title: ELT3-245-RAPA_20nM_24h_rep2


title: MII 111815_02 SOLO

status: Public on Sep 06 2018

type: SRA

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64 (SPIA libraries) & v2.7.6 (SoLo libraries)
Hisat2  to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Macaca mulatta

source_name: MII Oocyte

growth_protocol: Control ovarian stimulation protocol (COS) was used for the collection of oocytes. Rhesus macaques were observed daily for signs of menses. Within day 1-4 of menses, animals were administered an intramuscular injection of recombinant macaque FSH (r-mFSH; National Hormone and Peptide Program, A. F. Parlow, UCLA) twice daily for a total of 7 days. On day 8 a subset of animals was used for collection of GV oocytes and another subset of animals were administrated an intramuscular injection of 1000 IU of human chorionic gonadotropin (hCG; LaJ olla Discount Pharmacy, La Jolla, CA). On day 9, ultrasound-guided needle aspiration of follicles was used for the collection of oocytes. Oocytes were observed for maturation status for both normal GV and MII, and FTM oocytes.

extract_protocol:
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA).  After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011).  After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.
SoLo libraries: cDNA libraries were produced with Nugen Ovation SoLo RNA-Seq(NuGEN, San Carlos, CA). After bead purification, the cDNA was processed: end repair, adaptor ligation and first round library amplification and purification. Then 20 ng of each library was used for the remainder of library preparation, which included use of InDA-C primers for rRNA depletion, as well as 2nd round library amplification and purification steps. SoLo Custom R1 primer was used instead of a standard Illumina R1 sequencing primer for the sequencing of the libraries.

tag: tissue

value: oocyte

tag: developmental stage

value: MII

tag: library processing kit

value: SoLo


title: SO DS, rep4

type: RNA

city: UPM Serdang

first: King Hwa

last: Ling

state: Selangor

address: Faculty of Medicine and Health Sciences

department: Department of Biomedical Sciences

country: Malaysia

institute: Universiti Putra Malaysia

description: Gene expression of SO DS.

hyb_protocol: 600 ng 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 25 ul containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K chip 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 SureScan Microarray Scanner using AgilentG3_GX_1color setting (G3 format, standard mode).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 028005_D_F_20140728 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Soleus tissue, DS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

extract_protocol: RNA was prepared using the MasterPure™ RNA Purification Kit (Epicentre, U.S.A.) following the manufacturer's recommendations. The protocol includes RNase-Free DNase I digestion. RNA was quantified using a NanoVue™ Plus Spectrophotometer (GE Healthcare, UK) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain/background

tag: genotype/variation

value: Skeletal muscle

tag: muscle type

value: soleus (SO)


title: ELT3-245_DMSO_rep2

city: Memphis

first: Aristotelis

last: Astrinidis

state: TN

address: 50 N Dunlap

department: Pediatrics

institute: University of Tennessee Health Sciences Center

description: Gene expression data from rapamycin-resistant cell line ELT3-245 (DMSO control)

hyb_protocol: Hybridization was performed using GeneChip WT PLUS Reagent Kit (Applied Biosystems).

scan_protocol: Microarrays were scanned on a GeneChip Scanner (Affymertrix) according to GeneChip WT PLUS Reagent Kit (Applied Biosystems).

data_processing: Data was normalized and log transformed using ThermoFisher TAC console with RMA.

label: biotin

organism: Rattus norvegicus

source_name: ELT3-245 cell line

label_protocol: cDNA was labelled using GeneChip WT PLUS Reagent Kit (Applied Biosystems).

growth_protocol: Cells (200,000-400,000 per 100 mm cell culture plate) were grown in triplicate in 10 ml media (IIA complete media supplemented with 10% FBS) for 24 hours.

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer instructions.

treatment_protocol: Rapamycin (10 ul from a stock of 20 mM in DMSO, final concentration 20 nM) or DMSO (10 ul) was added to the cultures, and cells were incubated for 24 hours.

tag: cell line

tag: treatment

value: DMSO


title: H23.HOTAIR-N.siRNA.Sample3

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed of sequencing adapters, primers, and low quality reads with autoadapt.pl 0.2 using default settings
Trimmed FASTQ files were aligned to HG19 using STAR 2.6.0c. Gene and isoform expression values were determined using RSEM 1.3.0 rsem-calculate-expression with “--star”, “--star-gzipped-read-file”, “--output-genome-bam”, and “-p 48” options
Genome_build: hg19
Supplementary_files_format_and_content: text file with expression signal in expected_count, TPM, FPKM

organism: Homo sapiens

source_name: Lung cancer cell line H23_HOTAIR-N siRNA

growth_protocol: H23 cells were cultured in RPM1640 with 10% FBS.

extract_protocol:
Total cell RNA was extracted from the treated cells at 48 hrs after transfection using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: HOTAIR-N-specific siRNA and control siRNA were transfected into H23 cells using RNAiMAX.

tag: cell type

value: lung cancer

value: Lung


title: MII 021916_01 SOLO


title: H23.HOTAIR-N.siRNA.Sample1


title: Fat_Meishan_5-months_4

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

country: Japan

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

description: Biological replicate 4 of 7. Liver, Meishan crossbred pig, 5 months old.

hyb_protocol: Hybridization was carried out using Gene Expression Hybridization kit (Agilent) in SureHyb Hybridization chambers. Each array slide was washed with Gene Expression Wash Pack (Agilent).

scan_protocol: Microarray slides were scanned at 5 microns/pixel resolution using Agilent DNA Microarray Scanner G2505B.

data_processing: Microarray images were analyzed with Agilent Feature Extraction Software (ver. 9.5) using the GE2-v5_95_Feb07 FE extraction protocol.

organism: Sus scrofa

label_protocol: Quick Amp Labeling Kit (Agilent)

growth_protocol: All animals were fed a diet according to the Japanese Feeding Standard for Swine.

extract_protocol: Rneasy Midi Kit (QIAGEN)

treatment_protocol: All animals were handled humanely under the guidelines of the Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO).

value: Subcutaneous adipose tissue

tag: Sex

value: female

tag: breed

value: LWD x Meishan (LWDM)

tag: age

value: Liver

value: LWD


title: H23.CTLsi.Sample3

source_name: Lung cancer cell line H23_control siRNA


title: FTM 112712_01 SPIA

data_processing:
Illumina Real Time Analysis (RTA) v2.7.6
Hisat2  to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: read counts

source_name: Failed to mature oocyte

extract_protocol:
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA).  After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011).  After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.

value: FTM oocyte


title: ELT3-245_DMSO_rep3


title: H23.CTLsi.Sample2


title: FTM 111312_01 SPIA


title: SO WT, rep4

description: Gene expression of SO WT.

source_name: Soleus tissue, WT

value: WT


title: H23.HOTAIR-N.siRNA.Sample2


title: FTM 042613_03 SPIA


title: Fat_Meishan_5-months_3

description: Biological replicate 3 of 7. Liver, Meishan crossbred pig, 5 months old.


title: SO DS, rep3

description: Gene expression of SO DS.


title: Millipore-2ug_IP

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

country: Canada

institute: UHN

data_processing:
MeRIP-seq reads were aligned to the hg38 genome assembly using STAR2 version 2.4.2a. For the pair-end read mates were pooled and treated as single-end reads.
m6A peaks were called using MeTpeak
Genome_build: hg38
Supplementary_files_format_and_content: BED file for m6A peak

source_name: A549 cell line

growth_protocol: Human lung cancer cell line A549 was maintained in RPMI-1640 medium with 10% fetal bovine serum.

extract_protocol:
Total RNA from cells in culture was extracted using Trizol reagent (Thermo Fisher Scientific, Waltham, MA), and then treated with DNase I (04 716 728 001, Roche Diagnostics, Indianapolis, IN) for 20 min at 37°C to remove DNA contamination.
RNA libraries were prepared  using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian.

value: A549 cell line

tag: merip-seq antibody

value: anti-m6A(ABE572, Millipore)


title: SO WT, rep3

description: Gene expression of SO WT.


title: FTM 042613_02 SPIA

value: oocyte


title: Fat_Landrace_5-months_8

description: Biological replicate 8 of 8. Liver, Landrace crossbred pig, 5 months old.

value: LWD x Landrace (LWDL)


title: SO DS, rep2

description: Gene expression of SO DS.


title: Fat_Meishan_5-months_1

description: Biological replicate 1 of 7. Liver, Meishan crossbred pig, 5 months old.


title: SO WT, rep2

description: Gene expression of SO WT.


title: Fat_Meishan_5-months_2

description: Biological replicate 2 of 7. Liver, Meishan crossbred pig, 5 months old.


title: Millipore-6ug_IP


title: EDL DS, rep3

description: Gene expression of EDL DS.

source_name: EDL tissue, DS

value: extensor digitorum longus (EDL)


title: Fat_Landrace_5-months_7

description: Biological replicate 7 of 8. Liver, Landrace crossbred pig, 5 months old.


title: SO DS, rep1

description: Gene expression of SO DS.

value: Skeletal muscle


title: FTM 042613_01 SPIA


title: Fat_Landrace_5-months_6

description: Biological replicate 6 of 8. Liver, Landrace crossbred pig, 5 months old.


title: SO WT, rep1

description: Gene expression of SO WT.

value: soleus (SO)


title: EDL WT, rep3

description: Gene expression of EDL WT.

source_name: EDL tissue, WT


title: EDL DS, rep2

description: Gene expression of EDL DS.


title: FTM 040611_03 SPIA


title: H23.CTLsi.Sample1


title: Millipore-12ug_IP


title: Millipore-32ug_IP


title: Normal2

city: Shanghai

first: Feng

last: Liu

address: 600 Yishan Road

department: Department of Otolaryngology-Head and Neck Surgery

country: China

institute: Shanghai JiaoTong University Affiliated Sixth People's Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value. miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Genome_build: hg38

source_name: PBMC

growth_protocol: PBMCs were directly isolated from blood from health donors and TB patients

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: No Extra treatments were performed

value: PBMC

tag: diagnosis

value: Healthy


title: Normal3


title: Synaptic-32ug_IP

value: anti-m6A(202 203, Synaptic)


title: NEB-32ug_IP

value: anti-m6A(E1610S, NEB)


title: Normal1


title: FTM 011513_05 SPIA


title: FTM 040611_01 SPIA


title: FTM 011513_06 SPIA


title: FTM 011513_04 SPIA


title: Input


title: Sick3

value: Tuberculosis


title: CMS_Lut_H

city: Yangling

first: Yingxue

last: Fu

state: Shaanxi

address: Taicheng Road 3

institute: Northwest A&F University

data_processing:
Quality control of raw sequences from each sample was investigated using FastQC (v0.11.5).
Reads were then mapped to the Ensembl rat genome sequence (Rnor_6.0) using HISAT2 (v2.0.4) and assembled into transcripts by StringTie (v1.2.4) using a UCSC rn6 GTF (general transfer format) file.
FPKM (fragment per kilobase per million mapped reads) values were used to estimate the transcript abundance.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM values for all Samples

source_name: hippocampus

extract_protocol:
Total RNA was extracted and purified from ~30 mg tissue using the RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA-seq was performed at Genminix Informatics Ltd.,Co.(Shanghai, China) using Illumina HiSeq ×10 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On Week 7, the hippocampi and PFC of the rat brains were dissected from one normal rat and two CUMS rats treated with either saline or 100 mM/kg MGO.

tag: strain

value: Sprague-Dawley

tag: development stage

value: adult

value: male

value: CMS+luteolin

value: hippocampus


title: FTM 010813_01 SPIA

value: FTM oocyte


title: Sick2


title: Fat_Landrace_5-months_5

description: Biological replicate 5 of 8. Liver, Landrace crossbred pig, 5 months old.

value: Subcutaneous adipose tissue

value: female

value: Liver

value: LWD


title: Fat_Landrace_5-months_3

description: Biological replicate 3 of 8. Liver, Landrace crossbred pig, 5 months old.

value: LWD x Landrace (LWDL)


title: EDL WT, rep2

description: Gene expression of EDL WT.

value: WT

value: Skeletal muscle

value: extensor digitorum longus (EDL)


title: GV 050613_04 SPIA

source_name: Germinal vesicle oocyte

value: oocyte

value: GV


title: GV 050613_02 SPIA


title: CMS_MGO_H

value: CMS+methylglyoxal


title: CMS_MGO_F

source_name: prefrontal cortex

value: Sprague-Dawley

value: prefrontal cortex


title: Sick1

value: PBMC

value: Tuberculosis


title: AON-MBNL1-3

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
RNA-seq reads were mapped to the mm9 mouse genome assembly using STAR version 2.4.2a with the following parameters : --sjdbOverhang 99 --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outFilterMultimapNmax 40 --twopassMode Basic
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of genome read density were generated using bamCoverage from the deepTools package

growth_protocol: PC3 cells were cultured in RPMI medium supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
RNA was isolated using TRIZOL and subsequently AMBION RNA PureLink mini Kit
For RNA-Seq library preparation we followed the Illumina TruSeq RNA Sample Preparation Kit v2 manual.

treatment_protocol: PC3 cells were transfected with 100nM AON in a 6 well plate using 4ul of RNAiMAX (Invitrogen) following manufacturer protocol

value: Prostate cancer cell line

tag: transfected with

value: AON directed against MBNL1 exon 7

tag: time point

value: 72h post-transfection


title: GV 050613_01 SPIA

tag: tissue

tag: developmental stage


title: Fat_Landrace_5-months_2

description: Biological replicate 2 of 8. Liver, Landrace crossbred pig, 5 months old.

value: Subcutaneous adipose tissue

value: female


title: Fat_Landrace_5-months_1

description: Biological replicate 1 of 8. Liver, Landrace crossbred pig, 5 months old.

value: Liver

value: LWD


title: Fat_Landrace_5-months_4

description: Biological replicate 4 of 8. Liver, Landrace crossbred pig, 5 months old.

value: LWD x Landrace (LWDL)


title: Fat_Meishan_12-days_6

description: Biological replicate 6 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.

value: LWD x Meishan (LWDM)


title: Fat_Meishan_12-days_4

description: Biological replicate 4 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.


title: Fat_Meishan_12-days_5

description: Biological replicate 5 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.


title: Fat_Meishan_12-days_3

description: Biological replicate 3 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.


title: AON-MBNL1-2


title: CMS_H

value: adult

value: male

value: CMS+saline

value: hippocampus


title: EDL DS, rep1

description: Gene expression of EDL DS.

tag: strain/background

value: Skeletal muscle

value: extensor digitorum longus (EDL)


title: EDL WT, rep1

description: Gene expression of EDL WT.

tag: genotype/variation

value: WT


title: GV 030711_04 SPIA

value: oocyte

value: GV


title: AON-MBNL1-1

value: Prostate cancer cell line

value: AON directed against MBNL1 exon 7


title: Fat_Meishan_12-days_2

description: Biological replicate 2 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.

value: Subcutaneous adipose tissue


title: CMS_F

value: Sprague-Dawley

value: prefrontal cortex


title: CMS_Lut_F

value: CMS+luteolin


title: Fat_Landrace_12-days_5

description: Biological replicate 5 of 5. Subcutaneous adipose tissue, Landrace crossbred pig, 12 days old.

value: female

value: LWD x Landrace (LWDL)

value: Liver

value: LWD


title: Control_H

value: adult

value: male

value: saline


title: AON-SCR-3

value: 100nM of a scrambled antisense oligonucleotide (AON)

value: 72h post-transfection


title: GV 030711_03 SPIA

value: oocyte


title: AON-SCR-2


title: GV 030711_02 SPIA

value: GV


title: Control_F


title: GV 030711_01 SPIA


title: AON-SCR-1

value: Prostate cancer cell line


title: Fat_Meishan_12-days_1

description: Biological replicate 1 of 6. Subcutaneous adipose tissue, Meishan crossbred pig, 12 days old.

value: LWD x Meishan (LWDM)


title: A549 cells transfected with SUMO vector and infected with PR8∆NS1, replicate 2

status: Public on Sep 05 2018

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
After adapter removal with cutadapt (Martin, 2011) and base quality trimming to remove 3’ read sequences if more than 20 bases with Q < 20 were present, paired-end reads were mapped to the human (hg38) reference genome using STAR (Dobin et al., 2013) and gene count summaries were generated using featureCounts (Liao et al., 2014). Raw read counts were then combined into a numeric matrix, with genes in rows and experiments in columns and used as input for differential gene expression analysis with the Bioconductor Limma package (Ritchie et al., 2015) after multiple filtering steps to remove low-expressed genes. First, gene counts were converted to FPKM (fragments per kb per million reads) using the RSEM package (Li et al., 2011) with default settings in strand specific mode and only genes with expression levels above 1 FPKM in at least 50% of samples were retained for further analysis. Additional filtering removed genes with less than 50 total reads across all samples or less than 200 nucleotides in length. Finally, normalization factors were computed on the filtered data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom (Law et al., 2014) mean-variance transformation in preparation for Limma linear modeling. Data was fitted to a design matrix containing all sample groups and pairwise comparisons were performed between sample groups. eBayes adjusted P-values were corrected for multiple testing using the Benjamin-Hochberg (BH) method and used to select genes with significant expression differences.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing the Gene ID, raw counts and the normalized Log2 count per million reads.

growth_protocol: A549 cells were infected by the indicated viruses at an MOI of 2 for indicated hours.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, adding 600 μls RLT Buffer and 6 μls of B-mercaptoethanol to each sample.
One ug of DNase-treated RNA was depleted of rRNAs using the Ribo-Zero Gold rRNA  Removal Kit (Human/Mouse/Rat) according to the manufacturer’s instructions and purified  post-depletion with 1.6X volume AMPure XP beads. Barcoded directional RNA-Seq libraries  were then prepared using the TruSeq Directional Library Prep kit (Illumina), per kit  instructions. PCR products were purified with 1.8X volume AMPure XP beads and fragments  of 300-500 bp were size-selected using BluePippin 2% M1 gels (Sage Scientific). Afterwards,  libraries were sequenced on the Illumina HiSeq 2500 platform in a 100 bp single-end read run  Format.

value: transfected with SUMO vector

tag: infection

value: PR8∆NS1 virus

tag: time

value: 4 hours post-infection


title: A549 cells transfected with SUMO vector and infected with PR8∆NS1, replicate 1

tag: cell line

tag: treatment


title: A549 cells transfected with GFP vector, replicate 2

value: transfected with GFP vector


title: A549 cells transfected with SUMO vector, replicate 2


title: A549 cells transfected with empty vector, replicate 1

value: transfected with empty vector


title: A549 cells transfected with empty vector and infected with PR8∆NS1, replicate 1


title: A549 cells transfected with SUMO vector, replicate 1


title: A549 cells transfected with GFP vector, replicate 1


title: A549 cells transfected with empty vector and infected with PR8∆NS1, replicate 2


title: Fat_Landrace_12-days_1

description: Biological replicate 1 of 5. Subcutaneous adipose tissue, Landrace crossbred pig, 12 days old.

value: Subcutaneous adipose tissue

tag: Sex

value: female

value: LWD x Landrace (LWDL)


title: A549 cells transfected with empty vector, replicate 2


title: Fat_Landrace_12-days_3

description: Biological replicate 3 of 5. Subcutaneous adipose tissue, Landrace crossbred pig, 12 days old.

tag: breed

value: Liver

value: LWD


title: A549 cells depleted for Ubiquitin Conjugating Enzyme E2 (siUBE2I), Replicate 1


title: A549 cells depleted for control, replicate 2

value: depleted for control (siCtrl)


title: A549 cells depleted for control, replicate 1


title: CAPH2 ChIPseq 2

city: Kansas City

first: Jennifer

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline
ChIPseq reads from samples were aligned to the human genome UCSC hg19
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files that contain continuous data to be displayed in the genome browser

molecule: genomic DNA

source_name: Human embryonic kidney cells 293

growth_protocol: HEK293 cells were cultured in DMEM media in 150 mm dishes. The media was changed daily until 80% confluent, when the cells were harvested for ChIP.

extract_protocol:
Standard ChIP protocol was used. Briefly, nuclei were isolated using nuclearlysis buffer, followed by being lysed with SDS buffer to extract chromatin. The chromatin was sheared by Covaris sonicator to a size range of 300-700 base pairs. The chromatin samples were incubated with 6 μL antibodies overnight at 4°C with rotation, followed by incubation with Protein A/G dynabeads for 2 hours at 4°C with rotation. . The beads were washed twice with 0.1% SDS Lysis Buffer for 5 min each at 4°C, followed by washing twice with High Salt Wash Buffer for 5 min each at 4°C, followed by washing twice with Lithium Chloride Wash Buffer for 5 min each at 4°C. After that, the beads were washed with TE buffer with 0.2% Triton. Chromatin was eluted by adding elution buffer. Eluted chromatin was reverse cross-linked by adding 0.3M NaCl and incubating it overnight at 65°C, which is followed by treatment of 6 μL proteinase K. Chromatin was purified by Qiagen PCR purification kit (Qiagen, 28106), following the manufacturer’s protocol.
The Illumina adaptors were added to each chromatin sample for Solexa sequencing.

tag: cell type

value: human embryonic kidney cells

tag: passages

value: 10-13 passages

tag: antibody

value: NCAPH2 (Bethyl:A302-275A)


title: TFIIIC ChIPseq 2

value: TFIIIC (Bethyl:A301-291A)


title: CAPH2 ChIPseq 1


title: TFIIIC ChIPseq 1


title: S5_P4_Tomato+ cells

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_Matrix.txt").

source_name: Spinal Cord

growth_protocol: Transgenic mice were aged to 6 weeks of age under specific pathogen free conditions and subsequently Experimental Autoimmune Encephalmyelitis (EAE) was induced.

extract_protocol:
Mice were sacrificed and spinal cords were isolated and transferred to ice-cold PBS (Sigma-Aldrich). Tissue was then cut in small pieces and digested in RPMI containing 2% fetal calf serum (Sigma-Aldrich), 25mM HEPES (Sigma-Aldrich), DNase I (10ng/ml, StemCell Technologies) and Collagenase D (0,8mg/ml, Roche) for 30 min at 37°C. Reaction was stopped by addition 1:100 dilution of a 0.5M EDTA (Sigma-Aldrich) solution. Suspension was filtered through 70 µm cell strainers (Falcon) and resuspended in a 30% solution of Percoll (Sigma-Aldrich). After 30 min of gradient centrifugation at 10.800 r.p.m., the top (myelin) and lower (red cells) layers were removed and the remaining solution was filtered through 70µm cell strainers (Falcon) before further analysis. Cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: Active EAE was induced in adult mice by injecting 400μg of purified recombinant MOG (N1-125) in complete Freund's adjuvant (containing 10mg/ml Mycobacterium tuberculosis H37 Ra, Sigma-Aldrich). At day 0 and 2, 400ng of pertussis toxin (Sigma-Aldrich) was administered intraperitoneally.

tag: strain background

value: spinal cord

tag: genotype

value: Arginase-YFP x iNOS-tdTomato

tag: cell markers

value: Tomato+ cells


title: S5_P3_Unpolarized

value: Unpolarized


title: Fat_Landrace_12-days_2

description: Biological replicate 2 of 5. Subcutaneous adipose tissue, Landrace crossbred pig, 12 days old.

tag: age


title: S5_P2_Tomato+ YFP+ cells

tag: tissue

value: Tomato+ YFP+ cells


title: Fat_Landrace_12-days_4

description: Biological replicate 4 of 5. Subcutaneous adipose tissue, Landrace crossbred pig, 12 days old.


title: S5_P1_YFP+ cells

value: YFP+ cells


title: B6_P4_Tomato+ cells


title: B6_P1_YFP+ cells


title: B5_P4_Tomato+ cells


title: B5_P3_Unpolarized


title: A549 cells depleted for Ubiquitin Conjugating Enzyme E2 (siUBE2I), Replicate 2


title: B1_P3_Unpolarized


title: B5_P1_YFP+ cells


title: B5_P2_Tomato+ YFP+ cells


title: B1_P2_Tomato+ YFP+ cells


title: B1_P4_Tomato+ cells


title: MCF7-antiAGO2-FT-exp3-rep2

city: Palermo

first: Claudia

last: Coronnello

address: via Bandiera 11

country: Italy

institute: Fondazione RiMED

hyb_protocol: Cy3-labelled RNA, in a reaction volume of 45 ul containing 1x Agilent blocking agent and 1x Agilent Hi-RPM hybridization buffer following the manufacturers instructions was hybridized to Agilent Human miRNA Microarray 8x15K (Agilent-G4470C) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 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 (G2505B) using one color scan setting for 8x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol: miRNA-v1_95 and Grid: 021827_D_20081121) to obtain background subtracted and spatially detrended processed signal intensities. gTotalGeneSignal values were quantile normalized.

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 3, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions (Agilent protocol: G4170-90011_miRNA_ver_3.1.1).

growth_protocol: The MCF-7 human breast cancer cell line was purchased from American Type Culture Collection (ATCC, Rockville, MD, USA). Cells were cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), glutamine (4 mM) and penicillin/streptomycin (100 μg/ml).

extract_protocol: Total RNA (i.e. including mRNAs and microRNAs ) was extracted from IP fractions following the two-step method described in the RIP-Assay Kit, while total and unbound fractions were processed using TRIzol LS (ThermoFisher Scientific Inc.) according to the manufacturer’s instructions. In some cases, total RNA was isolated using the miRNeasy Mini Kit from Qiagen. RNA was quantified by NanoDrop (ThermoFisher Scientific Inc.) and RNA integrity and quality were assessed using the 2100 Agilent Bioanalyzer.

treatment_protocol: Immunoprecipitation (IP) of RISC proteins was performed using mouse monoclonal anti-AGO2 (clone 1B1-E2H5, RN003M), rabbit anti-GW182 (TNRC6A, RN033P) and the RIP-Assay Kit for microRNA (MBL International corporation). Briefly, cells (1.5x107) were suspended in 0.3 ml of miLysis buffer supplemented with protease and RNase inhibitors, after incubation on ice for 10min and one freeze-thaw cycle, the lysate was diluted five-times with lysis buffer and the cytoplasmic fraction was isolated by centrifugation at 12,000xg at 4 °C for 5 min. To eliminate nonspecific binding the lysate was incubated with protein A/G-agarose beads (SantaCruz) at 4 °C for 1 hour. The precleared lysates were then mixed with anti-AGO2 or anti-GW182 (25 ug of Ab/mg of lysate) armed beads, the use of preimmune mouse IgG isotype and rabbit IgG assessed the specificity of the precipitated immunocomplexes. After incubation overnight at 4 °C on a rocking platform, AGO2-IP and GW182-IP beads were washed three times with ice cold wash buffer.

tag: protein

tag: fraction

value: FT


title: MCF7-antiAGO2-IP-exp3-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 3, replicate 2

value: IP


title: MCF7-antiGW182-FT-exp1-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 1, replicate 2


title: MCF7-antiGW182-IP-exp3-rep2

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 3, replicate 2


title: MCF7-antiAGO2-IN-exp3-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 3, replicate 2

value: IN


title: MCF7-antiAGO2-IP-exp2-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 2, replicate 2


title: MCF7-antiGW182-FT-exp3-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 3, replicate 2


title: MCF7-antiAGO2-IP-exp1-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 1, replicate 2


title: MCF7-antiAGO2-IN-exp2-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 2, replicate 2


title: MCF7-antiAGO2-FT-exp2-rep2

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 2, replicate 2


title: MCF7-antiGW182-IP-exp3-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 3, replicate 1


title: MCF7-antiGW182-FT-exp2-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 2, replicate 2


title: MCF7-antiGW182-IN-exp3-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 3, replicate 2


title: MCF7-antiGW182-IP-exp2-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 2, replicate 1


title: MCF7-antiGW182-IN-exp3-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 3, replicate 1


title: FTVI-treated BMSC sample RP-003-P2

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 3µm

data_processing: Agilent Feature Extraction software version 11.0.1.1

source_name: Reference sample: pool of 5 samples of bone marrow-derived mesenchymal stromal cells

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: BM mononuclear cells (BMMNC) were isolated by density gradient centrifugation over Histopaque-1077 (Sigma-Aldrich, St Louis, MO).  Human Platelet Lysate was obtained from platelet concentrates, which were frozen at –80 ºC for at least 3 days, thawed at 37 oC, transferred to sterile tubes and centrifuged at 900 g for 30 min; the supernatants were pooled, aliquoted and stored at –20ºC. BMMNC were seeded in culture flasks at 160,000 cells/cm2 using low glucose DMEM (GIBCO Invitrogen Corporation, Gran Island, NY, USA) supplemented with 5 % HPL, plus 50 U/ml penicillin and 50 U/ml streptomycin, and heparin (2U/ml) incubated at 37oC in a humid atmosphere with 5 % CO2. First change of medium was performed at 24 h and from this point twice per week. First passage was made when cells achieved 60-80% confluence. Culture media was removed and culture flasks were washed with DPBS, then incubated with TrypLE Select reagent (GIBCO Invitrogen Corporation, Gran Island, NY, USA). Cells were pooled, centrifuged at 700 g for 5 min and seeded at a density of 1,000 cells/cm2. After the third passage, BM-hMSCs were harvested.

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: Five million detached BM-hMSCs were concentrated at 30 x 106 cells/ml in HBSS, without Ca2+ or Mg2+ (Gibco), containing 10 mM HEPES, 0.1 % human serum albumin (Sigma-Aldrich). Each sample was divided into two reaction tubes, buffer alone, and the other with 60 mU/ml of FTVI or FTVII (obtained from R&D Systems), as specified in each case, containing  1 mM GDP-fucose (Sigma-Aldrich) as enzyme substrate. Reactions were performed at 37 oC for 1 h with gentle shaking, followed by centrifugation and washing with DPBS.

tag: agent

source_name: Test sample: FTVI-treated bone marrow-derived mesenchymal stromal cells sample RP-003-P2

value: Bone marrow-derived mesenchymal stromal cells sample RP-003-P2

value: FTVI


title: FTVII-treated BMSC sample OSP-V001

source_name: Test sample: FTVII-treated bone marrow-derived mesenchymal stromal cells sample OSP_V001

value: Bone marrow-derived mesenchymal stromal cells sample OSP_V001

value: FTVII


title: FTVII-treated BMSC sample OSP-V001-P3

source_name: Test sample: FTVII-treated bone marrow-derived mesenchymal stromal cells sample OSP_V001-P3

value: Bone marrow-derived mesenchymal stromal cells sample OSP_V001-P3


title: Mock-treated BMSC sample OSP-V001-P3

value: Bone marrow-derived mesenchymal stromal cells

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample OSP_V001-P3

value: mock


title: MCF7-antiGW182-FT-exp3-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 3, replicate 1


title: MCF7-antiAGO2-IN-exp1-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 1, replicate 2.


title: MCF7-antiGW182-FT-exp2-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 2, replicate 1


title: MCF7-antiAGO2-FT-exp1-rep2

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 1, replicate 2


title: Mock-treated BMSC sample OSP-V002-P2

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample OSP_V002-P2

value: Bone marrow-derived mesenchymal stromal cells sample OSP_V002-P2


title: FTVII-treated BMSC sample OSP-V002-P2

source_name: Test sample: FTVII-treated bone marrow-derived mesenchymal stromal cells sample OSP_V002-P2


title: MCF7-antiGW182-IP-exp2-rep2

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 2, replicate 2


title: Mock-treated BMSC sample OSP-V001

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample OSP_V001


title: Mock-treated BMSC sample RP-003-P2

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample RP-003-P2


title: MCF7-antiGW182-IN-exp2-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 2, replicate 1


title: MCF7-antiGW182-IP-exp1-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 1, replicate 1


title: FTVI-treated BMSC sample M41-P3

source_name: Test sample: FTVI-treated bone marrow-derived mesenchymal stromal cells sample M41-P3

value: Bone marrow-derived mesenchymal stromal cells sample M41-P3


title: MCF7-antiAGO2-FT-exp2-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 2, replicate 1


title: MCF7-antiAGO2-IP-exp3-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 3, replicate 1


title: MCF7-antiGW182-FT-exp1-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 1, replicate 1


title: MCF7-antiAGO2-FT-exp3-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 3, replicate 1


title: MCF7-antiAGO2-IP-exp1-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 1, replicate 1


title: MCF7-antiAGO2-IP-exp2-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 2, replicate 1


title: MCF7-antiAGO2-IN-exp3-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 3, replicate 1


title: Mock-treated BMSC sample RP-002

source_name: Reference sample: pool of 5 samples of bone marrow-derived mesenchymal stromal cells

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample RP-002

value: Bone marrow-derived mesenchymal stromal cells sample RP-002


title: 2014-06-20_unstim_5_(HuGene-1_0-st-v1)

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from cell culture

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: T-Rex HeLa unstimulated, shRNA ANRIL silenced

growth_protocol: Cells were cultivated at 37°C and 5% CO2 in appropriate growth medium (EMEM, 10% FCS, 2mM Glutamine, 1% Penicillin-Streptomycin) with Blasticidin (5 µg/ml) and Zeocin (200 µg/ml).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen).

treatment_protocol: Monoclonal cell lines were induced with tetracycline (1 µg/ml) for 48h and for 96h.

tag: sample type

value: Cell culture


title: 2014-06-20_unstim_4_(HuGene-1_0-st-v1)

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: 2014-06-20_unstim_6_(HuGene-1_0-st-v1)_2


title: MCF7-antiGW182-IN-exp1-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 1, replicate 1.


title: 2014-06-20_unstim_3_(HuGene-1_0-st-v1)


title: MCF7-antiAGO2-IN-exp1-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 1, replicate 1.


title: FTVI-treated BMSC sample M48

source_name: Test sample: FTVI-treated bone marrow-derived mesenchymal stromal cells sample M48

value: Bone marrow-derived mesenchymal stromal cells sample M48


title: MCF7-antiAGO2-FT-exp1-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 1, replicate 1


title: FTVI-treated BMSC sample RP-002

source_name: Test sample: FTVI-treated bone marrow-derived mesenchymal stromal cells sample RP-002


title: 2014-06-20_Tetracyclin_96h_4_(HuGene-1_0-st-v1)

source_name: T-Rex HeLa stimulated with Tetracycline, shRNA ANRIL silenced for 96h


title: 2014-06-20_Tetracyclin_96h_5_(HuGene-1_0-st-v1)


title: Mock-treated BMSC sample M48

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample M48


title: MCF7-antiAGO2-IN-exp2-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 2, replicate 1


title: 2014-06-20_unstim_2_(HuGene-1_0-st-v1)


title: SAL 28 RS

city: Montreal

first: Anne Marie

middle: Lucie

last: Downey

state: Quebec

address: 3655 Promenade Sir William Osler, Room 115

department: Pharmacology and Therapeutics

institute: McGill University

description:
685_S001_miRNA_1105_Oct12_2_2
round spermatids from control rat #28

hyb_protocol: Cy3 labelled miRNA was hybridized to Agilent Sure Print Rat miRNA 8x15K  Release 16.0 microarrays at 55°C for 20 hours using the miRNA complete labeling and hyb kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned with Agilent SureScan G2600D DNA microarray scanner

data_processing:
Probe intensities were processed using Feature Extraction ver. 11.5.1.1 (Agilent Technologies) software with protocol miRNA_1105_Oct12 and grid 031189_D_F_20121224.
Quantile Normalized, Log2 transformed signal intensities, baseline transformation to 1 using Genespring software ver. 14.9 (Agilent Technonogies)

source_name: round spermatids from control rat

label_protocol: Cyanine-3 (Cy3) labelled RNA was prepared from 100ng total RNA using the miRNA complete labeling and hyb Kit (Agilent Technologies) following manufacturer's  instructions.

extract_protocol:
Germ cell isolation protocol: germ cells were isolated by unit gravity sedimentation using the STA-PUT method and frozen at -80°C
Total RNA was extracted using TRIzol reagent and cleaned up using RNeasy mini kit columns

treatment_protocol: Male rats were gavaged with 6 mg/Kg cyclophosphamide or saline 6 days/week for 4 weeks

tag: strain

value: Sprague-Dawley

tag: rat id

value: rat #28

value: male

value: round spermatids

value: control (saline)


title: SAL 25 RS

description:
685_S001_miRNA_1105_Oct12_2_1
round spermatids from control rat #25

value: rat #25

tag: treatment


title: SAL 16 RS

description:
604_S001_miRNA_1105_Oct12_1_2
round spermatids from control rat #16

value: rat #16

tag: Sex


title: SAL 17 RS

description:
685_S001_miRNA_1105_Oct12_1_2
round spermatids from control rat #17

value: rat #17


title: CPA 26 RS

description:
685_S001_miRNA_1105_Oct12_2_4
round spermatids from CPA treated rat #26

source_name: round spermatids from CPA treated rat

value: rat #26

value: cyclophpsphamide


title: 2014-06-20_Tetracyclin_96h_3_(HuGene-1_0-st-v1)


title: CPA 25 RS

description:
604_S001_miRNA_1105_Oct12_2_4
round spermatids from CPA treated rat #25


title: 2014-06-20_Tetracyclin_96h_6_(HuGene-1_0-st-v1)


title: CPA 14 RS

description:
603_S001_miRNA_1105_Oct12_1_1
round spermatids from CPA treated rat #14

value: rat #14


title: CPA 15 RS

description:
603_S001_miRNA_1105_Oct12_1_2
round spermatids from CPA treated rat #15

value: rat #15


title: CPA 16 RS

description:
603_S001_miRNA_1105_Oct12_1_3
round spermatids from CPA treated rat #16


title: SAL 28 P

description:
604_S001_miRNA_1105_Oct12_2_3
pachytene spermatocytes from control rat #28

value: pachytene spermatocyte


title: 2014-06-20_Tetracyclin_48h_4_(HuGene-1_0-st-v1)

source_name: T-Rex HeLa stimulated with Tetracycline, shRNA ANRIL silenced for 48h


title: 2014-06-20_Tetracyclin_48h_6_(HuGene-1_0-st-v1)


title: 2014-06-20_Tetracyclin_96h_2_(HuGene-1_0-st-v1)


title: CASIN_Aged_2

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Standard Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 using tophat
All downstream analysis including differential expression analysis, principal component analysis, between group analysis, and additional statistical tests related to RNA-seq were performed using R and bioconductor packages (R Core Team, 2015; Huber et al., 2015) and in-house developed scripts. The GSEA tool from broad MIT (Subramanian et al., 2005) was used for Gene Set Enrichment Analysis (GSEA).
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

source_name: CASIN treated LT-HSC sorted from aged mouse

growth_protocol: Cells were cultured in HBSS + 10% FBS and incubated for 16 hours in a water-jacketed incubator at 37°C, 5% CO2, and 3% O2.

extract_protocol:
Sorted cells were directly dropped into lysis buffer and were used in the downstream RNA-seq library protocol.
RNA-seq libraries were generated using Ovation® Single Cell RNA-Seq System (NuGEN Technologies Inc.). Cells were directly dropped into lysis buffer and reverse transcription was performed using oligo dT and selective primers to create first strand cDNA with randomly incorporated degradable nucleotide analog. Second strand cDNA priming was done using a forward adaptor with a random octamer attached to its 5’ end. After performing end repair, the free end of the newly synthesized double stranded cDNA was ligated to the reverse adaptor and final Enrichment PCR was performed.

treatment_protocol: 5µM CASIN (CASIN treatment) is added to the medium.

value: Aged

value: Long-term Hematopoietic stem cells (LT-HSC)

value: CASIN


title: CONTROL_Aged_2

source_name: Untreated (Control) LT-HSC sorted from aged mouse

value: CONTROL


title: CONTROL_Aged_4


title: CASIN_Aged_1


title: CASIN_Aged_3


title: SAL 15 RS

description:
603_S001_miRNA_1105_Oct12_1_4
round spermatids from control rat #15

value: Sprague-Dawley


title: 2014-06-20_Tetracyclin_48h_1_(HuGene-1_0-st-v1)_2

value: Cell culture


title: CONTROL_Aged_5


title: SAL 25 P

description:
604_S001_miRNA_1105_Oct12_1_1
pachytene spermatocytes from control rat #25

value: male


title: SAL 26 P

description:
604_S001_miRNA_1105_Oct12_2_2
pachytene spermatocytes from control rat #26


title: CONTROL_Young_4

source_name: Untreated (Control) LT-HSC sorted from young mouse

value: Young


title: SAL 13 P

description:
603_S001_miRNA_1105_Oct12_2_3
pachytene spermatocytes from control rat #13

value: rat #13

value: control (saline)


title: SAL 16 P

description:
603_S001_miRNA_1105_Oct12_2_4
pachytene spermatocytes from control rat #16

value: rat #16


title: CPA 29 P

description:
604_S001_miRNA_1105_Oct12_2_1
pachytene spermatocytes from CPA treated rat #29

value: rat #29


title: CONTROL_Aged_3


title: 2014-06-20_Tetracyclin_48h_3_(HuGene-1_0-st-v1)

description: mRNA expression profiles from cell culture


title: CONTROL_Young_2


title: CPA 16 2012 P

description:
604_S001_miRNA_1105_Oct12_1_4
pachytene spermatocytes from CPA treated rat #16 2012


title: CPA 15 P

description:
603_S001_miRNA_1105_Oct12_2_2
pachytene spermatocytes from CPA treated rat #15


title: CPA 16 2011 P

description:
604_S001_miRNA_1105_Oct12_1_3
pachytene spermatocytes from CPA treated rat #16 2011


title: CONTROL_Aged_0


title: D21_input genomic DNA

city: Montpellier

first: Thierry

last: Forné

address: 1919, Route de Mende

country: France

institute: CNRS

data_processing:
Library strategy: HRS-seq
Base calling was performed using the RTA software from Illumina
Trimming of adaptor sequences (remove the following sequence from the 3' end of reads : TCGTATGCCGTCTTCTGCTTG).
Only reads starting by the WWGG modif are kept (presence of a styI cut site)
Reads were aligned to the 129P2 genome assembled from the mm9 genome assembly using the  CASAVA version 1.8.2, script ELAND_standalone.pl) from Illumina.
Reads were counted for each StyI restriction fragment in the 129P2 reference genome assembled from the mm9 assembly.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each StyI fragment

source_name: Embryonic Stem Cells

growth_protocol: Mouse ESC (E14 strain, 129P2 genomic background) were maintained on gelatin in DMEM (Invitrogen) supplemented with 15% ES-certified FBS (Invitrogen), 0.1mM non-essential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen), 0.1mM Beta-mercaptoethanol (Sigma), 50U/ml penicillin/streptomycin and 10³ U/ml LIF (Millipore)

extract_protocol:
Nucleus preparations and HRS assays were performed as previously described in (Milligan et al. 2000 Oncogene 19, 5810-16) and (Braem et al. 2008 J. Biol. Chem. 283, 18612-20).
For each sequencing library, 150 ng of genomic DNA issued from the HRS or loop fractions of the assays were used. Briefly, a first biotinylated StyI DNA adaptor, containing a binding site for the MmeI type IIS restriction enzyme, is ligated to the StyI fragments. Ligated products are then captured onto streptavidin beads and digested with MmeI to homogenize the size of the StyI restriction fragments (~18 to 20 nucleotides). A second sequencing adaptor is ligated to MmeI restricted sites and DNA fragments are released from streptavidin beads, purified on an acrylamide gel and sequenced using high-throughput sequencing.

tag: cell line

value: E14Tg2a ESC


title: CONTROL_Young_3

tag: cell type


title: CONTROL_Young_5


title: 2014-06-20_Tetracyclin_48h_2_(HuGene-1_0-st-v1)


title: D12_input genomic DNA


title: MCF7-antiGW182-IP-exp3-rep2

hyb_protocol: 1.0 ug of Cy3- or Cy5-labelled cRNA (specific activity >9.0 pmol Cy/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K v2 (Agilent-G4845A) 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 (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channels PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol: GE2-v5_95 and Grid: 026652_D_F_20110325) to obtain background subtracted, dye normalized and spatially detrended processed signal intensities. The expression profiles, obtained by considering the gProcessedSignal and rProcessedSignal intensities were quantile normalized.

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 3, replicate 2

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 labeled cRNA was prepared from 100 ng RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions (Agilent protocol: G4140-90050_GeneExpression_TwoColor_ver._6.9.1), followed by RNAeasy mini kit column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer.

value: IP


title: CPA 7 P

description:
603_S001_miRNA_1105_Oct12_2_1
pachytene spermatocytes from CPA treated rat #7

value: rat #7

value: cyclophpsphamide


title: MCF7-antiGW182-IP-exp2-rep2

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 2, replicate 2


title: MCF7-antiGW182-IN-exp3-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 3, replicate 2

value: IN


title: MCF7-antiAGO2-IP-exp3-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 3, replicate 2


title: MCF7-antiGW182-FT-exp1-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 1, replicate 2

value: FT


title: MCF7-antiGW182-FT-exp3-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 3, replicate 2


title: MCF7-antiGW182-FT-exp2-rep2

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 2, replicate 2


title: MCF7-antiAGO2-FT-exp1-rep2

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 1, replicate 2


title: prdm14_puro_esc4_10000

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

description:
DamID
processed data file: prdm14_esc_10000cells_new.bedgraph

data_processing:
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline.
Processed data from the damidseq_pipeline software in bedgraph format were used for peak calling with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised fold enrichment of Dam-OCT4 or Dam-PRDM14 fusion protein over dam-alone.  Processed files are provided as averaged bedgraphs

source_name: Embryonic stem cells (2i)

extract_protocol:
gDNA was extracted using the QuiAmp® DNA Micro. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and pcr amplified.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion.  Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

tag: media

value: 2i and LIF

tag: flox cassette

value: GFP

value: Embryonic stem cells


title: prdm14_puro_esc5_10000


title: MCF7-antiAGO2-IN-exp2-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 2, replicate 2


title: MCF7-antiAGO2-FT-exp3-rep2

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 3, replicate 2


title: prdm14_puro_esc3_10000


title: MCF7-antiAGO2-IP-exp2-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 2, replicate 2


title: MCF7-antiAGO2-IN-exp1-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 1, replicate 2.


title: MCF7-antiAGO2-IN-exp3-rep2

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 3, replicate 2


title: MCF7-antiAGO2-IP-exp1-rep2

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 1, replicate 2


title: MCF7-antiGW182-FT-exp3-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 3, replicate 1


title: MCF7-antiGW182-IP-exp1-rep2

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 1, replicate 2


title: prdm14_puro_esc2_10000


title: dam_puro_esc5_10000


title: MCF7-antiGW182-IN-exp3-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 3, replicate 1


title: MCF7-antiGW182-IP-exp2-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 2, replicate 1


title: dam_puro_esc4_10000


title: MCF7-antiGW182-IP-exp3-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 3, replicate 1


title: MCF7-antiGW182-IN-exp2-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 2, replicate 1


title: MCF7-antiGW182-FT-exp2-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 2, replicate 1


title: dam_puro_esc3_10000


title: MCF7-antiGW182-FT-exp1-rep1

source_name: unbound sample resulting from anti-GW182 RIP, MCF7 cell line, experiment 1, replicate 1


title: MCF7-antiGW182-IP-exp1-rep1

source_name: anti-GW182 RIP sample, MCF7 cel l line, experiment 1, replicate 1


title: MCF7-antiAGO2-FT-exp2-rep2

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 2, replicate 2


title: MCF7-antiGW182-IN-exp1-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-GW182 RIP, experiment 1, replicate 1.


title: MCF7-antiAGO2-IP-exp1-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 1, replicate 1


title: MCF7-antiAGO2-IN-exp3-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 3, replicate 1


title: MCF7-antiAGO2-FT-exp3-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 3, replicate 1


title: MCF7-antiAGO2-IP-exp2-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 2, replicate 1


title: MCF7-antiAGO2-FT-exp1-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 1, replicate 1


title: MCF7-antiAGO2-IP-exp3-rep1

source_name: anti-AGO2 RIP sample, MCF7 cel l line, experiment 3, replicate 1


title: dam_puro_esc2_10000

source_name: Embryonic stem cells (2i)


title: MCF7-antiAGO2-IN-exp1-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 1, replicate 1.


title: MCF7-antiAGO2-IN-exp2-rep1

source_name: total RNA extracted from MCF-7 cell line, before anti-AGO2 RIP, experiment 2, replicate 1


title: MCF7-antiAGO2-FT-exp2-rep1

source_name: unbound sample resulting from anti-AGO2 RIP, MCF7 cell line, experiment 2, replicate 1


title: U87_rep4_4N

city: Newark

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

description: 3'READS human samples used in PolyA_DB version 3.2

data_processing:
Adpter trimming by Cutadapt:  cutadapt -a NNNNTGGAATTCTCGGGTGCCAAGG -n 1 -O 10 -m 25 -f fastq -q 10
3'READs and 3'READS+ reads were aligned to hg19 using bowtie2:
For the sample name ends with "3N":
bowtie2 --local --threads 24 -5 3 -x IndexFiles/bowtie2/hg19 -U sample_3N.trimmed.fastq -S sample_3N.sam
For the sample name ends with "4N":
bowtie2 --local --threads 24 -5 4 -x IndexFiles/bowtie2/hg19 -U sample_4N.trimmed.fastq -S sample_4N.sam
For the sample name ends with "6N":
bowtie2 --local --threads 24 -5 6 -x IndexFiles/bowtie2/hg19 -U sample_6N.trimmed.fastq -S sample_6N.sam
For 3'READs data, reads with a mapping quality score (MAPQ) >=10 were kept for further analysis. Reads with >=2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each PAS position coverved by PolyA_DB version 3.2

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).

tag: protocol

tag: purpose

tag: molecule type

value: total RNA


title: U87_rep3_4N

value: 3'READS human samples used in PolyA_DB version 3.2


title: ESC_rep7_4N

value: ESC


title: ESC_rep6_4N


title: MCF7_rep3_4N


title: MCF7_rep4_4N


title: MCF7_rep2_4N


title: sample8, dataset1

city: Brussels

first: Vinu

last: Jose

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

hyb_protocol: On GeneChip® HG-U133 Plus2.0 array using GeneChip® Hybridization, Wash, and Stain Kit, according to Affymetrix's standard procedure.

scan_protocol: Using GeneChip® scanner 3000 according to Affymetrix's standard procedure.

data_processing: Data set was RMA background corrected,quantile normalized and median-polish summarized using 'expresso' function available from bioconductor package affy.

source_name: breast tumor tissue

label_protocol: Total RNA was amplified and labeled using Affymetrix's GeneChip® 3' IVT Express kit according to Affymetrix's recommendations.

extract_protocol: Total RNA from frozen samples was extracted using TRIzol® Reagent according to Thermo Fisher Scientific's (Invitrogen) recommendations.

value: breast tumor

tag: er status

value: positive

tag: her2 status

tag: tissue preservation method

value: Fresh-Frozen


title: sample3, dataset2

extract_protocol: Total RNA from FFPE sections was extracted using miRNeasy FFPE kit according to Qiagen's recommendation.

tag: tissue

value: negative

value: FFPE


title: sample8, dataset2


title: sample6, dataset2


title: sample4, dataset2


title: Mock-treated BMSC sample M41-P3

source_name: Reference sample: pool of 5 samples of bone marrow-derived mesenchymal stromal cells

tag: agent

source_name: Test sample: mock-treated bone marrow-derived mesenchymal stromal cells sample M41-P3

value: Bone marrow-derived mesenchymal stromal cells sample M41-P3

value: mock


title: sample2, dataset2


title: MCF7_rep1_4N

first: Bin


title: sample5, dataset2


title: HeLa_rep24_4N

value: HeLa


title: sample7, dataset2


title: HeLa_rep25_4N


title: ESC_rep5_4N


title: sample1, dataset2


title: Tissue_mix_rep2_4N

value: Tissue mix


title: nosGAL4>bruRNAi-Poly Trial 2

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

data_processing:
Alignment was performed with HISAT2 2.0.5.2 using spliced alignment
Bam files were sorted withSortSam by coordinate order  2.7.1.1
Raw counts were generated with featureCounts  1.4.6.p5
Custom R script: To determine translation efficiencies (TE), CPMs (counts per million) values were calculated for all polysome-seq libraries. Any transcript having zero reads in any library was discarded from analysis. The log2 ratio of CPMs between the polysome fraction and total mRNA was calculated and averaged between replicates. This ratio represents TE. After TE of each sample was calculated and replicates were averaged, TE of pumRNAi and bruRNAi were compared to that of Control. This ratio represents △TE. Targets were defined as transcripts falling greater or less than one standard deviation from the median of △TE (Kronja et al. 2014).
bamCoverage 2.5.0
Genome_build: DMEL Release 6.01
Supplementary_files_format_and_content: Raw counts were generated using featureCounts  1.4.6.p5

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Crosses and control flies were grown at 29C.

extract_protocol:
~80 ovaries were dissected in PBS supplemented with cycloheximide and frozen immediately with liquid nitrogen. Tissue was homogenized in 200 μl of cold lysis buffer consisting of 1x Polysome buffer supplemented with 1% Triton-X and 1 protease inhibitor pill per 10 ml of buffer. The lysate was centrifuged at 15,000 x g at 4°C for 10 minutes. 20% of lysate was kept aside for “Input RNA” libraries. 750μl of cleared lysate was loaded onto 10-50% sucrose gradients (500 mM KCl; 15 mM Tris-HCl, pH 7.5; 15 mM MgCl2; and 100 μg/ml cycloheximide) in Beckman Coulter 9/16x3.5 PA tubes (Cat. #331372). Gradients were centrifuged at 35,000xg using a SW41 rotor for 3 hours at 4°C. Gradients were fractionated on a Brandel flow cell (Model #621140007) at 0.75 mls/min and 750μl was collected for each fraction with the sensitivity settings at 0.5 Abs. RNA was extracted from the fractions using standard acid phenol: chloroform extraction. The RNA pellet was washed with 80% ethanol and then air-dried. After air-drying the pellet was dissolved in 10 μl of nuclease-free water. RNA samples were subjected to a DNase treatment using the TURBO DNA-free Kit by Life Technologies (AM1907). poly(A)+ RNA was isolated by double selection with poly-dT beads, using the Turbo DNase treated samples, which is then followed by first- and second-strand synthesis. Sequencing libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific). Samples were single-end sequenced on a NextSeq 500.
Bioo Scientific Manufactures protocol

treatment_protocol: Flies were fattened with yeast a day before dissection and kept at 29C.

value: Ovary

tag: rna source

value: Polysome

tag: age

value: 2 Days Post Eclosion


title: nosGAL4>UAS-TKV

data_processing:
Alignment was performed with HISAT2 2.0.5.2 using spliced alignment
Bam files were sorted withSortSam by coordinate order  2.7.1.1
Raw counts were generated with featureCounts  1.4.6.p5
BigWig file was generated with bamCoverage 2.5.0
Genome_build: DMEL Release 6.01
Supplementary_files_format_and_content: BigWig file was generated with bamCoverage 2.5.0

growth_protocol: Crosses and control flies were grown at 25C.

extract_protocol:
ovaries were dissected in 1XPBS. After dissection, all the PBS was aspirated and 100 μl of Trizol reagent was added to the tissue. The tissue was homogenized. 900 μl of Trizol was added, mixed and incubated at RT for 3 minutes. After incubation, 200 μl of Chloroform was added to each sample and mixed vigorously and incubated at RT for 5 minutes. The samples were then centrifuged at 13,000 rpm for 20 minutes at 4C. The aqueous layer was then transferred to a new centrifuge tube. 2 volumes of 100% ethanol, 10% volume 3 M sodium acetate and 0.5 ul of glycol blue was added to the samples and incubated at -20C for 1 hour. The samples were then centrifuged at 13,000 rpm for 20 minutes at 4C. The pellet was then washed with 75% ethanol, air-dried and re-suspended in RNase free H2O. For efficient re-suspension of the isolated nucleic acid, the sample was incubated at 50C for 10 minutes. The concentration of the isolated RNA was determined using a Nanodrop. 10μg of nucleic acid was then taken and subjected to a DNase treatment using the TURBO DNA-free Kit by Life Technologies (AM1907). poly(A)+ RNA was isolated by double selection with poly-dT beads, using the Turbo DNase treated samples, which is then followed by first- and second-strand synthesis. Sequencing libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific). Samples were single-end sequenced on a NextSeq 500.
Bioo Scientific Manufactures protocol

treatment_protocol: Flies were fattened with yeast a day before dissection and kept at 25C.

value: Total

tag: strain/genotype


title: Tissue_mix_rep3_4N


title: Tissue_mix_rep1_4N


title: sample7, dataset1


title: sample5, dataset1


title: HeLa_rep22_4N


title: InVitro_ANBL-6_FAM46C_knockout_2

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in ANBL-6/FAM46C-KO_clone#2

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v3 8x60K Microarray  (G4851C-  072363) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, 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 GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ANBL-6_FAM46C-KO_2, Interleukin-6 (5 ng/mL)

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, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cells were then incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: myeloma cell line

tag: genotype

value: FAM46C KO

tag: gender

value: female

tag: representative genomic abnormality


title: sample3, dataset1


title: HEK293_rep3_4N

value: 3'READS human samples used in PolyA_DB version 3.2

value: total RNA


title: HEK293_rep4_4N


title: InVitro_ANBL-6_FAM46C_wildtype_2

description: Gene expression in ANBL-6/FAM46C-WT clone#2

source_name: ANBL-6_FAM46C-WT_2, Interleukin-6 (5 ng/mL)

tag: cell line

tag: cell type

value: WT


title: InVitro_KMS-11_FAM46C_knockout_2

description: Gene expression in KMS-11/FAM46C-KO_clone#2

source_name: KMS-11_FAM46C-KO_2, normal culture


title: sample1, dataset1

value: breast tumor

value: Fresh-Frozen


title: sample4, dataset1

value: positive

value: negative


title: sample2, dataset1


title: HeLa_rep23_4N


title: sample6, dataset1


title: InVitro_KMS-11_FAM46C_wildtype_2

description: Gene expression in KMS-11/FAM46C-WT clone#2

source_name: KMS-11_FAM46C-WT_2, normal culture


title: InVitro_KMS-11_FAM46C_wildtype_1

description: Gene expression in KMS-11/FAM46C-WT clone#1

source_name: KMS-11_FAM46C-WT_1, normal culture


title: nosGAL4>bruRNAi-Poly Trial 1

tag: strain


title: HEK293_rep7_4N

tag: protocol


title: InVitro_KMS-11_FAM46C_knockout_1

description: Gene expression in KMS-11/FAM46C-KO_clone#1

source_name: KMS-11_FAM46C-KO_1, normal culture


title: U87_rep2_4N

tag: purpose


title: InVitro_ANBL-6_FAM46C_knockout_1

description: Gene expression in ANBL-6/FAM46C-KO_clone#1

source_name: ANBL-6_FAM46C-KO_1, Interleukin-6 (5 ng/mL)


title: InVitro_ANBL-6_FAM46C_wildtype_1

description: Gene expression in ANBL-6/FAM46C-WT clone#1

source_name: ANBL-6_FAM46C-WT_1, Interleukin-6 (5 ng/mL)


title: Az_I_3 [RNA-seq]

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Read quality control using FastQC
Adaptor trimming and chopping using Trimmomatic
Genome alignment unig Bowtie and Oryza sativa MSU v7
sequeces are then formated to tag-count format
Genome_build: Oryza sativa MSU v7
Supplementary_files_format_and_content: Final trimmed and cropped output file in tag-count format

organism: Oryza sativa

source_name: Leaf

growth_protocol: Plants were grown in the greenhouse at 16h light/8h dark, 28ºC day- 22ºC night and 40-60% relative humidity, until the three-leaf stage

extract_protocol:
RNA was extracted using Trizol, follwing manufacturer's protocol
Indexed libraries were prepared from 1 ug/ea purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina), following manufacturer's protocol.

treatment_protocol: A suspension of spores (106 spores/mL) was sprayed to plants and these were further grown for 7 days

tag: condition

value: Infected

tag: replicate

tag: developmental stage

value: 3 weeks old


title: Az_I_1 [RNA-seq]


title: HEK293_rep6_4N

tag: molecule type


title: nosGAL4>pumRNAi-Poly Trial 2

tag: tissue


title: nosGAL4>pumRNAi-Poly Trial 1


title: Az_C_1 [RNA-seq]

value: Control


title: U87_rep1_4N


title: A549_rep1_4N


title: Ac-DCL1a_I_3 [RNA-seq]


title: Young nosGAL4-Poly Trial 1

value: Ovary

value: <8 Hrs


title: Ac-DCL1a_C_3 [RNA-seq]


title: Ac-DCL1a_I_1 [RNA-seq]


title: Ac-DCL1a_C_1 [RNA-seq]


title: Az_C_3 [RNA-seqe]


title: nosGAL4>pumRNAi-In Trial 2

value: Input

value: 2 Days Post Eclosion


title: nosGAL4>bruRNAi-In Trial 2


title: nosGAL4>bruRNAi-In Trial 1


title: HEK293_rep5_4N


title: Az_I_3 [ncRNA-seq]

extract_protocol:
RNA was extracted using Trizol, follwing manufacturer's protocol
Indexed libraries were prepared with TruSeq small RNA Library Prep Kit (Illumina), following manufacturer's protocol.


title: HeLa_rep17_4N

value: HeLa


title: Az_C_3 [ncRNA-seq]


title: HeLa_rep11_3N


title: HeLa_rep12_3N


title: Az_I_1 [ncRNA-seq]


title: HeLa_rep13_3N


title: HeLa_rep9_3N


title: HeLa_rep8_3N


title: nosGAL4>pumRNAi-In Trial 1


title: HeLa_rep10_3N


title: Young nosGAL4-In Trial 1


title: Young nosGAL4-In Trial 2


title: Ac-DCL1a_I_3 [ncRNA-seq]


title: HeLa_rep7_3N


title: Young nosGAL4-Poly Trial 2

value: Polysome


title: HeLa_rep6_3N


title: Ac-DCL1a_C_3 [ncRNA-seq]


title: Hr962X_p3

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

data_processing:
base-calling: bcl2fastq v2.17.1.14
reads aligned using Bowtie 2.2.9
identified transcript associated reads using TopHat 2.1.1
calculated transcript fpkm and gene fpkm values using Cufflinks 2.2.1
Genome_build: refseq annotation file: dm6 and BDGP6.Ensembl.85.gtf
Supplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status

source_name: posterior midgut

growth_protocol: Fertilized adult females were aged for 10-12 days, and provided with new food every other day. Female flies were kept in a controlled density with male flies at 25°C.

extract_protocol:
30-50 isolated regions per sample were transferred to 400 uL iced tripure. Each experimental condition was collected in triplicate. Collected midguts were homogenized and 600uL fresh tripure added. Samples then rested at room temperature for 10 minutes. 180uL chloroform was added and samples shaken by hand for 45 seconds followed by room temperature incubation for 10 minutes. Samples were then centrifuged for 15 minutes at 12,000 rpm at 4°C, and the aqueous layer moved to a fresh tube. RNA was then precipitated with 400 uL isopropanol.
cDNA libraries were constructed from poly(A)-selected RNA using Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: Pupae were transferred to specified diet before adulthood.

tag: Stage

value: 10-12 day old adult female

tag: subregion

value: p1-4 replicate 3

tag: diet

value: control diet


title: Hr962X_p2

value: p1-4 replicate 2


title: Hr962X_p1

value: p1-4 replicate 1


title: Ac-DCL1a_I_1 [ncRNA-seq]


title: Ac-DCL1a_C_1 [ncRNA-seq]


title: HTR8_rep1_3N

value: 3'READS human samples used in PolyA_DB version 3.2

value: total RNA


title: JEG3_rep1_3N


title: Hr962X_a3

source_name: anterior midgut

value: a1-3 replicate 3


title: Hr962X_a2

value: a1-3 replicate 2


title: Hr962X_a1

value: a1-3 replicate 1


title: ESC_rep4_3N

value: ESC


title: KUa27-5

city: Boston

first: Matthew

last: Booker

state: MA

address: 21-27 Burlington Ave.

department: Informatics

institute: Dana Farber Cancer Institute

data_processing:
ChIP-Seq reads aligned to fb5_22 release of Drosophila melanogaster genome using bowtie (rel 0.12.9) options -t -p 12 -m 1 -I 50 -X 500 --solexa-quals --best --chunkmbs 256
Peaks were called using MACS2 callpeak (version 2.1.1) and p-value threshold of 0.05. For MSL3 IP, the --broad flag was used.
Genome_build: fb5_22/dm3
Supplementary_files_format_and_content: bedgraph files were generated using MACS2 bdgcmp (version 2.1.1)  with the -m FE flag. Scores represent local fold enrichment.

source_name: sorted female-enriched embryos

growth_protocol: We grew flies  on standard sucrose/cornmeal media at 24 degrees C. We collected embryos on grape juice plates with yeast paste. Embyros were aged at 24 degrees C.

extract_protocol:
To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample.
We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009).

tag: nuclear cycle

value: Nuclear cycle = late 14

tag: chip antibody

value: CLAMP (3 μL of Novus/SDIX rabbit anti-CLAMP)


title: ESC_rep3_3N


title: 4XC_p3

value: 4x cholesterol diet (0.2% cholesterol)


title: ESC_rep2_3N


title: KUa30-5

value: Nuclear cycle = 13


title: ESC_rep1_3N


title: Az_C_1 [ncRNA-seq]

value: Control

value: 3 weeks old


title: KUa30-1

value: Nuclear cycle = 12


title: KUa28-5


title: MDA-MB-468_rep1_4N


title: KUa29-5


title: HeLa_rep5_3N

value: HeLa


title: 4XC_a3

value: 10-12 day old adult female


title: 4XC_p2

value: p1-4 replicate 2


title: 4XC_p1

value: p1-4 replicate 1


title: KUa28-1

value: Nuclear cycle = 11


title: 4XC_a2


title: KUa29-1


title: SKBR3_rep1_4N

value: 3'READS human samples used in PolyA_DB version 3.2

value: total RNA


title: KUa27-1

value: Nuclear cycle <=10


title: MDA-MB-231_rep1_4N


title: 4XC_a1

value: a1-3 replicate 1


title: T474_rep1_4N


title: Hr96_p3

value: p1-4 replicate 3

value: control diet


title: MCF10A_rep1_4N


title: Hr96_p2


title: Mammary_epithelial_rep1_4N

value: Mammary epithelial


title: Hr96_p1


title: HEK293_rep2_4N


title: HEK293_rep1_4N


title: Hr96_a3

value: a1-3 replicate 3


title: 1004-Memory_NK-U

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

data_processing:
Tn5 transposase adapters were trimmed with cutadapt version 1.13 with a minimum length of 20 and an overlap of 5 in paired-end mode.
Trimmed reads were aligned using bowtie2 version 2.2.9
Following removal of chrM reads we filtered with samtools version 1.4 and-f 2 and -F 1804 and MAPQ > 30, and removed duplicate reads with picard version 1.134
Used get_count function from nucleoATAC
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including read count for each sample in each peak

source_name: primary blood

extract_protocol: ATAC-seq libraries were prepared following the Fast-ATAC protocol (Corces et al., 2016). Briefly, frozen cells were thawed, washed in media, aliquoted and resuspended in Tn5 reaction buffer and incubated at 37℃ for 30 min. Transposed samples were purified using MinElute PCR purification columns according to the manufacturer’s protocol (Qiagen, Germany). Purified samples were amplified and indexed using custom Nextera barcoded PCR primers as described in Buenrostro et al (Buenrostro et al., 2013). Amplified libraries were purified using MinElute PCR purification columns followed by gel-based size selection to remove free PCR primers.

treatment_protocol:
Treatment 1: T lymphocytes were activated for 24 hours with dynabead conjugated CD3/CD28 antibodies at 1:1 ratio, supplemented with 50 unit/ml of human IL-2  or 300 unit/ml for regulatory T cells. B lymphocytes were activated for 24 hours with 10µg/ml  anti-IgG/IgM antibodies and 20ng/ml of human IL-4. Monocytes were activated with 1µg/ml of LPS for 24 hours. NK cells were activated with 200 unit/ml of human IL2 for 24 hours.
Treatment 2: Monocytes were activated with 100ng/ml of LPS for 6 hours. NK cells were activated with CD2 and CD355 coated beads at 1:2 cell to bead ratio supplemented with 500 unit/ml IL-2 for 48 hours.

tag: donor

tag: lineage

value: NK

tag: treatment


title: 1004-Mature_NK-S

tag: cell type


title: 1004-Monocytes-U

value: Monocytes

value: MYELOID


title: 1004-Monocytes-S


title: 1004-Mature_NK-U


title: HeLa_rep4_4N

value: polysome


title: Hr96_a2

tag: strain

value: a1-3 replicate 2


title: HeLa_rep3_4N

value: HeLa

tag: protocol


title: HeLa_rep1_4N

tag: purpose

value: Nucleus


title: HeLa_rep2_4N


title: LD_p2

value: 10-12 day old adult female

value: p1-4 replicate 2

value: lipid-depleted diet


title: Hr96_a1


title: 1004-Th2_precursors-U


title: LD_p3


title: 1004-Th2_precursors-S


title: 1004-Immature_NK-U


title: LD_a2


title: 1004-Th17_precursors-S


title: LD_a3


title: 1004-Th17_precursors-U


title: 1004-Th1_precursors-S


title: LD_a1


title: Jurkat_H3K4me1_ChIP-Seq

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Peaks calling for broad region using --broad parameter. Threshold for the peaks called is P-value < 1E-9
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Jurkat cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K4me1-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
Library construction and sequencing by Illumina Hiseq 4000 were performed by BGI Tech Solutions Co., Limited (Hongkong).

treatment_protocol: Not applicable.

tag: cell line

value: Jurkat

value: T-cell acute lymphoblastic leukemia (T-ALL) cell line

value: H3K4me1 (Abcam:ab8895)


title: CD_p3

value: p1-4 replicate 3


title: 1004-Th1_precursors-U


title: CD_p2

value: control diet


title: CD_a3


title: LD_p1

value: p1-4 replicate 1


title: CD_p1


title: 1004-Naive_Tregs-S


title: 1004-Naive_Teffs-S


title: CD_a2


title: 1004-Naive_Tregs-U


title: 1004-Regulatory_T-U


title: CD_a1

value: a1-3 replicate 1


title: 1010-Mature_NK-S

value: NK


title: 1004-Naive_Teffs-U


title: 1004-Memory_Tregs-U


title: 1004-Memory_Tregs-S


title: 1010-Memory_NK-U


title: 1010-Monocytes-S

value: Monocytes


title: 1004-Memory_Teffs-S


title: 1010-Naive_Tregs-S


title: 1010-Follicular_T_Helper-U


title: 1004-Follicular_T_Helper-S


title: 1010-Plasmablasts-U

value: Plasmablasts

value: B


title: 1011-Naive_Teffs-S


title: 1004-Memory_Teffs-U


title: 1008-Monocytes-S

value: MYELOID


title: 1008-Myeloid_DCs-U


title: 1004-Effector_CD4pos_T-U


title: 1008-Memory_NK-U


title: 1004-Naive_CD8_T-S


title: 1004-Follicular_T_Helper-U


title: 1004-Gamma_delta_T-S

value: GD


title: 1008-Mature_NK-S


title: 1004-Naive_CD8_T-U


title: 1004-Effector_memory_CD8pos_T-S


title: 1010-Mem_B-S


title: 1008-Immature_NK-U


title: sample8, dataset5

hyb_protocol: On Affymetrix® HG-U219 Array Plate using GeneTitan® System with GeneTitanTM Hybridization, Wash, and Stain Kit for 3'IVT Array, according to Affymetrix standard procedure.

scan_protocol: Using GeneTitan System according to Affymetrix standard procedure.

data_processing: Data set was RMA background corrected,quantile normalized and median-polish summarized using expresso function available from bioconductor package affy.

source_name: breast tumor tissue

label_protocol: Total RNA was amplified and labeled using Affymetrix's SensationPlusTM FFPE Amplification Kit and 3'IVT Labeling kit respectively, according to Affymetrix's recommendation.

extract_protocol: Total RNA from FFPE sections was extracted using miRNeasy FFPE kit according to Qiagen recommendation.

value: breast tumor

tag: er status

value: positive

tag: her2 status

tag: tissue preservation method

value: FFPE


title: 1004-Gamma_delta_T-U


title: 1004-Effector_memory_CD8pos_T-U


title: sample4, dataset5

tag: tissue

value: negative


title: sample6, dataset5


title: 1008-Naive_Tregs-U


title: sample2, dataset5


title: sample6, dataset4

label_protocol: Total RNA was amplified and labeled using Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module respectively, according to Nugen's recommendation.


title: 1008-Mature_NK-U


title: sample7, dataset5


title: sample5, dataset5


title: sample5, dataset4


title: sample8, dataset4


title: 1004-Central_memory_CD8pos_T-S


title: sample1, dataset5


title: sample3, dataset5


title: sample4, dataset4


title: 1004-Central_memory_CD8pos_T-U


title: 1004-CD8pos_T-U


title: 1004-Monocytes-S

data_processing:
Tn5 transposase adapters were trimmed with cutadapt version 1.13 with a minimum length of 20 and an overlap of 5 in paired-end mode.
RNA-seq reads were pseudoaligned using Kallisto version 0.43.0 (Bray et al., 2016). The Kallisto index was made with default parameters and the gencode v25lift37 fasta file (Harrow et al., 2012) and was run in quant mode with default parameters.
Gene abundances were computed using tximport version 1.2.0 (Soneson et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including gene abundance estimate for protein coding genes

extract_protocol: RNA sequencing libraries were prepared according to the Smart-seq2 protocol (Picelli et al. ,2014). Custom Nextera barcoded PCR primers (Buenrostro et al., 2015) were used for dual indexing. Amplified libraries were purified using AMPure XP beads (Beckman Coulter) using a 1:1 ratio.


title: 1004-Monocytes-U


title: 1004-Myeloid_DCs-U


title: 1004-Mature_NK-S


title: 1004-Naive_B-U


title: 1004-Mem_B-U


title: 1004-Mature_NK-U


title: 1004-Th2_precursors-S


title: 1004-Bulk_B-U


title: 1004-Th17_precursors-S


title: 1003-Monocytes-S

description:
Additional sequencing was performed on a NextSeq 500 and merged with this library.
ATAC_counts.txt.gz


title: sample7, dataset4


title: 1004-Regulatory_T-U


title: sample2, dataset4


title: 1003-Monocytes-U


title: 1003-Memory_NK-U


title: sample1, dataset4


title: sample6, dataset3

scan_protocol: Using GeneTitan® System according to Affymetrix standard procedure.

extract_protocol: Total RNA from frozen samples was extracted using TRIzol® Reagent according to Thermo Fisher Scientific (Invitrogen) recommendations.

value: Fresh-Frozen


title: sample2, dataset3


title: 1004-Naive_Tregs-S


title: 1003-Mature_NK-S


title: sample3, dataset3


title: sample3, dataset4


title: ERMS_3

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

data_processing:
Reads were aligned with STAR v2.4.0; PCR duplicates were removed with Picard v1.95 and reads aligning to ribosomal RNA were removed with RSeQC; gene counts were obtained from reads with an alignment quality of at least 10 using featureCounts and transformed to transcript per million (TPM) units.
Genome_build: GRCz10
Supplementary_files_format_and_content: Counts matrix provided as supplementary file.

organism: Danio rerio

source_name: embryonal rhabdomyosarcoma

growth_protocol: Animals were raised at 28 degrees celcius

extract_protocol:
Total RNA was extracted using RLT buffer (Qiagen) and purified using RNeasy kit (Qiagen) as per manufacturer instructions
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit

treatment_protocol: Tissue was harvested using 90% PBS + 5% FBS. FACS sorting was performed to obtain tumor cell fraction with 85% purity and 90% viability.

tag: genotype

value: CG1 tp53 homozygous mutant

tag: tumor type

tag: procedure

value: primary transplant, GFP FACS-sorted


title: GermCell_1

source_name: germ cell tumor

value: spontaneous


title: sample1, dataset3


title: 1003-Mature_NK-U


title: sample7, dataset3


title: sample8, dataset3


title: sample4, dataset3


title: 1004-Naive_Tregs-U


title: 1003-Immature_NK-U


title: 1004-Naive_Teffs-S


title: 1004-Th1_precursors-S


title: sample5, dataset3


title: 1003-Th2_precursors-S


title: 1004-Naive_Teffs-U


title: ERMS_1


title: 1003-Th2_precursors-U


title: MPNST_3

source_name: malignant peripheral nerve-sheath tumor

value: primary transplant, dissection


title: 1003-Th17_precursors-S


title: 1004-Regulatory_T-S


title: ERMS_2


title: MPNST_2


title: 1004-Memory_Tregs-U


title: 1004-Memory_Teffs-S


title: MPNST_1


title: 1003-Th1_precursors-U


title: 1003-Regulatory_T-S


title: Leukemia_3

source_name: Natural Killer cell leukemia


title: 1004-Follicular_T_Helper-S


title: 1004-Follicular_T_Helper-U


title: 1003-Naive_Teffs-S


title: 1003-Regulatory_T-U


title: Leukemia_1


title: 1004-Effector_CD4pos_T-S


title: Leukemia_2


title: Angiosarcoma_2

source_name: angiosarcoma


title: 1004-Memory_Tregs-S


title: 1004-Effector_CD4pos_T-U


title: 1003-Naive_Teffs-U


title: 1003-Th1_precursors-S


title: WholeFish_3

source_name: whole fish

value: bulk extraction


title: 1003-Memory_Tregs-U


title: 1004-Memory_Teffs-U


title: 1004-Gamma_delta_T-S


title: 1004-Gamma_delta_T-U


title: WholeFish_2


title: 1003-Memory_Teffs-S


title: 1004-Naive_CD8_T-S


title: 1003-Memory_Teffs-U


title: WholeFish_1


title: 1003-Memory_Tregs-S


title: 1004-Naive_CD8_T-U


title: 1003-Follicular_T_Helper-S


title: 1003-Follicular_T_Helper-U


title: 1004-Effector_memory_CD8pos_T-S


title: Angiosarcoma_1