Division of Tumor Immunology

country: South Korea

institute: National Cancer Center

description:
FPKM_from_2_and_3_mm10.transcript.addDesc.txt
FPKM_from_2_and_3_mm10.gene.addDesc.txt

data_processing:
Phred was used for base calling.
Adapter sequence were trimmed. Processed trimmed reads are mapped to known reference genomes through the TopHat program (version 2.0.13 ) and then create the aligned reads then mapped to UCSC mm10  by using Bowtie aligner (bowtie2 v2.2.3 ) which allows splice junction processing.
After read mapping, transcript assembly work was done through cufflinks program (version 2.2.1 ). As a result, the expression profile values for each sample were obtained for each transcript, and the FPKM (Fragment per Kilobase of Transcript per Million mapped reads) values were compiled based on the transcript / gene.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: B16F10-GFP melanoma

growth_protocol: HEK293T and B16F10-GFp cells were cultured in DMEM with 10% FBS. For coculture experiments HEK293T and B16F10-GFP clls were cultured in DMEM with 5% FBS and low bindiding plates (Corning) for 12 hours on 37°C, 5% CO2

extract_protocol:
Total RNA was extracted by using RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared by using TruSeq RNA library kit (Illumina) and standard Illumina RNA library preparation protocols.

treatment_protocol: For HEK293T and B16F10-GFP coculture experiments, HEK293T cells were transfected using lipofectamine 3000 (Invitrogen) with mammalian expression plasmid containing mouse Siglec1 (experimental samples) or empty plasmid (control samples) and cultured for 3 days before employing into coculture with B16F10-GFP cells.

value: B16F10 melanoma

tag: transfection


title: Melanoma cells culture with Siglec1 expressing HEK293T cells 1

description:
FPKM_from_1_mm10.transcript.addDesc.txt
FPKM_from_1_mm10.gene.addDesc.txt


title: Melanoma cells culture with Siglec1 expressing HEK293T cells 2


title: Melanoma cells culture with mock HEK293T cells 3

value: mock


title: Melanoma cells culture with mock HEK293T cells 1


title: Ca9-22_KPNA4i_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

description:
Gene expression three days after siRNA transfection.
Ca9-22_004

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: Ca9-22, KPNA4 knocked down cell, replicate 2

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

growth_protocol: 10% FBS DMEM + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Macherey-Nagel) according to the manufacturer's instructions.

tag: cell line

value: Ca9-22 cancer cell line

tag: genotype

value: KPNA4 knocked down


title: Melanoma cells culture with mock HEK293T cells 2


title: siSRSF1_rep1


title: Ca9-22_CTLi_rep2

description:
Gene expression three days after siRNA transfection.
Ca9-22_002

source_name: Ca9-22, negative control cell, replicate 2

value: control


title: shControl-Input-r2


title: smC122: Small RNA Cells ATG12-/- Biorep #2

first: Jayanta

last: Debnath

address: 513 Parnassus Ave, HSW-475 Campus Box 0502

institute: University of California, San Francisco

description: small RNAs

data_processing:
Raw reads were first trimmed using cutadapt (v2.3) by removing the polyA tail and the tri-nucleotide template switch.
Trimmed reads were then mapped to the human reference genome (GRCh38/hg38) using bowtie2 (v2.3).
Bedtoold (intersectBed) was used to count the number of reads that overlap annotated small RNA species (DASHRv2.0)
Differential expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include DESeq2 values for each sample

source_name: HEK293T cells

growth_protocol: Wild-type, ATG7-/- and ATG12-/- HEK293T cells were grown under normal conditions (DMEM, 10% FBS, 1x pen/strep)

extract_protocol:
Total RNA from wild-type, ATG7-/- and ATG12-/- HEK293T EVs and cells was isolated using the Macherey-Nagel NucleoSpin kit (# 740971) according to the manufacturer’s protocol.
Small RNA libraries were prepared using the SMARTer smRNA-Seq Kit for Illumina (Takara #635030), libraries were amplified for 12 cycles and subject to size selection using SPRI AMPure Beads (Beckman Coulter, #A63880).
RNA-seq: Single-end 50 bp read length on a HiSeq4000

treatment_protocol: Wild-type, ATG7-/- and ATG12-/- HEK293T cells were subject to serum starvation for 24h

tag: genotype/clone

value: ATG12-/- clone D9

tag: evs or cells

value: RNA from cells


title: smC73: Small RNA Cells ATG7-/- Biorep #3

description: small RNAs

value: ATG7-/- clone F2


title: smC121: Small RNA Cells ATG12-/- Biorep #1

description: small RNAs


title: Ca9-22_KPNA4i_rep1

description:
Gene expression three days after siRNA transfection.
Ca9-22_003

source_name: Ca9-22, KPNA4 knocked down cell, replicate 1


title: smC72: Small RNA Cells ATG7-/- Biorep #2

description: small RNAs


title: Ca9-22_CTLi_rep1

description:
Gene expression three days after siRNA transfection.
Ca9-22_001

source_name: Ca9-22, negative control cell, replicate 1


title: smC71: Small RNA Cells ATG7-/- Biorep #1

description: small RNAs


title: smCWT2: Small RNA Cells Wild-type Biorep #2

description: small RNAs

value: wild-type


title: smCWT1: Small RNA Cells Wild-type Biorep #1

description: small RNAs


title: smE123: Small RNA EVs ATG12-/- Biorep #3

description: small RNAs

value: RNA from extracellular vesicles


title: smCWT3: Small RNA Cells Wild-type Biorep #3

description: small RNAs


title: smE73: Small RNA EVs ATG7-/- Biorep #3

description: small RNAs


title: smE72: Small RNA EVs ATG7-/- Biorep #2

description: small RNAs


title: smE71: Small RNA EVs ATG7-/- Biorep #1

description: small RNAs


title: smE122: Small RNA EVs ATG12-/- Biorep #2

description: small RNAs


title: smEWT2: Small RNA EVs wild-type Biorep #2

description: small RNAs


title: smEWT1: Small RNA EVs wild-type Biorep #1

description: small RNAs


title: smC123: Small RNA Cells ATG12-/- Biorep #3

description: small RNAs


title: lrgC123: Large RNA Cells ATG12-/- Biorep #3

data_processing:
Salmon (v0.14) was used to map raw reads to the human transcriptome (Gencode v28) and this data was imported into R using tximport.
DESeq2 was then used to perform differential gene expression analysis.
Genome_build: Gencode v28
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 values for each sample

extract_protocol:
Total RNA from wild-type, ATG7-/- and ATG12-/- HEK293T EVs and cells was isolated using the Macherey-Nagel NucleoSpin kit (# 740971) according to the manufacturer’s protocol.
Large RNA libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit - HI (Takara # 634875), purified using SPRI AMPure Beads (Beckman Coulter, #A63880), and amplified for 22 cycles.
RNA-seq: Single-end 50 bp read length on a HiSeq4000


title: siWTAP_rep1

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Reads mapping to features residing within introns (e.g. miRNAs, snoRNA, and other RNAs) were removed bedtools (intersectBed).
MISO was then used to quantify changes in intron retention for introns that are bound by TARBP2. In comparison, a set of randomly selected introns without TARBP2 binding were investigated as controls.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

extract_protocol:
RNA samples were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on an Illumina NextSeq 500.

value: siWTAP


title: lrgC122: Large RNA Cells ATG12-/- Biorep #2


title: siWTAP_rep2


title: siControl_rep1


title: lrgC121: Large RNA Cells ATG12-/- Biorep #1


title: smEWT3: Small RNA EVs wild-type Biorep #3

description: small RNAs


title: lrgC73: Large RNA Cells ATG7-/- Biorep #3


title: shTARBP2_nuclear_r1

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Cufflinks and cuffmerge (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and consolidated results across the samples.
Reads mapping to features residing within introns (e.g. miRNAs, snoRNA, and other RNAs) were removed bedtools (intersectBed).
featureCounts (v1.6) was then used to count intronic reads in each replicate and DESeq2 (Bioconductor 3.6) was used to compare samples.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

extract_protocol:
Nuclear RNA samples were collected using Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on an Illumina NextSeq instrument.

treatment_protocol: 100k cells from shControl or shTARBP2 cells (MDA-LM2 background) were seeded 2 days prior to RNA exatrction.


title: lrgC72: Large RNA Cells ATG7-/- Biorep #2


title: shTARBP2_nuclear_r2


title: shControl_nuclear_r2

value: shControl


title: shControl_nuclear_r1


title: smE121: Small RNA EVs ATG12-/- Biorep #1

description: small RNAs


title: siControl_rep2


title: siTPR_rep2

value: siTPR


title: lrgCWT3: Large RNA Cells Wild-type Biorep #3


title: lrgCWT2: Large RNA Cells Wild-type Biorep #2


title: shTARBP2_r1

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Cufflinks, cuffmerge, and cuffdiff (v.2.2.1) were then used to calculate reads per kilo base per million (RPKM) and compare samples. REMBRANDTS (Alkallas et al, 2018) was used to compare changes in RNA stability.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

extract_protocol:
RNA samples were extracted 48 hours later using total RNA isolation kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina NextSeq 500.

treatment_protocol: Hairpins targeting TARBP2 or non-targeting controls were used in this experiment.


title: lrgCWT1: Large RNA Cells Wild-type Biorep #1


title: lrgE123: Large RNA EVs ATG12-/- Biorep #3


title: siTPR_rep1


title: lrgE122: Large RNA EVs ATG12-/- Biorep #2


title: lrgC71: Large RNA Cells ATG7-/- Biorep #1


title: shControl_r1


title: lrgE73: Large RNA EVs ATG7-/- Biorep #3


title: lrgE72: Large RNA EVs ATG7-/- Biorep #2


title: lrgE71: Large RNA EVs ATG7-/- Biorep #1


title: NEET5-4_rep3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated file included normalized counts for each sample

source_name: complete seedling

growth_protocol: 7-day-old seedlings of Col, 3 NEET lines and 3 H89C lines were grown in liquid cultures (0.5x MS) were immediately frozen in liquid culture

extract_protocol:
Total RNA was isolated using TRIzol following the manufacturer’s instructions and purified using a NucleoSpin RNA Clean-up kit
TruSeqHT

treatment_protocol: 7-day-old seedlings of Col, 3 NEET lines and 3 H89C lines growing  in liquid cultures (0.5x MS) were immediately frozen in liquid culture

value: NEET5-4 transgenic line

value: complete seedling


title: lrgEWT2: Large RNA EVs Wild-type Biorep #2


title: lrgEWT1: Large RNA EVs Wild-type Biorep #1


title: NEET11-9_rep3

value: NEET11-9 transgenic line


title: NEET11-9_rep2


title: lrgEWT3: Large RNA EVs Wild-type Biorep #3


title: shTARBP2_r2


title: NEET5-4_rep1


title: NEET5-4_rep2


title: swarm1_2017July

source_name: PA14 cells

tag: strain

tag: condition

value: swarming


title: NEET10-10_rep3

value: NEET10-10 transgenic line


title: BGI EC109 plenti6

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description: strand-specific RNA-Seq

data_processing:
Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SAOPnuke software.
Read mapping was performed by using STAR (v2.5) with the reference human genome version 19 (hg19) as the annotation library.
For the splicing analysis, mapped reads were filtered and classified into the following three groups based on their distance and location around the annotated splice sites: 1) reads mapped to exon-exon junctions, 2) reads bridging exon-intron junctions, and 3) reads mapped completely to introns.
The reads in Group 3 were used for intron retention coverage and depth calculations. The reads in Groups 1 and 2 were used for the calculation of splicing index (SI) for each splice site for the selection of potential differential splicing candidates.
To identify the various types of splicing events including exon skipping, intron retention and alternative splice sites, the SI calculation was adjusted for each type of splicing events.
All potential splicing candidates were classified into either known/annotated alternative splicing or novel splicing events that are not represented in the annotation library, and were assessed by Fisher’s exact test and SI change.
For this study, only candidates with total junction reads≥15, |ΔSI| ≥ 10% with a FDR<0.2 in the opposite direction of change for KD and OE samples were selected.
Genome_build: hg19
Supplementary_files_format_and_content: spreadsheet file include ADAR1 or ADAR2 knockdown or overexpression specific high confidence alternative splicing events (intron retention, casette exon and alternative splice site)

source_name: human esophageal squamous carcinoma cells

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silecing ADAR1/2 or transfected with expression construct for overexpressing ADAR1/2.

tag: treatment

value: Empty vector control


title: IMP2 IP rep3

city: Boston

first: Ning

last: Dai

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using STAR
Transcript abundance was calculated using HTseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: IMP2 IP

growth_protocol: Mouse embryonic fiboblast (MEF) cells  were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
QIAGEN RNase kit
libraries were constructed according to Illumina TruSeq high throughput kit

treatment_protocol: MEF cells are deleted for IMP1 or IMP2

value: mouse embryonic fiboblast (MEF)

tag: molecule subtype

value: mRNA interacting with IMP2 protein


title: NEET10-10_rep2


title: NEET10-10_rep1


title: shControl_r2


title: IMP2 IP rep2

tag: cell type


title: BGI EC109 plenti ADAR2

description: strand-specific RNA-Seq

value: human esophageal squamous carcinoma cells

value: ADAR2 over expression


title: H89C4-7_rep3

value: H89C4-7 transgenic line


title: NEET11-9_rep1


title: H89C4-7_rep2


title: lrgE121: Large RNA EVs ATG12-/- Biorep #1

value: ATG12-/- clone D9


title: H89C23-10_rep2

value: H89C23-10 transgenic line


title: IMP1 IP rep2

source_name: IMP1 IP

value: mRNA interacting with IMP1 protein


title: BGI EC109 shAR2 #942

description: strand-specific RNA-Seq

value: ADAR2 knockdown


title: H89C4-7_rep1


title: H89C23-10_rep3


title: BGI EC109 shAR2 #939

description: strand-specific RNA-Seq


title: IMP1 IP rep3


title: H89C23-10_rep1


title: BGI EC109 shAR1 #9

description: strand-specific RNA-Seq

value: ADAR1 knockdown


title: H89C11-7_rep3

value: H89C11-7 transgenic line


title: BGI EC109 shAR1 #3

description: strand-specific RNA-Seq


title: IMP1 IP rep1


title: RNA IP IgG rep3

source_name: RNA IP IgG

value: mRNA interacting with IigG


title: H89C11-7_rep1

value: complete seedling


title: Col_rep3

value: wild type


title: IMP2 IP rep1


title: BGI EC109 Scr

description: strand-specific RNA-Seq

value: scramble shRNA treated


title: RNA IP IgG rep2


title: Col_rep1


title: SRSF1_CLIP_r2

data_processing:
After linker sequence removal and quality trimming (cutadapt; -u 5 -q 15 -m 20 -a GTGTCAGTCACTTCCAGCGG), sequence mapping was performed using BWA (v.0.7; -t 12 -n 0.06 -q 20) with default parameters (build hg19).
The binding sites were identified using the CTK package (Zhang and Darnell, Nature biotech, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: Identified HITS-CLIP peaks

growth_protocol: cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

extract_protocol:
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).


title: RNA IP IgG rep1


title: SRSF1_CLIP_r1


title: Col_rep2


title: IMP2 KO MEFs total RNA

source_name: IMP2 KO Total RNA

tag: genotype/variation

value: IMP2 KO

value: total mRNA


title: IMP1 KO MEFs total RNA

source_name: IMP1 KO Total RNA

value: mouse embryonic fiboblast (MEF)

value: IMP1 KO


title: siMETTL3_nuclear_r2

data_processing:
Tophat (v. 2.1.1) was used to map the reads to the human transcriptome (build hg19).
Reads mapping to features residing within introns (e.g. miRNAs, snoRNA, and other RNAs) were removed bedtools (intersectBed).
featureCounts (v1.6) was then used to count intronic reads in each replicate and DESeq2 (Bioconductor 3.6) was used to compare samples.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

extract_protocol:
Nuclear RNA samples were collected using Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek) with DNAse I treatment followed by Ribo-Zero Gold rRNA removal (Epicentre).
Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on an HiSeq 4000 Instrument.

tag: shRNA


title: siMETTL3_nuclear_r1


title: Fam46c KO repeat2

city: Beijing

first: Xiwen

last: Lin

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology,CAS

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs.

source_name: testes

extract_protocol:
Total RNA from testis was isolated by TRIzol. The RNA libraries were constructed by Illumina library preparation protocols. High-throughput sequencing was performed on Illumina HiSeq X10 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: background strain

value: DBA/C57 F1

value: testes

tag: gender

value: male

tag: development stage

value: Adult

value: Fam46c KO


title: Fam46c KO repeat1

tag: tissue


title: IMP2 WT MEFs total RNA

source_name: IMP2 WT Total RNA


title: H89C11-7_rep2

tag: replicate


title: siControl_nuclear_r2

value: siControl


title: WT repeat 2

value: WT


title: IMP1 WT MEFs total RNA

source_name: IMP1 WT Total RNA


title: WT repeat 1


title: shXRN2-r2

data_processing:
STAR (v. 2.5) was used to map the reads to the human transcriptome (build hg19).
HTSeq-count (v.0.7) was then used to count reads in each gene and DESeq2 was used to compare samples.
Genome_build: hg19
Supplementary_files_format_and_content: Gene count files

extract_protocol:
RNA samples were collected using total RNA Purification Kit (Norgen Biotek).
Libraries were generated using QuantSeq 3’ mRNA-Seq library prep kit fwd (Lexogen) and run on an HiSeq 4000 Instrument.

treatment_protocol: EXOSC10 and XRN2 knockdown cells, along with shControl cells, in biological replicates were used for this experiment.


title: siControl_nuclear_r1


title: siFOXD3 rep3

middle: Xiang

last: jun

state: Shanghai

address: 500 Dongchuan Rd

department: the Institute of Biomedical Sciences and School of Life Sciences

institute: East China Normal University

data_processing:
Sequencing tags were mapped to the human (Homo sapiens) genome (version hg19) using the software TopHat
Transcript abundance was estimated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: lung cancer cell line

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

value: lung cancer cell line


title: shEXOSC10-r2


title: siFOXD3 rep2


title: shXRN2-r1


title: urinary_HC_rep4

description: Gene expression in urine from healthy controls.

hyb_protocol: Cy3-labeled miRNA samples were hybridized in a reaction volume of 45 µl containing 1x Hi-PRM hybridization buffer and 1x GE blocking agent following the manufacturer's instructions. The mixed samples were hybridized to Agilent Human miRNA Microarrays (G4872A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_miRNA and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: urinary_007, collected from healthy controls, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from urinary RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions. T4 RNA ligase and Cy-3-pCp were used for labeling the miRNA samples.

extract_protocol: miRNA was extracted with miRNeasy Serum/Plasma Kit (Qiagen, Valencia, CA)  according to the manufacturer's instructions.

tag: sample type

value: urine sample