title: 4422_10_A549_Etoposide_R2

city: Amsterdam

first: Liqin

last: Wang

address: Plesmanlaan 121

country: Netherlands

institute: NKI-AVL

description:
A549 etoposide treated cells
A549 Etoposide, Aurora treated.txt

data_processing:
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38, using Tophat 2.1 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: KRAS mutant lung

growth_protocol: A375 cells grow in DMEM-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. A549 cell grow in RPMI-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine.

extract_protocol:
RNA was isolated using TRIZOL
polyA+ Stranded RNA libraries were prepared for sequencing according to Illumina instructions

treatment_protocol: A375 cells were infected with gRNAs gSMARCB1 virus and cultured for 8 days. A549 cells were treated with 0.2μM tozasertib, 1μM alisertib or 1μM  barasertib for 7 days.

tag: disease state

value: Lung cancer

tag: cell line

tag: agent

value: etoposide


title: BR_WR_0_5d_M24_exp1

status: Public on Sep 21 2017

type: SRA

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

country: USA

institute: The University of Chicago

description:
Whole tissue
raw_counts_exp1_day7_day21.txt

library_source: transcriptomic

data_processing:
Fastq files were demultiplexed with custom scripts and quality checked with FastQC.
Read mapping using STAR aligner with mm10 genome.
FeatureCounts was used to count mapped reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample. Rows = genes, and columns = whole-tissue or sorted CD8+ cell samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
For whole organs, samples were lysed in Trizol and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (Thermoscientific). For sorted cell populations, CD8+ T cell populations (5,000-10,000 cells per sample) were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and total RNA was extracted with Dynabeads MyOne Silane beads. After bead-based enrichment, total RNA samples were purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA concentration was normalized across samples prior library construction.
Total RNA was heat-fragmented to an average size of 500 bp fragments and reverse transcribed with barcoded oligo(dT) primers containing an Illumina-compatible adapter sequence. After RNA degradation, barcoded, single-stranded cDNA samples were pooled and flanked by an Illumina-compatible adapter sequence in their 3’ end using a ‘primer extension’ method with DNA Pol I, Large Klenow Fragment exo minus. cDNA pools flanked on both ends with illumina sequences were then amplified by PCR and sequenced on Illumina sequencers.

tag: strain

tag: cohort

value: WR

tag: days post infection

tag: mouse id

tag: experiment id

tag: sequencing batch


title: BR_MVA_3d_M80_exp1

value: MVA


title: BR_MVA_5d_M104_exp1


title: BR_MVA_3d_M79_exp1


title: BR_MVA_5d_M105_exp1


title: BR_MVA_5d_M103_exp1


title: BR_MVA_WR_0_5d_M25_exp1


title: 4422_8_A549_MLN8237_R2

description:
A549 MLN8237 treated cells
A549 Etoposide, Aurora treated.txt

organism: Homo sapiens


title: BR_MVA_5d_M102_exp1


title: 4422_9_A549_Etoposide_R1


title: BR_MVA_WR_5d_M110_exp1


title: BR_MVA_3d_M78_exp1


title: 4422_6_A549_AZD1132_R2

description:
A549 AZD1132 treated cells
A549 Etoposide, Aurora treated.txt


title: BR_MVA_WR_3d_M86_exp1


title: BR_MVA_1_5d_M56_exp1


title: BR_MVA_1_5d_M54_exp1


title: 4422_7_A549_MLN8237_R1


title: BR_MVA_1_5d_M53_exp1


title: BR_MVA_1_5d_M55_exp1


title: 4422_5_A549_AZD1132_R1


title: BR_MVA_0_5d_M19_exp1


title: BR_MVA_0_5d_M17_exp1


title: 4422_4_A549_VX680_R2

description:
A549 VX680 treated cells
A549 Etoposide, Aurora treated.txt


title: BR_MVA_0_5d_M18_exp1


title: BR__control_M140_exp1

value: Uninfected


title: BR_MVA_0_5d_M20_exp1


title: BR__control_M139_exp1


title: 4422_3_A549_VX680_R1


title: BR__control_M138_exp1


title: 4422_2_A549_untreated_R2

description:
A549 Parental cells
A549 Etoposide, Aurora treated.txt

value: Parental cells


title: BM_WR_5d_M109_exp1

source_name: Bone marrow


title: 4422_1_A549_untreated_R1


title: BM_WR_5d_M108_exp1


title: BM_WR_5d_M107_exp1


title: 4222_2_A375-crSMARCB1

description:
A375 SMARCB1 KO cells
A375 gSMARCB1.txt

source_name: BRAF mutant melanoma

value: skin cancer

tag: genotype/variation

value: SMARCB1 KO


title: 4222_1_A375-NTC

description:
A375 Parental cells
A375 gSMARCB1.txt


title: BM_WR_3d_M83_exp1


title: BM_WR_3d_M82_exp1


title: BM_WR_3d_M84_exp1


title: BM_WR_5d_M106_exp1


title: BM_WR_1_5d_M60_exp1


title: BR_MVA_3d_M77_exp1


title: BM_WR_1_5d_M59_exp1


title: BM_WR_1_5d_M57_exp1


title: BM_WR_0_5d_M23_exp1


title: BM_WR_1_5d_M58_exp1


title: BM_WR_0_5d_M22_exp1


title: BM_MVA_WR_5d_M113_exp1


title: BM_WR_0_5d_M24_exp1


title: BM_MVA_WR_5d_M111_exp1


title: BM_MVA_WR_5d_M112_exp1


title: RNAseq Koptk1-ASO2

city: New York

first: Iannis

last: Aifantis

state: NY

address: 550 First Avenue, Smilow Research Building Room 1301

department: Pathology

institute: New York University School of Medicine

data_processing:
reads were aligned using STAR aligner v1.4.2 with default parameters
raw counts are calculated by STAR aligner
raw counts were inputed into DESeq2 for differential expression analyiss and normalized count generation
Genome_build: hg19/GENCODE_v19
Supplementary_files_format_and_content: normalized counts in tab delimited file

molecule: total RNA

source_name: T cell leukemia

growth_protocol: cells are growth in RMPI 10% FBS

extract_protocol:
RNA extranction is carried out by RNAeasy plus kit
RNAseq library were prepare by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina ( cat #E7420L)

treatment_protocol: long non coding RNA knockdown is achieved by either infecting cells with lentivirus carrying CRISPR components or antisense oligo (ASO) are added directly in cell culture to 1uM

tag: cell type

value: T cell leukemia


title: BM_MVA_WR_5d_M110_exp1


title: BM_MVA_WR_3d_M88_exp1


title: RNAseq Koptk1-ASO1


title: BM_MVA_WR_3d_M87_exp1


title: BM_MVA_WR_3d_M86_exp1


title: BM_MVA_WR_1_5d_M64_exp1


title: BM_MVA_WR_3d_M85_exp1


title: RNAseq Koptk1-scamble ASO


title: BM_MVA_WR_0_5d_M28_exp1


title: BM_WR_3d_M81_exp1


title: BM_MVA_WR_1_5d_M63_exp1


title: BM_WR_0_5d_M21_exp1


title: MBO25 (F) rep1

city: Birmingham

first: W

middle: Edward

last: Swords

state: Alabama

address: 1918 University Blvd. McCallum bldg, Room 798

department: Medicine, Division of Pulmonary, Allergy and Critical Care Medicine

institute: Univ. of Alabama at Birmingham

description:
replicate 1
F1

data_processing:
Illumina Casava (bcl2fastq) version 1.8.4 software used for basecalling.
Reads were mapped to the reference S. pneumoniae TIGR4 genome (accession- NC_003028.3) using Bowtie2 2.2.9 (default parameters), and transcript abundance was calculated using summarizeOverlaps function from R package GenomicAlignments
The differential expression analyses were carried out using R package DeSeq2 alognwith generation of normalized read count matrix
Genome_build: NC_003028.3
Supplementary_files_format_and_content: Normalized read count matrix for all samples

organism: Streptococcus pneumoniae

source_name: Bacteria planktonic culture harvested at OD600nm 0.8.

growth_protocol: For each pneumococcal strain, three independent cultures were grown in 8 mL of Todd-Hewitt broth supplemented with 0.5 % yeast extract in a 37°C water bath. Cultures were harvested at mid-log phase (OD600nm 0.8), centrifuged (12,000 rpm) for 5 min and resuspended in 1 mL PBS containing lysozyme (2 mg/mL). Samples were immediately processed for RNA extraction.

extract_protocol:
RNA was extracted from bacteria pellets with lysozyme, followed by clean-up and DNase I treatment with NucleoSpinRNA II kit kit per manufacturer’s recommendations.
The ribosomal RNA was removed from the total bacterial RNA using ribosome reduction for Gram positive bacteria (ArrayStar, Rockville MD).  The purified RNA was then processed using the SureSelect Strand Specific RNA-Seq library prep kit from Agilent Technologies (San Diego, CA) following the manufacturer’s protocol. The resulting libraries were quantitated with quantitative PCR (KapaBiosystems, Woburn MA) and the size distribution of the inserts were checked on the Agilent 2100 BioAnalyzer on a High Sensitivity DNA Chip. Library concentration was normalized to 2nM

tag: hsds allele

value: F

tag: hsds allele target recognition domains

tag: colony phenotype

value: 100% transparent


title: MBO25 (F) rep2

description:
replicate 2
F2


title: BM_MVA_WR_1_5d_M61_exp1


title: MBO25 (F) rep3

description:
replicate 3
F3


title: RNAseq CUTLL1-scamble ASO


title: RNAseq CUTLL1-ASO1


title: MBO24 (E) rep3

description:
replicate 3
E3

value: E


title: BM_MVA_WR_0_5d_M25_exp1


title: BM_MVA_5d_M105_exp1


title: BM_MVA_5d_M104_exp1


title: RNAseq CUTLL1-ASO2


title: MBO24 (E) rep2

description:
replicate 2
E2


title: RNAseq HpbALL-sgRNA2

value: HpbALL


title: BM_MVA_5d_M103_exp1


title: MBO24 (E) rep1

description:
replicate 1
E1


title: RNAseq HpbALL-non-targeting guide_2


title: BM_MVA_5d_M102_exp1


title: BM_MVA_3d_M80_exp1


title: MBO23 (D) rep3

description:
replicate 3
D3

value: D


title: BM_MVA_3d_M79_exp1


title: BM_MVA_3d_M78_exp1


title: BM_MVA_WR_0_5d_M27_exp1


title: BM_MVA_3d_M77_exp1


title: MBO23 (D) rep2

description:
replicate 2
D2


title: BM_MVA_1_5d_M56_exp1


title: RNAseq Koptk1-sgRNA2


title: MBO23 (D) rep1

description:
replicate 1
D1


title: RNAseq Koptk1-non-targeting guide


title: RNAseq Koptk1-sgRNA1


title: MBO22 (C) rep2

description:
replicate 2
C2

value: C


title: MBO22 (C) rep3

description:
replicate 3
C3


title: RNAseq CUTLL1-sgRNA2


title: BM_MVA_0_5d_M18_exp1


title: BM_MVA_1_5d_M53_exp1


title: BM_MVA_0_5d_M17_exp1


title: MBO22 (C) rep1

description:
replicate 1
C1


title: BM_MVA_1_5d_M54_exp1


title: RNAseq CUTLL1-sgRNA1


title: MBO21 (B) rep3

description:
replicate 3
B3

value: B

value: 100% opaque


title: RNAseq CUTLL1-non-targeting guide


title: BM__control_M139_exp1


title: mESC_Serum_RB20

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

data_processing:
Quality control with FastQC v0.11.5
Adapter removal with Cutadapt v1.3
Alignment with Bowtie v1.1.2
Abundance measurement with featureCounts v1.5
miARma processing pipeline v1.5
Genome_build: mm10
Supplementary_files_format_and_content: [FeatureCounts.txt] non-normalized abundance measurements
Supplementary_files_format_and_content: [NormalizedExpression.txt] Normalized expression levels (log2)

source_name: Embryonic stem cells (ESCs)

growth_protocol: ESC lines were initially derived from C57BL/6 mice using the R2i+LIF protocol (Hassani ei al., 2014). Isolated R2i cells were either maintained under 2i+LIF conditions or transferred to media containing serum+LIF. Cells were passaged at least 10 times to derive stable 2i and serum cell lines. Pluripotency of established cell lines was confirmed by chimera formation and germline contribution as previously reported (Hassani et al., 2014).

extract_protocol:
Total RNA was extracted from the mESC samples using miRVana miRNA Isolation Kit (Invitrogen)
Total RNA was extracted from the mESC samples and used to generate small RNA libraries from which cDNA libraries were prepared at LC Sciences. The purified cDNA libraries were then used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx (Illumina HiSeq 1000/Illumina GAIIx) according to the vendor’s instruction for running the instrument. Raw sequencing reads (up to 45 nt) were obtained using Illumina’s Sequencing Control Studio software version 2.8 following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (LC Sciences).
Illumina Standard Small RNA sequencing library construction protocol

treatment_protocol: ESC lines were maintained at 37˚C in 5% CO2, cultivated on gelatinized tissue-culture plates and dishes (Sigma-Aldrich), and passaged every other day. Serum ESCs were cultured in Knockout™ DMEM (Invitrogen) supplemented with 15% ES-qualified fetal bovine serum (HyClone), 0.1 mM β-mercaptoethanol (Sigma-Aldrich), 0.1 mM non-essential amino acids (Invitrogen), 2 mM L-glutamine (Invitrogen), 100 U/ml penicillin, 100 μg/ml streptomycin (Invitrogen), and 1000 U/ml mouse LIF (mLIF, Royan Biotech). 2i and R2i cells were cultured in N2B27 media that consisted of Neurobasal® medium and DMEM/F-12 (both from Invitrogen) at a 1:1 ratio, 1% N2 supplement (Invitrogen), 1% B27 supplement (Invitrogen), 0.1 mM β-mercaptoethanol, 5 mg/ml BSA (Invitrogen), 2 mM L-glutamine, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, and 1000 U/ml mLIF. Small-molecule chemicals used in 2i and R2i cultures were added at the following concentrations: 1 μM PD0325901 (Stemgent), 10 μM SB431542 (Sigma-Aldrich), and 3 μM CHIR99021 (Stemgent).

value: ESC

tag: culture conditions

value: cultured in serum

tag: passages


title: BM__control_M138_exp1


title: mESC_Serum_RB18


title: BM_MVA_0_5d_M20_exp1


title: MBO20 (A) rep3

description:
replicate 3
A3

value: A


title: MBO20 (A) rep2

description:
replicate 2
A2


title: mESC_2i_RB20

value: cultured in 2i


title: mESC_2i_RB18


title: MBO20 (A) rep1

description:
replicate 1
A1


title: 1-6-BWTStr

city: Worcester

first: Neil

last: Aronin

state: MA

address: 368 Plantation St.

institute: University of Massachusetts Medical School

data_processing:
software used for basecalling was Illumina CASAVA version 1.8.2.
We sorted indexed reads into samples and removed the barcode and randomer with cutadapt version 1.9 (parameter -u 12). Cutadapt trimmed the 3′ polyA tail (parameter -a AAAAAAA) and low quality bases (phred<25), excluding reads less than 15 nucleotides (parameter -q 25 -m 15). We mapped remaining reads to the hg19 or mm10 genome with Bowtie version 1.0.0. Samtools version 0.0.19 converted sam files to bam files, and Bedtools version 2.25.0 converted the bam files to bed files and computed the read 3′ end coverage of each coordinate (parameters -bg -3 -i).
Because the site of cleavage and polyA is heterogeneous, we wrote a peak-calling program to combine reads within 24 nucleotides of the coordinate with the most 3′ end coverage for each polyA site.
We mapped peaks with more than 5 reads to gene ORF or 3′UTRs using intersectBed (BedTools), excluding peaks with non-unique mapping. For each gene, we defined the 3′UTR as the terminal (most 3′) coordinates from the UCSC table browser.
We used CleanUpdTSeq to remove genomically-primed peaks.
We identified alternatively polyadenylated genes as genes with more than one 3′UTR peak. For differential expression analysis, we combined all reads mapping to a gene, either the ORF or the 3′UTR.
Our peak-calling program generated slightly different coordinates between samples for the same isoform due to small inter-sample variations in isoform 3′ end coverage. We considered isoform peaks between samples to be the same if they were within 40 nucleotides of each other. We normalized the expression of each isoform in APA genes by dividing the isoform abundance by the total reads mapping to the gene 3′UTR.
We compared the normalized isoform abundance between HD and control samples using t-tests with or without multiple-hypothesis testing correction using the Benjamini-Hochburg procedure. We considered an adjusted p-value <0.1 to be significant unless otherwise stated (false discovery rate<10%). We did not place a fold or percent change cutoff because small changes in isoform abundances of some genes may affect cellular functions. Only isoforms represented in at least five disease and control samples were considered.
The total reads mapping to each gene were compared between patients and controls using the DESeq2 differential expression package. We considered genes with a fold change greater than 50% and false discovery rate <10% (Benjamini Hochburg correction) significantly expressed differently.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: For human brain sequencing, TSV files were obtained by combining the raw number of reads corresponding to each gene for each sample, or the isoform abundance (normalized to total 3′UTR reads) corresponding to each isoform for each sample.  For mouse brain sequencing,  isoform peaks mappint to huntingtin were extracted from total peaks for each sample.
Supplementary_files_format_and_content: Gr1MCx_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: Gr2MCx_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: HumMCx_all_gene_coverageGr1.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: HumMCx_all_gene_coverageGr2.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: MCxgr1_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: MCxgr2_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: MCxgr1_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: MCxgr2_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: CB_combinedisos.tsv: raw read counts for each isoform peak for all samples
Supplementary_files_format_and_content: HumCB_all_gene_coverage.tsv: raw read counts for each gene for all samples
Supplementary_files_format_and_content: CB_analyzed_isos.tsv: analyzed isoform expression (HD vs control)
Supplementary_files_format_and_content: CB_analyzed_DE.tsv: analyzed gene expression (HD vs control)
Supplementary_files_format_and_content: Mouse_combinedHTTpeaks.tsv: raw read counts for each HTT isoform peak for all mouse samples

source_name: striatum tissue

extract_protocol:
5-10μg total RNA was collected from homogenized tissue using Trizol (Ambion), and RNA quality was assessed by Bioanalyzer (Agilent). RNA was treated with TurboDNAse (Ambion) and cleaned with Clean and Concentrator columns (Zymo).
Cleaned RNA was fragmented in 1x SuperScript III first strand buffer (Invitrogen) at 94°C for 5 minutes 30 seconds and immediately placed on ice. SuperScript III (Invitrogen) reverse transcribed fragmented RNA from the custom Passeq oligo d(T) primer, and 20 minute incubation with RNAse I hydrolyzed remaining RNA (Life Technologies). Samples were run on a denaturing 8M urea, 10% acrylamide gel, and 160-200 nucleotide cDNA fragments were eluted overnight in elution buffer (300mM NaCl, 10mM EDTA). Spin-X columns (Corning) removed remaining gel pieces, and eluted cDNA was precipitated by incubation with 50% isopropanol at -20°C for 30 minutes followed by centrifugation at maximum speed for 45 minutes at 4°C. The pellet was washed with 70% ethanol and collected by spinning at maximum speed for 10 minutes 4°C. Dried pellets were resuspended in water. cDNA was circularized by incubation with CircLigase II (Epicentre) at 60°C for 4 hours. Phusion polymerase (NEB) amplified the insert and adaptors with PE 1.0 and PE 2.0 primers by incubation at 98°C for 30 seconds; 14 cycles of 98°C for 5 seconds, 62°C for 10 seconds, and 72°C for 10 seconds; and a final extension of 72°C for 2 minutes. The PCR products were run on a non-denaturing 10% polyacrylamide gel. The 215-254 nucleotide library was extracted and eluted and precipitated as above. Libraries were Bioanalyzed (Agilent) for quality control and sequenced with single-end 100 base-pair sequencing on the HiSeq 2000 machine (Illumina).
Passeq

tag: genotype

value: wild-type mouse


title: A426WTStr


title: A425WTStr


title: mESC_R2i_RB18

value: cultured in R2i


title: H2O2 rep2

city: Toronto

first: Stefanie

last: Mak

state: Ontario

address: 661 University Avenue, Suite 1600

department: Biochemistry

country: Canada

institute: University of Toronto

data_processing:
Base-calling was performed by MiSeq Reporter.
Sequenced reads were mapped to Staphylococcus aureus ATCC 29213 using Bowtie v2.2.8
Reads were counted using HTSeq 0.6.1
Differentially expressed genes were identified using DESeq2 v3.4. The following were the cutoffs for the actinorhodin dataset: adjusted P-value ≤0.05; fold-change ≥2. The following were the cutoffs for the H2O2 dataset: adjusted P-value ≤0.05; fold-change ≥1.5. Data from duplicate experiments were processed together by DESeq2; gene expression of actinorhodin-treated and H2O2-treated cells were compared with that of dioxane-treated cells in order to generate a list of differentially expressed genes.
Genome_build: Staphylococcus aureus subsp. aureus ATCC 29213 (GenBank accession: GCA_001267715.1)
Supplementary_files_format_and_content: Comma-separated value files were generated with DESeq2, showing a list of differentially expressed genes with its normalized abundance measurement, log2 fold change, and adjusted P-values. ACT_upreg_gene_list.csv & ACT_downreg_gene_list.csv show list of genes which were upregulated and downregulated with actinorhodin treatment, respectively. Genes listed have adjusted P-values ≤0.05 and fold-change ≥2. H2O2_upreg_gene_list.csv & H2O2_downreg_gene_list.csv show list of genes which were upregulated and downregulated with H2O2 treatment, respectively. Genese listed have adjusted P-value ≤0.05 and fold-change ≥1.5.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus ATCC 29213

growth_protocol: S. aureus was grown to OD600 ~0.4 before treatment with compounds.

extract_protocol:
Harvested cells were lysed using Rususpension Buffer (10 mM Tris-HCl pH 7.5; 30 mM MgCl2; 30 mM NH4Cl) containing 500 µg/mL lysostaphin. RNA was extracted with the Qiagen RNeasy Mini kit and then treated with DNase I. Ribosomal depletion was performed using the Illumina Ribo-Zero rRNA Removal (Bacteria) kit.
RNA libraries were prepared for sequencing using NEBNext Ultra Directional RNA Library Preparation kit for Illumina.

treatment_protocol: Cultures were treated with either actinorhodin (4 µg/mL), H2O2 (10 mM), or dioxane (equivalent volume) before RNA extraction.

tag: treatment of cells

value: 10 mM H2O2


title: MBO15 (15) rep2

description:
replicate 2
15_2

value: deletion


title: BM__control_M140_exp1

value: Uninfected


title: A396Q140Str

value: Q140 mouse model


title: MBO21 (B) rep2

description:
replicate 2
B2


title: BM_MVA_WR_0_5d_M26_exp1


title: Diox rep2

value: dioxane


title: MBO21 (B) rep1

description:
replicate 1
B1


title: MBO15 (15) rep1

description:
replicate 1
15_1

value: 100% transparent


title: L4 ChIP-seq

city: Monroe

first: Chris

middle: R

last: Gissendanner

state: LA

address: 700 University Avenue

institute: University of Louisiana Monroe

library_source: genomic

data_processing:
ChIP sequence fragments were mapped to the C. elegans genome (version ce6) using the Short Read Mapping Package (SHRiMP) alignment tool using the R/Bioconductor package BSgenome.Celegans.UCSC.ce6
Peaks were called using the Model-based analysis of ChIP-Seq (MACS) with the band width set at 300 and a p-value cutoff of 1.00 e-05
Enriched ChIP peaks were annotated with the R/Bioconductor package ChIPseeker using the annotation package TxDB.Celegans.UCSC.ce6.ensGene

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole animal L4 stage

growth_protocol: Egg preparations were produced from ten large (100 mm) agar plates, containing growing cultures of NHR-6::GFP animals, by alkaline hypochlorite treatment. Hatched, synchronized L1 arrested larvae from this procedure were then added to 20 large plates seeded with OP50 E. coli such that ~4,000 animals were placed on each plate. Animals were collected for both the late L3/Early L4 and early-mid L4/mid L4 time points at 34-37 hours and 37-42 hours after plating respectively. A minimum of 20 animals were examined at high magnification (60x) with Nomarski optics to ensure nematodes were at the correct developmental stage before proceeding. Crosslinking of collected animals was then performed as previously described to obtain multiple 1.5 mL Eppendorf tubes with 0.1 mL of packed animals each.

extract_protocol:
Fragmented chromatin was obtained by sonicating animal pellets on ice in 0.7 mL HLB buffer using a Misonix Ultrasonic Liquid Sonicator S-4000 with the following settings; 50% amplitude, 5 second pulses with a 1 minute pulse-off period between each set of pulses. Each immunoprecipitation was performed using 2.2 mg of protein equivalent in the lysate as previously described with either rabbit anti-GFP IgG fraction (Life Technologies) or control normal rabbit IgG (Life Technologies) antibodies. 50 mL of total lysate was used as non-treated input control.  Immunoprecipitated DNA was collected by phenol-chloroform-isoamyl alcohol recovery. DNA from each immunoprecipitation was run on a 1% agarose gel with ethidium bromide staining and fragments of length 100-300 bp were excised and gel purified using the Omega Gel Extraction Kit (Omega BioTek) as per the manufacturer’s protocol. Immunoprecipitated DNA samples along with purified input DNA for each developmental time point were sent to the Genomics Core Facility at Louisiana State University Pennington Biomedical Research Center for quality control analysis and next-generation sequencing using the Life Technologies SOLiD 5500xl system.
5500 SOLiD Fragment Library Core Kit (4464415)

value: sgIs2 (Strain I)

tag: tissue

value: whole animal

tag: developmental stage


title: A395Q140Str

tag: strain


title: Diox rep1


title: A394Q140Str


title: L3 input

source_name: whole animal L3 stage

value: sgIs1 (Strain F)


title: Act rep2

value: 4 µg/mL actinorhodin


title: TIGR4 (WT) rep2

description:
replicate 2
W2

value: wild-type

value: All

value: 100% opaque


title: H2O2 rep1


title: A351Q140Str


title: A350Q140Str


title: L3 ChiP-seq


title: TIGR4 (WT) rep1

description:
replicate 1
W1


title: Act rep1


title: S2 PABP Fab2 IP

status: Public on Sep 20 2017

first: Olivia

last: Rissland

address: 686 Bay Street

institute: The Hospital for Sick Children

data_processing:
RNA-seq reads were mapped to the genome by STAR 2.5.2a
Read abundance was calculated using representative gene models and HT-seq count
For those genes with sufficient abundance, occupancies were calculated by normalizing reads in the input sample by those in the total RNA sample
PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths as described (Subtelny et al., 2014).
Genome_build: dm6, hg19
Supplementary_files_format_and_content: PABP_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: eIF4G_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: DDX6_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: Occupancies.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs
Supplementary_files_format_and_content: S2_Occupancies.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs
Supplementary_files_format_and_content: Input_for_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: PABP_pUC_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: miR-124_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: miR-155_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: Total_pUC_DDX_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_pUC_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_124_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_155_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: 293 cells (ATCC) were cultured as recommended by the manufacturer, in DMEM supplemented with 10% fetal bovine serum (Clontech) and penicillin/streptomycin. Drosophila S2 cells (Invitrogen) were cultured as described (Djuranovic et al. 2012).

extract_protocol:
Trizol
Illumina TRU-seq

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Invitrogen) and either 100 nM miRNA duplex or 5 μg pUC19 per 5 million cells, as recommended by the manufacturer. After 24 hours, cells were harvested. EZ view protein G Sepharose (Sigma) was washed twice with lysis Buffer A (100 mM KCl, 0.1 mM EDTA, 20 mM Hepes, pH 7.6, 0.4% NP-40, 10% glycerol, with freshly added 20U/ml SUPERase•In [Ambion], 1 mM DTT and complete mini EDTA-free protease inhibitors [Roche; one tablet per 25 ml lysis buffer]). 100 μl slurry was used per 5 million cells. The beads were then blocked by an overnight incubation, rotating at 4°C, with 500 μg salmon-sperm DNA (Sigma) and 1 ml Buffer A. The next day, cells were washed with 1X PBS (137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.47 mM KH2PO4, pH 7.4) and then lysed with 2 ml ice-cold buffer A per 5 million cells. After clarification by spinning at 15,000 x g for 10 minutes at 4°C, lysates were incubated with antibodies for one hour, rotating at 4°C. Blocked Protein G beads were spun to remove the supernatant, resuspended in an equal volume of Buffer A, added, and the lysates were further incubated for one hour, rotating at 4°C. The beads were washed 3 times with lysis Buffer A, and then TRI-reagent was used to extract RNA. The AGO2 monoclonal 4G8 antibody was purchased from Wako Diagnostics; eIF4E and eIF4G1 antibodies were purchased from MBL international; PABPC1 and DDX6 antibodies were purchased from Abcam (ab21060 and ab40684, respectively). For Fab immunoprecipitations, control C1, anti-PABP (Fab1: P3D9; Fab2: P3D12) and anti-eIF4G (P2A8) Fabs were purified as described (Na et al. 2016). Anti-FLAG Sepharose (Sigma) was washed twice with lysis Buffer A, and then incubated overnight with the appropriate FLAG-tagged Fab and salmon-sperm DNA (Sigma), as above. Immunoprecipitations were performed as with standard antibodies, except that the Fab-bead conjugates were added directly to lysates and incubated for 2 hours rotating at 4°C.

tag: ip

value: PABP 2 (Fab D035)

tag: transfection

value: Mock

tag: enrichment

value: Oligo(dT)

tag: sequencing type

value: RNA-seq


title: S2 Input

value: Input


title: S2 PABP Fab1 IP

value: PABP 1 (Fab D032)


title: Tomato_PSTVd-RG1

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

institute: Université de Sherbrooke

description: RNA isolated from PSTVd-RG1 used for PARE analysis

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
Sequence containing the 5' adapter sequences (GTCCGAC) were filtered
The filtered sequences were searched against the tomato genome  (taxid:4081) by BLAST in order to detect 5' end of the cleaved site.
Genome_build: Chloride channel protein CLC-b-like mRNA and the 40S ribosomal protein S3a-like of tomato
Supplementary_files_format_and_content: PARE analysis; Excel  files containing the 5' RACE sequences of chloride channel protein CLC-b-like mRNA and the 40S ribosomal protein S3a-like.

organism: Solanum lycopersicum

source_name: leaf tissue

growth_protocol: Plants were grown in a growth chamber at a temperature of 25ºC with 16 h of light and 8 h of darkness.

extract_protocol:
Total RNA from the leaf samples was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA), with modifications. Briefly, 100 mg of leaf sample was ground with 800 µl of Lysis/Binding buffer. Then, 80 µl of miRNA homogenate was added and the resulting solution was mixed by vortexing.  RNA was separated by acid phenol-chloroform extraction followed by DNase RQ1 (Promega, MA) treatment. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies, California, USA).
Total RNA obtained from 21-days post inoculation (dpi) plants were subjected for mRNA purification using GenElute mRNA Mini Prep kit according to the manufacturers instructions (Sigma-Aldrich). An RNA adapter-containing MmeI restriction endonuclease site, 5’-PARE RNA adapter, was ligated to the 5’ uncapped ends of the purified mRNA by incubating at 37ºC for 1 h in the presence of T4 RNA ligase I (New England Biolabs, Inc, MA, USA). The unligated adaptor was removed with GenElute mRNA Mini Prep kit. Obtained RNA products were subjected to cDNA synthesise using Target RT-primer followed by 7 cycles of PCR amplification using 5’-cDNA PCR primer and 3’-cDNA PCR primer. The amplicons were subjected to MmeI restriction endonuclease digestion for 1 h according to the manufacturers instructions (New England Biolabs Inc, MA, USA). The products of were separated on 5% polyacrylamide gel and then the nucleic acid band of approximately 70-bp was eluted using elution buffer (10 mM magnesium acetate tetrahydrate, 0.5 M ammonium acetate, 1 mM EDTA [pH 8.0], 0.1% [w/v] SDS). The eluted products were subjected to 15 cycles of PCR amplification using Illumina universal primer along with Indexed TruSeq 3’ index primers.
RNA-seq 5’ RACE

treatment_protocol: Tomato plants were inoculated with the 1 µg of the dimeric PSTVd-RG1 transcripts.

tag: cultivar

value: cv. Rutgers

tag: inoculated with

value: leaf tissue


title: Tomato_Control (PARE)

description: RNA isolated from control used for PARE analysis

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
Sequence containing the 5' adapter sequences (GTCCGAC) were filtered
The filtered sequences were searched against the tomato genome  (taxid:4081) by BLAST in order to detect 5' end of the cleaved site.
Genome_build: tomato  (taxid:4081)
Supplementary_files_format_and_content: Excel file containing the 5' RACE sequences of chloride channel protein CLC-b-like mRNA and the 40S ribosomal protein S3a-like.

extract_protocol:
Total RNA from the leaf samples was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA), with modifications. Briefly, 100 mg of leaf sample was ground with 800 µl of Lysis/Binding buffer. Then, 80 µl of miRNA homogenate was added and the resulting solution was mixed by vortexing.  RNA was separated by acid phenol-chloroform extraction followed by DNase RQ1 (Promega, MA) treatment. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies, California, USA).
Total RNA obtained from 21-days post inoculation (dpi) plants were subjected for mRNA purification using GenElute mRNA Mini Prep kit according to the manufacturers instructions (Sigma-Aldrich). An RNA adapter-containing MmeI restriction endonuclease site, 5’-PARE RNA adapter, was ligated to the 5’ uncapped ends of the purified mRNA by incubating at 37ºC for 1 h in the presence of T4 RNA ligase I (New England Biolabs, Inc, MA, USA). The unligated adaptor was removed with GenElute mRNA Mini Prep kit. Obtained RNA products were subjected to cDNA synthesise using Target RT-primer followed by 7 cycles of PCR amplification using 5’-cDNA PCR primer and 3’-cDNA PCR primer. The amplicons were subjected to MmeI restriction endonuclease digestion for 1 h according to the manufacturers instructions (New England Biolabs Inc, MA, USA). The products of were separated on 5% polyacrylamide gel and then the nucleic acid band of approximately 70-bp was eluted using elution buffer (10 mM magnesium acetate tetrahydrate, 0.5 M ammonium acetate, 1 mM EDTA [pH 8.0], 0.1% [w/v] SDS). The eluted products were subjected to 15 cycles of PCR amplification using Illumina universal primer along with Indexed TruSeq 3’ index primers.

treatment_protocol: Tomato plants were inoculated with the inoculation buffer.

value: Rutgers

tag: infection

value: Mock inoculated

value: leaf


title: RNAseq HpbALL-non-targeting guide_1

tag: cell line

value: HpbALL

tag: cell type

value: T cell leukemia


title: S2 eIF4G Fab IP

value: eIF4G (Fab190)


title: TIGR4 (WT) rep3

description:
replicate 3
W3

tag: hsds allele

value: wild-type

tag: hsds allele target recognition domains

tag: colony phenotype


title: S24-2_18C_mmPCR

city: Stanford

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Drive, Alway M-341

department: Genetics

institute: Stanford University

data_processing:
RNA editing comparisons between populations: The first 19 bases of the read (representing the primer sequence) and the bases after the 143rd base were trimmed.
RNA editing comparisons between populations: Trimmed reads were mapped to the dm3 genome in addition to 120bp of exonic sequence surrounding known splice junctions using BWA, allowing 6 mismatches per read.
RNA editing comparisons between populations: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing comparisons between populations: RNA editing levels were calculated as the percentage of G reads at each site.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: RNA editing comparisons between populations: The processed data files contain editing levels for each Evolution Canyon fly line, including replicates.  The tab-delimited columns are formatted as: chromosome, position, number of edited reads, sequencing coverage, editing level.  Editing sites for which there was no coverage are not included.
RNA editing comparisons between those temperatures: The first 19 bases of the read (representing the primer sequence) and the bases after the 75th base were trimmed.
RNA editing comparisons between those temperatures: Trimmed reads were mapped as single-end reads to the dm3 genome in addition to 52bp of exonic sequence surrounding known splice junctions using BWA, allowing 6 mismatches per read.
RNA editing comparisons between those temperatures: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing comparisons between those temperatures: RNA editing levels were calculated as the percentage of G reads at each site.
Supplementary_files_format_and_content: RNA editing comparisons between those temperatures: The processed data files contain editing levels for each Evolution Canyon fly line, including replicates.  The tab-delimited columns are formatted as: chromosome, position, number of edited reads, sequencing coverage, editing level.   Editing sites for which there was no coverage are not included.

source_name: Male whole body

growth_protocol: Whole bodies were collected from 3-5 day old male adult flies raised at 25˚C or 18˚C.

extract_protocol:
Total RNA was extracted using the Agencourt RNAdvance Tissue Kit, followed by DNAse I treatment (Thermo Fisher Scientific).  cDNA synthesis was performed using the iScript Advanced cDNA synthesis kit (BioRad).
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq)

value: Whole body

tag: replicate

tag: temperature


title: S24-1_18C_mmPCR

tag: tissue


title: S15-1_18C_mmPCR


title: S16-1_18C_mmPCR


title: S16-2_18C_mmPCR


title: Tomato_PSTVd-I

description:
RNA isolated from PSTVd-I used for PARE analysis
Lycopersicum esculentum
RNA-seq 5’ RACE

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
Sequence containing the 5' adapter sequences (GTCCGAC) were filtered
The filtered sequences were searched against the tomato genome by BLAST in order to detect 5' end of the cleaved site.
Supplementary_files_format_and_content: Excel  file containing the 5' RACE sequences of chloride channel protein CLC-b-like mRNA and the 40S ribosomal protein S3a-like.

treatment_protocol: Tomato plants were inoculated with the 1 µg of the dimeric PSTVd-I RNA transcripts.

value: PSTVd-I infected


title: S15-2_18C_mmPCR


title: S14-2_18C_mmPCR


title: S14-1_18C_mmPCR


title: Tomato-Control

description:
RNA isolated for small RNA analysis
Lycopersicum esculentum cv. Rutgers

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
21- to 24-nt long small RNAs were filtered
Obtained 21- to 24-nt small RNAs were mapped on PSTVd in order to detect the possible tomato small RNA exhibiting similarity with PSTVd.  Two PSTVd variants were used for mapping: PSTVd-RG1 (GenBank Acc. No. U23058)  PSTVd-I; GenBank Acc. No. AY937179.
Genome_build: PSTVd-RG1 (U23058); PSTVd-I (AY937179)
Supplementary_files_format_and_content: .xlsx file reports tomato sRNAs exhibiting sequence identity with PSTVd variants

growth_protocol: Plants were maintained at a temperature of 25ºC with 16 h of light and 8 h of darkness.

extract_protocol:
Total RNA from the leaf samples was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA), with modifications. Briefly, 100 mg of leaf sample was ground with 800 µl of Lysis/Binding buffer. Then, 80 µl of miRNA homogenate was added and the resulting solution was mixed by vortexing. RNA was separated by acid phenol-chloroform followed by DNase RQ1 (Promega, MA) treatment. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies, California, USA).
For high-throughput sequencing of small RNAs, the small RNA of 15-50 nt was purified from the total RNA. The purified samples were then subjected for small RNA (sRNA) library preparation using NEBNext Multiplex Small RNA Library Prep Set for Illumina according to manufacturers instructions (New England Biolabs).

treatment_protocol: Plants were inoculated with the inoculation buffer containing 1% benthonite.

value: mock inoculated


title: S11-2_18C_mmPCR


title: S13-2_18C_mmPCR


title: S12-1_18C_mmPCR


title: S11-1_18C_mmPCR


title: S10-2_18C_mmPCR


title: S13-1_18C_mmPCR


title: S10-1_18C_mmPCR


title: BM_MVA_0_5d_M19_exp1

tag: cohort

value: MVA

tag: days post infection

tag: mouse id

tag: experiment id

tag: sequencing batch


title: S8-1_18C_mmPCR


title: S9-1_18C_mmPCR


title: S9-2_18C_mmPCR


title: S7-2_18C_mmPCR


title: S8-2_18C_mmPCR


title: S7-1_18C_mmPCR


title: L4 input

tag: strain

value: sgIs2 (Strain I)

value: whole animal

tag: developmental stage


title: S4-1_18C_mmPCR


title: S4-2_18C_mmPCR


title: S6-1_18C_mmPCR


title: S5-2_18C_mmPCR


title: S12-2_18C_mmPCR


title: S6-2_18C_mmPCR


title: S5-1_18C_mmPCR


title: S3-1_18C_mmPCR


title: S3-2_18C_mmPCR


title: N15-2_18C_mmPCR


title: N15-1_18C_mmPCR


title: N14-1_18C_mmPCR


title: S2-1_18C_mmPCR


title: N16-2_18C_mmPCR


title: N14-2_18C_mmPCR


title: N13-1_18C_mmPCR


title: N13-2_18C_mmPCR


title: N12-1_18C_mmPCR


title: N11-1_18C_mmPCR


title: N12-2_18C_mmPCR


title: N11-2_18C_mmPCR


title: N10-1_18C_mmPCR


title: S2-2_18C_mmPCR


title: N9-1_18C_mmPCR


title: N9-2_18C_mmPCR


title: N16-1_18C_mmPCR


title: N10-2_18C_mmPCR


title: N7-1_18C_mmPCR


title: N7-2_18C_mmPCR


title: N6-2_18C_mmPCR


title: N5-2_18C_mmPCR


title: N8-1_18C_mmPCR


title: N6-1_18C_mmPCR


title: N5-1_18C_mmPCR


title: N4-2_18C_mmPCR


title: BM_MVA_1_5d_M55_exp1


title: N3-2_18C_mmPCR


title: S24-1_25C_mmPCR


title: S16-2_25C_mmPCR


title: N1-1_18C_mmPCR


title: N8-2_18C_mmPCR


title: N3-1_18C_mmPCR


title: S15-2_25C_mmPCR


title: N2-1_18C_mmPCR


title: S24-2_25C_mmPCR


title: N1-2_18C_mmPCR


title: S13-2_25C_mmPCR


title: N2-2_18C_mmPCR


title: S13-1_25C_mmPCR


title: N4-1_18C_mmPCR


title: S10-2_25C_mmPCR


title: MBO15 (15) rep3

description:
replicate 3
15_3

value: deletion

value: 100% transparent


title: S11-1_25C_mmPCR


title: S15-1_25C_mmPCR


title: S11-2_25C_mmPCR


title: Tomato_PSTVd-RG1

description: RNA isolated from PSTVd-RG1 used for viroid derived small RNA analysis

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
21- to 24-nt long small RNAs were filtered
Obtained small RNA reads were mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. Resulted figure will be presented in the manuscript
Genome_build: sRNA was mapped on the genomic and antigenomic strand of the PSTVd-RG1 (GenBank Acc. No. U23058).
Supplementary_files_format_and_content: filtered 21- to 24-nt long total sRNA used for mapping in the PSTVd-RG1 genomic and anti-genomic strand; used for the final data analysis.

organism: Potato spindle tuber viroid

source_name: PSTVd-RG1 infected leaf tissue

treatment_protocol: Plants were inoculated with the 1 µg of the dimeric PSTVd-RG1 RNA transcripts.

value: RG 1

tag: host

value: Lycopersicum esculentum


title: Tomato_PSTVd-I

description: RNA isolated from PSTVd-I used for viroid derived small RNA analysis

data_processing:
CASAVA version 1.6 was used for base-calling.
The primers were trimmed
21- to 24-nt long small RNAs were filtered
Obtained small RNA reads were mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. Resulted figure will be presented in the manuscript
Genome_build: sRNA was mapped on the genomic and antigenomic strand of the PSTVd-I (GenBank Acc. No. AY937179).
Supplementary_files_format_and_content: tab-delimited text files include the 21 to 24-nt long sRNA used for the final data analysis.

source_name: PSTVd-I infected leaf tissue

treatment_protocol: Plants were inoculated with the 1 µg of the dimeric PSTVd-I RNA transcripts.

value: PSTVd-I


title: RNAseq HpbALL-sgRNA1


title: NonDM1_diff_control

city: Gainesville

first: Eric

middle: T

state: FL

address: 2033 Mowry Rd

institute: University of Florida

description:
Low serum, treated with dCas9 and control gRNA
kallisto.txt

data_processing:
Base-calling: Illumina RTA v2
Alignment: Hisat2 was used to align reads to the human genome.
Mixture-of-isoforms (MISO) was used to quantify splicing regulation.
Gene expression quantitation: Kallisto was used to quantify gene expression. Cyclic Loess (R code) was used to normalize gene expression values.
Genome_build: hg19
Supplementary_files_format_and_content: nonUTRevents_monotonic.txt: Tab-delimited file summarizing splicing regulation between the NonDM1 and DM1 lines. Includes chromosomal location of regulated exon (Event), gene symbol (Symb), Number of significant positive comparisons minus number of significant negative comparisons (Trueval), Mean "Trueval" of shuffled comparisons (Mean), Standard deviation of "Trueval" of shuffled comparisons (Std), NonDM1_psi, DM1_psi, difference between NonDM1 and DM1 psi values (delta_psi), and monotonicity score (Z-score).
Supplementary_files_format_and_content: DM05_diff_CAG_vs_DM05_diff_empty.miso.txt:  Tab-delimited file including chromosomal location of regulated exon (event), low confidence interval for psi, mean psi estimate, and high confidence interval for psi for all samples, Bayes Factors for all pair-wise comparisons between samples, name of the gene (gene), gene symbol (symb), and description of gene (desc).
Supplementary_files_format_and_content: kallisto.txt:  Tab-delimited file including gene names and estimated transcripts per million.

source_name: Primary human myoblasts

growth_protocol: Human myoblasts were maintained in Skeletal Muscle Cell Growth Medium-2, Lonza, #CC 3245 supplemented with 10% FBS (high serum) at 37°C and 5% CO2. For low serum conditions, DMEM-F12 supplemented with 2% horse serum was used for 3 days.

extract_protocol:
Total RNA was isolated from myoblasts using Direct-zol RNA columns (Zymo Research) according to manufacturer's instructions. RNAseq libraries were generated using the KAPA RiboMinus Stranded RNAseq kit, except for the two non-DM1 cells treated with dCas9 - the NEB Ultra kit with ribosomal RNA subtraction was used instead.
RNA was converted to libraries using the KAPA Biosystems RiboZero Stranded RNA-Seq kit of the NEB Ultra Stranded Kit with Ribosomal RNA depletion.

treatment_protocol: AAV2/6 treatments were performed for 3 days prior to harvesting of cells. AAV genomes contained deactivated S. aureus Cas9 and control or (CAG)6 gRNA.


title: DM1_diff_control

description:
Low serum, treated with dCas9 and control gRNA
DM05_diff_CAG_vs_DM05_diff_empty.miso.txt


title: DM1_diff_CAG

description:
Low serum, treated with dCas9 and CAG gRNA
DM05_diff_CAG_vs_DM05_diff_empty.miso.txt


title: NonDM1_diff_CAG

description:
Low serum, treated with dCas9 and CAG gRNA
kallisto.txt


title: S9-1_25C_mmPCR


title: S12-2_25C_mmPCR


title: S8-1_25C_mmPCR


title: S12-1_25C_mmPCR


title: S9-2_25C_mmPCR


title: DM1_diff2

description:
Low serum
nonUTRevents_monotonic.txt


title: S16-1_25C_mmPCR


title: S10-1_25C_mmPCR


title: S8-2_25C_mmPCR


title: S7-2_25C_mmPCR


title: NonDM1_diff

description:
Low serum
nonUTRevents_monotonic.txt


title: S6-2_25C_mmPCR


title: mESC_R2i_RB20

value: ESC

tag: culture conditions

value: cultured in R2i

tag: passages


title: S6-1_25C_mmPCR


title: DM1_undiff1

description:
High serum
nonUTRevents_monotonic.txt

tag: cell type


title: S5-2_25C_mmPCR


title: BM__control_M1_exp1

value: Uninfected


title: S4-1_25C_mmPCR


title: 35.RNA.270Y.3.5.2015

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

data_processing:
RNA-seq reads were aligned to hg19 using Tophat-1.3.3
Read counts were generated using featureCounts
Differentially expressed genes were identified with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq read counts for each sample/run were provided as an Excel spreadsheet

source_name: Human Embryonic stem cells

growth_protocol: Human primed and naïve ESC: Isogenic pairs of undifferentiated human pluripotent stem cells were plated at a density of ~ 1.0 x 10^6 cells onto 6-well tissue culture plates pre-coated with 1.5 % Geltrex in mTeSR1 supplemented with 10 µM Rho-kinase inhibitor (Y27632). Subsequently, mTeSR1 media was exchanged daily for four days until the cells reached confluence. RNA was prepared using the RNEasy Mini Kit (Qiagen). The experiment was performed on a total of three different days using a total of six different cell lines (three control and three PODXL-/-).

extract_protocol:
RNA was prepared from isogenic sets of hPSCs using the RNEasy Mini Kit (Qiagen), checked for high integrity on an Agilent Bioanalyzer, and prepared using the TruSeq stranded mRNA library kit (Illumina).
Samples were subsequently sequenced on an Illumina NextSeq500 75x75 paired end high output run

value: human pluripotent stem cells

tag: genotype

value: PODXL wild type/control


title: S5-1_25C_mmPCR


title: NonDM1_undiff

description:
High serum
nonUTRevents_monotonic.txt


title: DM1_undiff2

description:
High serum
nonUTRevents_monotonic.txt


title: N16-2_25C_mmPCR


title: S3-2_25C_mmPCR


title: S2-1_25C_mmPCR


title: S4-2_25C_mmPCR


title: N16-1_25C_mmPCR


title: DM1_diff1

description:
Low serum
nonUTRevents_monotonic.txt


title: S3-1_25C_mmPCR


title: 36.RNA.400Y.3.11.2015


title: N15-1_25C_mmPCR


title: S7-1_25C_mmPCR


title: 34.RNA.450Y.3.11.2015


title: S2-2_25C_mmPCR


title: N15-2_25C_mmPCR


title: 34.RNA.3707.3.5.2015


title: N14-2_25C_mmPCR


title: N14-1_25C_mmPCR


title: 24.RNA.370Y.3.11.2015

value: PODXL mutant


title: N13-1_25C_mmPCR

value: Whole body


title: N12-2_25C_mmPCR


title: 34.RNA.225Y.226.2015


title: N12-1_25C_mmPCR


title: 19.RNA.400Y


title: 35.RNA.215Y.2.26.2015


title: 19.RNA.370Y.3.5.2015


title: 19.2.26.15


title: N10-2_25C_mmPCR


title: 18.RNA.450Y.3.4.2015


title: N9-2_25C_mmPCR


title: N11-1_25C_mmPCR


title: N10-1_25C_mmPCR


title: 18.2.26.15


title: N9-1_25C_mmPCR


title: NoEUE

city: Philadelphia

first: Katherine

middle: Claire

last: Palozola

state: PA

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
EU-RNA
replicate E, unlabeled asynchronous population with spike-ins
processed data file:  NoEU.unique.NoEU.bw, File available on GSM2679533.

data_processing:
sequenced fragments were demultiplexed with bcl2fastq
fragments were trimmed to 35 nucleotides
fragments were aligned with Bowtie2 2.2.9, using the tophat "very sensitive" option in end-to-end mode
aligned BAM files were converted to BED files with bamToBed
BED files were reduced to unique, non-PCR duplicated fragments
fragments were extended to a total length of 300 nucleotides
BED files were normalized to the genome-wide RPM to make bedGraphs
NoEU signal was subtracted on a per base pair basis from each experimental sample
negative values were removed from all NoEU-subtracted samples
FPKM for every hg19 RefSeq was measured with a custom script, available upon request
converted bedGraphs to bigWigs with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig UCSC Genome Browser tracks

source_name: HUH7 hepatoma cell line

growth_protocol: HUH7 human hepatoma cells were cultured in DMEM High Glucose with L-glutamine (Invitrogen, 11965), 10% FBS (HyClone), and 1% penicillin-streptomycin (Invitrogen) at 37˚C in 5% CO2. For mitotic arrest experiments, the cells were synchronized at the G1/S transition by culturing for 24 hr in complete DMEM supplemented with 2 mM thymidine (Sigma, T1895). The thymidine media was removed and cells were washed once with PBS. The cells were then cultured for 2 hr in complete DMEM to complete synchronization. The media was then supplemented with nocodazole (Sigma, M1404) for a final concentration of 0.06 ug/mL, and incubated at 37˚C for 16 hours. Mitotic cells were manually collected by shake-off. To release the cells from arrest, mitotic cells were washed twice with PBS and re-plated in complete DMEM.

extract_protocol:
The media was removed and the cells were collected with TRIzol Reagent (Ambion). Total RNA was isolated using miRNeasy (Qiagen). Biotin-azide was then tethered to EU with the Click-iT Nascent RNA Capture Kit (Invitrogen). Cutsom, biotin-RNA sequences were added as spike-in controls. Biotin-EU-RNAs were pulled down from total RNA using streptavidin-coated magnetic beads (Invitrogen).
The streptavidin bead-tethered biotin-EU-RNA was used for stranded, ribo-depleted cDNA library generation (Ovation Human FFPE RNA-seq Multiplex System).

treatment_protocol: Cells were pulse labeled with 0.5 mM EU in standard growth media for 40 minutes at 37˚C

tag: cell line

tag: time point

value: NoEU


title: N7-2_25C_mmPCR

tag: replicate


title: N13-2_25C_mmPCR

tag: temperature


title: asyncE

description:
EU-RNA
replicate E, labeled with EU in an asynchronous population with spike-ins
processed data file:  async.unique.NoEU.bw, File available on GSM2679530.

value: asynchronous


title: asyncF

description:
EU-RNA
replicate F, labeled with EU in an asynchronous population with spike-ins
processed data file:  async.unique.NoEU.bw, File available on GSM2679530.


title: N8-1_25C_mmPCR

tag: tissue


title: N8-2_25C_mmPCR


title: NoEUD

description:
EU-RNA
replicate D, unlabeled asynchronous population with spike-ins
processed data file:  NoEU.unique.NoEU.bw


title: N7-1_25C_mmPCR


title: asyncD

description:
EU-RNA
replicate D, labeled with EU in an asynchronous population with spike-ins
processed data file:  async.unique.NoEU.bw


title: N6-1_25C_mmPCR


title: N5-2_25C_mmPCR


title: mitE

description:
EU-RNA
replicate E, labeled with EU at 0 minutes of release from nocodazole block with spike-ins
processed data file: mit.unique.NoEU.bw. File available on GSM2679527.

value: mitotic


title: mitD

description:
EU-RNA
replicate D, labeled with EU at 0 minutes of release from nocodazole block with spike-ins
processed data file: mit.unique.NoEU.bw


title: N6-2_25C_mmPCR


title: N11-2_25C_mmPCR


title: NoEUC

description:
EU-RNA
replicate C, unlabeled asynchronous population

data_processing:
sequenced fragments were demultiplexed with bcl2fastq
fragments were trimmed to 35 nucleotides
fragments were aligned with Bowtie2 2.2.9, using the tophat "very sensitive" option in end-to-end mode
aligned BAM files were converted to BED files with bamToBed
BED files were reduced to unique, non-PCR duplicated fragments
fragments were extended to a total length of 300 nucleotides
BED files were normalized to the genome-wide RPM to make bedGraphs
NoEU signal was subtracted on a per base pair basis from each experimental sample
negative values were removed from all NoEU-subtracted samples
FPKM for every hg19 RefSeq was measured with a custom script, available upon request
converted bedGraphs to bigWigs with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig UCSC Genome Browser tracks on sample records, FKPM file on series record.

extract_protocol:
The media was removed and the cells were collected with TRIzol Reagent (Ambion). Total RNA was isolated using miRNeasy (Qiagen). Biotin-azide was then tethered to EU with the Click-iT Nascent RNA Capture Kit (Invitrogen). Biotin-EU-RNAs were pulled down from total RNA using streptavidin-coated magnetic beads (Invitrogen).
The streptavidin bead-tethered biotin-EU-RNA was used for stranded, ribo-depleted cDNA library generation (Ovation Human FFPE RNA-seq Multiplex System).


title: NoEUB

description:
EU-RNA
replicate B, unlabeled asynchronous population


title: NoEUA

description:
EU-RNA
replicate A, unlabeled asynchronous population


title: N4-2_25C_mmPCR


title: N4-1_25C_mmPCR


title: N3-2_25C_mmPCR


title: N5-1_25C_mmPCR


title: N2-2_25C_mmPCR


title: asyncC

description:
EU-RNA
replicate C, labeled with EU in an asynchronous population


title: asyncA

description:
EU-RNA
replicate A, labeled with EU in an asynchronous population


title: asyncB

description:
EU-RNA
replicate B, labeled with EU in an asynchronous population


title: 300C

description:
EU-RNA
replicate C, labeled with EU at 300 minutes of release from nocodazole block


title: mitF

description:
EU-RNA
replicate F, labeled with EU at 0 minutes of release from nocodazole block with spike-ins
processed data file: mit.unique.NoEU.bw. File available on GSM2679527.


title: N3-1_25C_mmPCR


title: N2-1_25C_mmPCR


title: S11_WGS

data_processing:
Library strategy: WGS-seq
n/a

growth_protocol: The whole bodies of male adult flies were collected.

extract_protocol:
For each sample, genomic DNA was extracted from a single male adult fly using the Qiagen DNeasy Blood & Tissue Kit.
Libraries were produced using the Nextera DNA Sample Prep Kit.

value: whole body


title: N1-1_25C_mmPCR


title: N1-2_25C_mmPCR


title: 300B

description:
EU-RNA
replicate B, labeled with EU at 300 minutes of release from nocodazole block


title: S10_WGS


title: S2_WGS


title: 105C

description:
EU-RNA
replicate C, labeled with EU at 105 minutes of release from nocodazole block


title: 300A

description:
EU-RNA
replicate A, labeled with EU at 300 minutes of release from nocodazole block


title: 165A

description:
EU-RNA
replicate A, labeled with EU at 165 minutes of release from nocodazole block


title: 165B

description:
EU-RNA
replicate B, labeled with EU at 165 minutes of release from nocodazole block


title: 165C

description:
EU-RNA
replicate C, labeled with EU at 165 minutes of release from nocodazole block


title: N12_WGS


title: N10_WGS


title: N5_WGS


title: 105B

description:
EU-RNA
replicate B, labeled with EU at 105 minutes of release from nocodazole block


title: 105A

description:
EU-RNA
replicate A, labeled with EU at 105 minutes of release from nocodazole block


title: N1_WGS


title: 80B

description:
EU-RNA
replicate B, labeled with EU at 80 minutes of release from nocodazole block


title: 80A

description:
EU-RNA
replicate A, labeled with EU at 80 minutes of release from nocodazole block


title: S24_WB_RNAseq

description: rRNA-depleted RNA

data_processing:
gene expression: fastx_trimmer was used to trim the 75th and 76th base from reads.
gene expression: Trimmed reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations, using the parameters "-N 5 --segment-mismatches 3 --read-edit-dist 5".
gene expression: Read counts were obtained using featureCounts from the Subread package.
gene expression: DESeq2 was used to obtain gene expression levels.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: gene expression: The processed data files contain gene expression counts for each sample that served as input for DESeq2.  The tab-delimited columns are formatted as: gene name, gene expression count.
RNA editing levels: fastx_trimmer was used to trim the 75th and 76th base from reads.
RNA editing levels: Trimmed reads were mapped to the dm3 genome in addition to 70bp of exonic sequence surrounding known splice junctions using BWA, with the default settings.
RNA editing levels: Duplicate reads were marked using Picard, and duplicate and unmapped reads were removed using Samtools, as well as reads with a mapping quality less than 10
RNA editing levels: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing levels: RNA editing levels were calculated as the number of 'G' reads divided by the number of 'A' and 'G' reads at each site, for bases that had a quality score of at least 20.
Supplementary_files_format_and_content: RNA editing levels: The processed data files contain editing levels for each Evolution Canyon fly line.  The tab-delimited columns are formatted as: chromosome, position, number of A reads, number of G reads, editing level.  Editing sites for which there was no coverage are not included.

source_name: Male whole bodies

growth_protocol: For each sample, 5 heads or whole bodies were collected from 3-5 day old male adult flies that were raised at 25˚C.

extract_protocol:
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), and depleted of ribosomal RNA.
Libraries produced using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 76-bp cycles.


title: S16_WB_RNAseq

description: rRNA-depleted RNA


title: 40B

description:
EU-RNA
replicate B, labeled with EU at 40 minutes of release from nocodazole block


title: 40C

description:
EU-RNA
replicate C, labeled with EU at 40 minutes of release from nocodazole block


title: S15_WB_RNAseq

description: rRNA-depleted RNA


title: S14_WB_RNAseq

description: rRNA-depleted RNA


title: 40A

description:
EU-RNA
replicate A, labeled with EU at 40 minutes of release from nocodazole block


title: S13_WB_RNAseq

description: rRNA-depleted RNA


title: 0C

description:
EU-RNA
replicate C, labeled with EU at 0 minutes of release from nocodazole block


title: 0A

description:
EU-RNA
replicate A, labeled with EU at 0 minutes of release from nocodazole block


title: S10_WB_RNAseq

description: rRNA-depleted RNA


title: M9_ATAC_seq

city: Farmington

first: Michael

last: Stitzel

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
processed data file:
Mouse_aTC1_bTC6_mm9_ATAC_seq_TMM_normalized_read_counts.csv

data_processing:
ATAC-seq. Paired-end ATAC-seq reads were quality trimmed using Trimmomatic version 0.32 and parameters “TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”. Trimmed reads were aligned to mouse genome (mm9) using BWA version 0.7.9a specifically using the bwa mem –M option. Duplicate reads were removed using “MarkDuplicates” from Picard-tools version 1.95. After preprocessing and quality filtering, peaks were called on alignments with MACS version 2.1.0 using the parameters “-g 'mm' --nomodel -f BAMPE -q 0.01”. The peak sets from all samples were merged to generate one consensus peak set (N = 65,053) by using R package DiffBind_2.2.5. Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized using the effective library size (total number of reads in consensus peaks) and using the trimmed mean of M-values normalization method (TMM). Consensus peaks were annotated using HOMER version 4.6 and were classified into two groups i) distal peaks (peaks whose distance to a gene TSS is > 2kb) and ii) promoter peaks (peaks whose distance to TSS is < 2kb). Spearman rank-order correlation was calculated for all pure and mixture samples within consensus peaks using deepTools version 2.4.2.
RNA-seq. Paired-end RNA-seq reads with Phred quality scores < 30 and adaptor sequences were removed using Trim Galore! version 0.40 and reads with < 50bp after trimming were discarded. Trimmed reads were aligned to mouse genome (mm9) using Bowtie 2 version 2.23 with default parameters and expression levels of all genes were determined using RSEM version 1.2.12 with default parameters and reference transcript annotations (NCBI37/mm9, Ensembl v67). A total of 24,531 protein-coding genes and long intergenic non-coding RNAs (lincRNAs) were considered in the study.
Genome_build: ATAC-seq and RNA-seq reads were aligned to mouse genome NCBI37/mm9 and mouse transcriptome NCBI37 ensembl version 67 respectively.
Supplementary_files_format_and_content: Comma-separated value files contain RSEM determined FPKM/expected count values, or TMM normalized read counts. The files are matrices with rows representing features (genes or peaks) and columns representing samples.

growth_protocol: alpha TC1 clone 6 (aTC1) (ATCC® CRL-2934™) and beta-TC-6 (bTC6) (ATCC® CRL-11506™) were purchased from American Type Culture Collection (ATCC) Manassas, VA. aTC1 cells were cultured in Dulbecco's Modified Eagle's Medium (Gibco 11885-076) supplemented with 10% heat-inactivated fetal bovine serum (Seradigm), 15 mM HEPES (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.02% bovine serum albumin (Sigma), 2 g/L glucose at 37C and 5% CO2. bTC6 cells were cultured in Dulbecco's Modified Eagle's Medium (Gibco 11965-084) supplemented with 15% heat-inactivated fetal bovine serum (Seradigm) and 10% sodium pyruvate (Gibco) at 37C and 5% CO2.

extract_protocol: aTC1 and bTC6 cells were counted and mixed in 10% increments to create mixture samples consisting of 100,000 total cells (i.e. 90,000 bTC6 and 10,000 aTC1). In addition, five replicates of 100,000 pure aTC1 and bTC6 cells were processed as controls. ATAC-seq libraries for all samples were prepared as detailed in (Buenrostro et al 2013: http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html) and sequenced on an Illumina NextSeq 500 with 2 x 75 bp cycles

value: Mixture

tag: tissue source

value: Pancreas

tag: sample type

value: Mixed culture


title: M8_ATAC_seq


title: M5_ATAC_seq


title: M6_ATAC_seq


title: 80C

description:
EU-RNA
replicate C, labeled with EU at 80 minutes of release from nocodazole block


title: M4_ATAC_seq


title: S5_WB_RNAseq

description: rRNA-depleted RNA


title: S8_WB_RNAseq

description: rRNA-depleted RNA


title: S7_WB_RNAseq

description: rRNA-depleted RNA


title: S6_WB_RNAseq

description: rRNA-depleted RNA


title: S4_WB_RNAseq

description: rRNA-depleted RNA


title: M3_ATAC_seq


title: S3_WB_RNAseq

description: rRNA-depleted RNA


title: B5_ATAC_seq

value: beta-TC-6 (ATCC CRL-11506)

value: cell culture


title: S2_WB_RNAseq

description: rRNA-depleted RNA


title: N16_WB_RNAseq

description: rRNA-depleted RNA


title: N15_WB_RNAseq

description: rRNA-depleted RNA


title: N14_WB_RNAseq

description: rRNA-depleted RNA


title: B3_RNA_seq

description:
processed data file:
Mouse_aTC1_bTC6_mm9_RNA_seq_rsem_expected_counts.csv
Mouse_aTC1_bTC6_mm9_RNA_seq_rsem_FPKM.csv

extract_protocol: Total RNA was extracted and purified from three aTC1 and bTC6 samples using Trizol (Life Technologies) according to the manufacturer’s instructions, ERCC spike ins (Life Technologies) were added and library prepared using the Kapa Biosystems KAPA stranded mRNA-seq kit according to the manufacturer’s instructions. All sequencing was performed on an Illumina NextSeq 500 with 2 x 100 bp cycles.


title: M1_ATAC_seq


title: 0B

description:
EU-RNA
replicate B, labeled with EU at 0 minutes of release from nocodazole block


title: S11_WB_RNAseq

description: rRNA-depleted RNA


title: M2_ATAC_seq


title: B4_ATAC_seq


title: S12_WB_RNAseq

description: rRNA-depleted RNA


title: N13_WB_RNAseq

description: rRNA-depleted RNA


title: M7_ATAC_seq


title: B2_RNA_seq


title: S9_WB_RNAseq

description: rRNA-depleted RNA


title: B3_ATAC_seq


title: N12_WB_RNAseq

description: rRNA-depleted RNA


title: N11_WB_RNAseq

description: rRNA-depleted RNA


title: N10_WB_RNAseq

description: rRNA-depleted RNA


title: B1_ATAC_seq


title: B1_RNA_seq


title: A5_ATAC_seq

source_name: alpha TC1 clone 6_ATAC-seq

value: alpha TC1 clone 6 (ATCC CRL-2934)


title: B2_ATAC_seq


title: N8_WB_RNAseq

description: rRNA-depleted RNA


title: N7_WB_RNAseq

description: rRNA-depleted RNA


title: A4_ATAC_seq


title: A3_RNA_seq

source_name: alpha TC1 clone 6_RNA-Seq


title: N5_WB_RNAseq

description: rRNA-depleted RNA


title: A3_ATAC_seq


title: N6_WB_RNAseq

description: rRNA-depleted RNA


title: N2_WB_RNAseq

description: rRNA-depleted RNA


title: A2_ATAC_seq


title: A2_RNA_seq


title: A1_ATAC_seq


title: N1_WB_RNAseq

description: rRNA-depleted RNA


title: DDX6 IP polyA miR155

source_name: 293 cells

tag: ip

value: DDX6 (Abcam, ab 40684)

tag: transfection

tag: enrichment

value: Oligo(dT)

tag: sequencing type

value: PAL-seq


title: A1_RNA_seq


title: DDX6 IP polyA miR124


title: S15_heads_RNAseq

description: rRNA-depleted RNA

source_name: Male heads

value: head


title: DDX6 IP polyA pUC

value: Mock


title: S16_heads_RNAseq

description: rRNA-depleted RNA


title: DDX6 polyA input

value: Input


title: N9_WB_RNAseq

description: rRNA-depleted RNA


title: S14_heads_RNAseq

description: rRNA-depleted RNA


title: S13_heads_RNAseq

description: rRNA-depleted RNA


title: PABP IP polyA pUC

value: PABP (abcam, ab21060)


title: S12_heads_RNAseq

description: rRNA-depleted RNA


title: PABP IP polyA miR155


title: PABP IP polyA miR124


title: S10_heads_RNAseq

description: rRNA-depleted RNA


title: S11_heads_RNAseq

description: rRNA-depleted RNA


title: PABP polyA input


title: N4_WB_RNAseq

description: rRNA-depleted RNA


title: S9_heads_RNAseq

description: rRNA-depleted RNA


title: S24_heads_RNAseq

description: rRNA-depleted RNA


title: S8_heads_RNAseq

description: rRNA-depleted RNA


title: N3_WB_RNAseq

description: rRNA-depleted RNA


title: MutL222P replicate 3

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

country: Italy

institute: Universita' degli Studi di Verona

data_processing:
CASAVA 1.8.2
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded
Reads were then clipped from adapter sequences using Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 10 nt window) were trimmed with Sickle (https://github.com/vsbuffalo/sickle).
Alignment of reads to reference human genome (hg19) was performed using TopHat 2 (http://tophat.cbcb.umd.edu/)
Transcripts isoforms were reconstructed using alignments from Reference Annotation Based Transcript (RABT) assembly with cufflinks program (from Cufflinks 2 package (http://cufflinks.cbcb.umd.edu/)) using current RefSeq annotation as a reference and merged with cuffmerge.
Genome_build: hg19
Supplementary_files_format_and_content: expression data table contains expression values (RPKM) as calculated by Cufflinks 2

source_name: SH-SY5Y cell line

growth_protocol: Human neuroblastoma SH-SY5Y cells (catalogue number #94030304 European Collection of Cell Cultures) were cultured in DMEM-High glucose medium supplemented with 15% Foetal Bovine Serum (FBS), 2 mM L-glutamine and 1% non-essential amino acids (all from Euroclone), at 37°C in humified atmosphere with 5% CO2.

extract_protocol:
TRI-reagent
Indexed directional cDNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to manufacturer's instructions. Adapter-ligated cDNA libraries with an insert size of 200-250 bp were size selected on 1.5% agarose gel cassettes using Pippin Prep instrument (Sage Science, Beverly, MA, USA).

treatment_protocol: RA-NBM differentiation paradigm: transfected SH-SY5Y cells were pre-differentiated in DMEM/HIGH supplemented with 5% FBS and 10 μM RA (Sigma-Aldrich) for 6 days, and then grown for further 3 days in Neurobasal medium (GIBCO) enriched with 50 ng/ml recombinant human BDNF (rhBDNF, Peprotech), 2 mM db-cAMP (Sigma-Aldrich), 20 mM KCl, B27 supplement and 1% GlutaMAX (GIBCO) (Pezzini et al, Cell Mol Neurobiol, 2017, 37:665-682).

tag: treatment

value: RA-NBM differentiated cells

tag: transfected with

value: muant CLN1 L222P


title: Mut169dupA replicate 1

value: mutant CLN1 169dupA


title: MutL222P replicate 2


title: Mut169dupA replicate 2


title: S5_heads_RNAseq

description: rRNA-depleted RNA


title: Mut169dupA replicate 3


title: MutL222P replicate 1


title: S6_heads_RNAseq

description: rRNA-depleted RNA


title: WildType replicate 3

value: wildtype CLN1


title: N16_heads_RNAseq

description: rRNA-depleted RNA


title: S2_heads_RNAseq

description: rRNA-depleted RNA


title: S3_heads_RNAseq

description: rRNA-depleted RNA


title: N15_heads_RNAseq

description: rRNA-depleted RNA


title: WildType replicate 2


title: Empty-vector replicate 3

value: empty vector


title: N14_heads_RNAseq

description: rRNA-depleted RNA


title: Empty-vector replicate 2


title: Empty-vector replicate 1


title: N12_heads_RNAseq

description: rRNA-depleted RNA


title: S7_heads_RNAseq

description: rRNA-depleted RNA


title: N11_heads_RNAseq

description: rRNA-depleted RNA


title: rheumatoid arthritis tissue 38 (RA_pre_19)

city: Spring House

first: Alice

last: Walsh

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

data_processing:
Reads were trimmed for adaptors and sequence quality. The average number of clusters (post-trimming) per sample was 89 million.
Trimmed reads were aligned to human b37.3 reference genome using the STAR v2.4 aligner (Dobin et al., 2013).
Aligned reads were quantified using RSEM v1.2.14 algorithm (Li and Dewey, 2011) with UCSC transcriptome model (accessed on 03/17/2014) that included lincRNAs from Ensembl v75. This transcriptome model has a total of 34495 genes and 88933 isoforms
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

source_name: synovial biopsy

extract_protocol:
Total RNA was extracted from RA synovial samples and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer
Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina. Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cells. Raw read quality was evaluated using FastQC.

tag: Sex

value: M

tag: age

tag: subject number

tag: disease duration in weeks

tag: disease

value: Rheumatoid arthritis (early)

value: Baseline

tag: acpa positivity

value: Positive


title: rheumatoid arthritis tissue 37 (RA_post_19)

tag: time point

value: 6 mo tDMARD


title: rheumatoid arthritis tissue 35 (RA_post_18)

value: F


title: N9_heads_RNAseq

description: rRNA-depleted RNA


title: N8_heads_RNAseq

description: rRNA-depleted RNA


title: rheumatoid arthritis tissue 32 (RA_pre_16)


title: N7_heads_RNAseq

description: rRNA-depleted RNA


title: N5_heads_RNAseq

description: rRNA-depleted RNA


title: N4_heads_RNAseq

description: rRNA-depleted RNA


title: N6_heads_RNAseq

description: rRNA-depleted RNA


title: N3_heads_RNAseq

description: rRNA-depleted RNA


title: rheumatoid arthritis tissue 29 (RA_post_15)


title: rheumatoid arthritis tissue 28 (RA_pre_14)


title: rheumatoid arthritis tissue 34 (RA_pre_17)


title: N13_heads_RNAseq

description: rRNA-depleted RNA


title: rheumatoid arthritis tissue 26 (RA_pre_13)


title: rheumatoid arthritis tissue 25 (RA_post_13)


title: rheumatoid arthritis tissue 27 (RA_post_14)


title: N1_heads_RNAseq

description: rRNA-depleted RNA


title: WildType replicate 1

tag: cell line


title: N10_heads_RNAseq

description: rRNA-depleted RNA

tag: tissue


title: rheumatoid arthritis tissue 36 (RA_pre_18)


title: rheumatoid arthritis tissue 31 (RA_post_16)


title: rheumatoid arthritis tissue 23 (RA_post_12)


title: rheumatoid arthritis tissue 30 (RA_pre_15)


title: N2_heads_RNAseq

description: rRNA-depleted RNA


title: rheumatoid arthritis tissue 24 (RA_pre_12)


title: rheumatoid arthritis tissue 22 (RA_pre_11)


title: rheumatoid arthritis tissue 21 (RA_post_11)


title: S14-2_25C_mmPCR

value: Whole body

tag: replicate

tag: temperature


title: rheumatoid arthritis tissue 33 (RA_post_17)


title: rheumatoid arthritis tissue 20 (RA_pre_10)


title: S14-1_25C_mmPCR


title: rheumatoid arthritis tissue 19 (RA_post_10)


title: rheumatoid arthritis tissue 18 (RA_pre_9)


title: rheumatoid arthritis tissue 17 (RA_post_9)


title: rheumatoid arthritis tissue 16 (RA_pre_8)


title: PLC_NTC

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (‘N’) and reads with more than 50% of the bases.
The high quality reads were aligned to the human transcriptome (hg19), followed by quantification of expression using RSEM 1.2.21 (Li and Dewey, 2011). Identification of differential gene expression was performed with EBSeq (Leng et al, 2013). All data was expressed as Transcript Per Million (TPM) and fold changes in transcript levels relative to the PLC/PRF/5 NTC group.

source_name: Hepatocellular Carcinoma Cell Line

growth_protocol: Huh7 cells were cultured in DMEM-HG supplemented with 10%FBS and 1%PS. PLC/PRF/5 cells were cultured in DMEM-HG supplemented with 10%FBS and 1%PS

extract_protocol:
Total RNA were extracted using TRIzol Reagent, and the quality of total RNA was checked by Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shRNAs targeting SCD1(shSCD1#13) and non-target control (NTC) were delivered into Huh7 cells by lenti-viruses. The stably transduced cells were selected by puromycin. shRNAs targeting SCD1(shSCD1#13) and non-target control (NTC) were delivered into PLC/PRF/5 cells by lenti-viruses. The stably transduced cells were selected by puromycin.

tag: genotype/variation

value: vector control


title: PLC_shSCD1

value: SCD1 knockdown


title: Huh7_NTC


title: Huh7_shSCD1


title: rheumatoid arthritis tissue 11 (RA_post_6)


title: rheumatoid arthritis tissue 14 (RA_pre_7)


title: rheumatoid arthritis tissue 13 (RA_post_7)


title: rheumatoid arthritis tissue 12 (RA_pre_6)


title: Individual 32

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

data_processing:
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using DRAP version 1.7 and the Trinity assembler (www.sigenae.org/drap)
Genome_build: Margaritifera_assembly.fas
Supplementary_files_format_and_content: raw counts : comma-separated csv file including count values for each sample / assembly : fasta file

organism: Margaritifera margaritifera

extract_protocol:
SV Total RNA isolation system kit (Promega) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2

tag: location

value: downstream

tag: year

tag: age class

value: young

value: kidney


title: Individual 31


title: Individual 28


title: rheumatoid arthritis tissue 10 (RA_pre_5)


title: rheumatoid arthritis tissue 9 (RA_post_5)


title: Individual 30

value: middle-aged


title: PABP IP

description: Occupancies.txt

data_processing:
RNA-seq reads were mapped to the genome by STAR 2.5.2a
Read abundance was calculated using representative gene models and HT-seq count
For those genes with sufficient abundance, occupancies were calculated by normalizing reads in the input sample by those in the total RNA sample
PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths as described (Subtelny et al., 2014).
Genome_build: dm6, hg19
Supplementary_files_format_and_content: PABP_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: eIF4G_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: DDX6_miRNA_processed.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs, as well as microRNA targeting features
Supplementary_files_format_and_content: Occupancies.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs
Supplementary_files_format_and_content: S2_Occupancies.txt: Processed data file contains RNA abundance measurements in total and IP samples for genes that passed expression cutoffs
Supplementary_files_format_and_content: Input_for_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: PABP_pUC_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: miR-124_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: miR-155_PABP.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: Total_pUC_DDX_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_pUC_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_124_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs
Supplementary_files_format_and_content: DDX6_155_pA.txt: Processed data file contains mean poly(A) tail lengths for genes that passed expression cutoffs

extract_protocol:
Trizol
Illumina TRU-seq

tag: ip

value: PABP (abcam, ab21060)

tag: transfection

value: Mock

tag: enrichment

value: Oligo(dT)

tag: sequencing type

value: RNA-seq


title: Individual 29

value: old


title: Individual 27


title: rheumatoid arthritis tissue 8 (RA_pre_4)

tag: Sex

value: M

tag: age

tag: subject number

value: Rheumatoid arthritis (early)


title: eIF4E IP

description: Occupancies.txt

value: eIF4E (MBL)


title: Individual 26


title: Total RNA

description: Occupancies.txt

value: Input


title: eIF4G IP

description: Occupancies.txt

value: eIF4G (MBL)


title: rheumatoid arthritis tissue 7 (RA_post_4)

tag: disease

value: 6 mo tDMARD

tag: acpa positivity

value: Positive


title: Individual 25


title: DDX6 IP miR124

value: DDX6 (Abcam, ab 40684)

value: Ribozero


title: rheumatoid arthritis tissue 15 (RA_post_8)

tag: time point


title: S24_WGS

tag: tissue

value: whole body


title: Individual 24

value: upstream

value: young

value: kidney


title: rheumatoid arthritis tissue 5 (RA_post_3)

value: F


title: S16_WGS


title: DDX6 IP pUC

value: Mock


title: S15_WGS


title: rheumatoid arthritis tissue 4 (RA_pre_2)

tag: disease duration in weeks

value: Baseline


title: Total RNA for DDX6 miR155

value: RNA-seq


title: Individual 23


title: Total RNA for DDX6 miR124


title: Individual 22


title: S14_WGS


title: Individual 21

value: old


title: S13_WGS


title: Total RNA for DDX6 pUC


title: rheumatoid arthritis tissue 1 (RA_post_1)

value: Rheumatoid arthritis (early)


title: S12_WGS


title: Individual 19

value: middle-aged


title: eIF4G IP miR155

value: Oligo(dT)


title: rheumatoid arthritis tissue 6 (RA_pre_3)


title: Individual 20


title: DDX6 IP miR155


title: eIF4G IP miR124

value: eIF4G (MBL)


title: Individual 18


title: eIF4G IP pUC


title: S9_WGS


title: S8_WGS


title: Individual 17


title: LUHMES_rep2

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to hg38 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Combine all chromosome percent methylation bed files into a single file
Genome_build: hg38
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

source_name: LUHMES

growth_protocol: LUHMES cells were grown at 37°C in a humidified 95% air, 5% CO2 atmosphere. Proliferating cells were enzymatically dissociated with trypsin (138 mM NaCl, 5.4 mM KCl, 6.9 mM NaHCO3, 5.6 mM d-Glucose, 0.54 mM EDTA, 0.5 g/L trypsin from bovine pancreas type-II-S; Sigma-Aldrich) and passaged 1 : 10 when they reached 80% confluency. For differentiation, 8 × 106 LUHMES were seeded into a T175 flask in proliferation medium and differentiation was started after 24 h, that is, on day 0 (d0), by changing to +/+, −/−, +/− or −/+ differentiation medium. After 2 days of cultivation in culture flasks, cells were trypsinized and seeded into poly-l-ornithine/fibronectin pre-coated multi-well plates at a cell density of 1.5 × 105 cells/cm2.

extract_protocol:
Extracted and purified using the Qiagen Puregene kit
WGBS libraries were prepared using 500 ng of DNA bisulfite converted using Zymo’s EZ DNA Methylation-Lightning kit according to the manufacturer’s instructions. Then, 100 ng of converted DNA was used to prepare the library using the EpiGnome/TruSeq DNA Methylation. The manufacturer’s instructions were followed except we performed 14 cycles of amplification instead of 10 in the last PCR step.

tag: cell line

value: LUHMES

tag: gender

value: Female

tag: passage number


title: Total RNA for eIF4G miR155

value: Input


title: rheumatoid arthritis tissue 3 (RA_post_2)

value: 6 mo tDMARD

value: Positive


title: rheumatoid arthritis tissue 2 (RA_pre_1)


title: S7_WGS

value: whole body


title: Individual 16

tag: location

value: downstream

tag: year


title: EPI-NCSC

source_name: EPI-NCSC

growth_protocol: The explants were incubated in a humidified atmosphere at 37°C, 5% CO2 and 5% O2. To protect cells against oxidative stress, we routinely culture neural crest stem cells at low oxygen tension (see e.g., ref 44). It needs to be noted that 5% oxygen does not constitute hypoxia for hEPI-NCSC, as hypoxia is defined as O2 tension below the normoxic value in a given tissue [45] and oxygen tension in hair follicles ranges between 2.5% and 0.1% O2. [46]. Culture medium was NeuroCult XF (Stem Cell Technologies, Grenoble, France Cat# 05761) supplemented with 10 ng/ml rhFGF2 (R&D Systems, Abingdon, UK Cat# 233-FB), 20 ng/ml rhEGF (R&D Systems Cat# 236-EG), 1X ITS+3 (Sigma, Poole, UK Cat# I-2771), 1% (v/v) FBS (HyClone, Thermo Fisher, Cramlington, UK Cat# SH30070.02), 1X GlutaMAX (Invitrogen, Cat# 35050–038), 1X Penicillin/Streptomycin (Sigma Cat# P0781) and 2.5 μg/ml Amphotericin B (Sigma Cat# A2942).

value: EPI-NCSC

value: Male


title: S6_WGS


title: Individual 15

tag: age class

value: kidney


title: Total RNA for eIF4G pUC

tag: ip

tag: transfection

value: Mock


title: PABP IP miR155

value: PABP (abcam, ab21060)

tag: enrichment

tag: sequencing type

value: RNA-seq


title: Individual 14

value: old


title: S4_WGS


title: S5_WGS


title: DPSC_Dup15q_rep2

source_name: Dental Pulp Stem Cells

growth_protocol: Dental pulp tissues were minced and then digested in a solution of 3 mg/ml collagenase type I and 4 mg/ml dispase type II for 1 h at 37 °C. After centrifugation, cells were resuspended in culture media, and passed through a 70 μm strainer to obtain single-cell suspension. Cells were seeded in culture dishes and maintained under standard conditions (37 °C, 100% humidity, 5% CO2) in αMEM medium, supplemented with 100 μM ascorbic acid 2-phosphate, 2 mM l-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal calf serum (FCS). Subconfluent cultures were regularly passaged by treatment with 0.05% trypsin in phosphate-buffered saline (PBS, pH 7.4) and seeded at a density of 104 cells/cm2.

tag: disease state

value: Dup15q Syndrome

value: Dental Pulp Stem Cells


title: DPSC_Dup15q_rep3


title: Individual 13


title: DPSC_Dup15q_rep1


title: LUHMES_rep1


title: S3_WGS

source_name: Male whole body


title: Individual 12


title: PABP IP pUC

value: Oligo(dT)


title: DPSC_Control_rep5

value: control


title: Total RNA for PABP miR155


title: N16_WGS


title: N15_WGS


title: Total RNA for eIF4G miR124


title: Individual 10


title: DPSC_Dup15qDupChr17

value: Dup15q Syndrome and duplication of part of chromosome 17


title: DPSC_Control_rep4


title: DPSC_Dup15q_rep4

value: Female


title: DPSC_Control_rep3


title: N14_WGS


title: Individual 9


title: PABP IP miR124


title: Total RNA for PABP pUC

value: Input


title: DPSC_Control_rep1


title: N13_WGS


title: DPSC_Control_rep2


title: Meg3 (M5) - even

city: Bethesda

first: Sunita

middle: K

last: Agarwal

state: MD

address: Bldg. 10, Room 8C-101

department: NIDDK

institute: National Institutes of Health

description:
ChIRP
Meg3 even probe mix was used to isolate Meg3 with chromatin DNA fragments

data_processing:
Library strategy: ChIRP-Seq
Base calling, alignment, filtering, peak calling,normalization of the ChIRP-Seq data was outsourced to Genomatix
Genome_build: NCBI Build 37 mm9
Supplementary_files_format_and_content: Bed file of Genomic DNA uniquely captured by Meg3-ChIRP (odd and even probes) from the Meg3 expressing MIN6-4N stable cell line (M5).

source_name: MIN6-4N cells

growth_protocol: MIN6-4N cells were cultured in complete medium (DMEM low glucose medium supplemented with 15% FBS and, antibiotic and antimycotic), at 37˚C and 5% CO2

extract_protocol:
Cells treated with 1% Glutaraldehyde for cross-linking were used for preparing chromatin with standard protocols recommended for ChIRP-Seq (SigmaAldrich).
Diagenode's MicroPlex Library Preparation kit and SX-8G IP-Star Compact protocol was used to construct total 6 libraries of genomic DNA fragments: V3 (input, odd probe Meg3-ChIRP and even probe Meg3-ChIRP) and M5 (input, odd probe Meg3-ChIRP and even probe Meg3-ChIRP). Library multiplex index/tags were as follows: V3_INPUT (ATCACG), V3_ODD (TTAGGC), V3_EVEN (TGACCA), M5_INPUT (CGATGT), M5_ODD (ACAGTG), M5_EVEN (GCCAAT)

treatment_protocol: MIN6-4N cells were transfected with pcDNA3.1 Vector or pcDNA3.1-Meg3 using lipofectamine 2000. Stable clones were selected in complete medium containing 750 µg/ml of G418 and picked using cloning cylinders. RT-PCR confirmed stable clones containing Vector (V3) or Meg3 (M5) were expanded in complete medium containing 500 µg/ml of G418. Glutaraldehyde cross-linked chromatin was prepared using standard protocols for ChIRP-Seq (Sigma).

value: Mouse Insulinoma cells

tag: cell type


title: Individual 7

value: upstream

value: young


title: N11_WGS

value: whole body


title: Individual 6


title: Individual 11

value: downstream

value: middle-aged


title: ScWLR27H2

city: yantai

first: cheng-gang

last: ren

state: shandong

address: 17 Chunhui Road, Laishan District

country: China

institute: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, China

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample:
1. Clean data were mapped back onto the assembled transcriptome
2. Readcount for each gene was obtained from the mapping results
Genome_build: De novo transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sesbania cannabina

source_name: root

extract_protocol:
Total RNA from the samples was isolated in two biological replicates using TRIzol (Invitrogen, USA) following the manufacture’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: root

tag: developmental stage

value: 30 days old seedling

tag: genotype

value: wild type


title: N8_WGS


title: Individual 5

value: kidney


title: Meg3 (M5) - odd

description:
ChIRP
Meg3 odd probe mix was used to isolate Meg3 with chromatin DNA fragments


title: N7_WGS


title: Meg3 (M5) - input

description:
Chromatin
No probe was used


title: N6_WGS


title: Total RNA for PABP miR124

value: RNA-seq


title: Individual 4


title: Individual 3


title: ScWLR3H2


title: ScWLR3H1


title: Vector (V3) - even


title: N4_WGS


title: Vector (V3) - odd


title: N9_WGS


title: N3_WGS


title: Individual 1


title: ScR 2


title: Vector (V3) - input

description:
Chromatin
No probe was used


title: N2_WGS


title: Individual 8


title: cKit_PRC1dKO_rep2

status: Public on Sep 19 2017

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the mm10 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
Genome_build: mm10

source_name: cKit+ spermatogonia

extract_protocol: Total RNA was purified using an RNeasy micro kit (Qiagen) according to the manual provided. RNA quality and quantity were checked using Bioanalyzer (Agilent) and Qubit (Life technologies), respectively. The initial amplification step was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. Libraries were then created by Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced with Illumina HiSeq 2500.

value: cKit+ spermatogonia

tag: strain

value: testis

tag: age

tag: biowardrobe ides


title: cKit_PRC1dKO_rep1

tag: tissue


title: cKit_PRC1ctrl_rep2


title: Thy1_PRC1dKO_rep2

source_name: Thy1+ spermatogonia

value: Thy1+ spermatogonia


title: ScWLR27H1


title: cKit_PRC1ctrl_rep1


title: Thy1_PRC1ctrl_rep1


title: Thy1_PRC1ctrl_rep2


title: TOM3

city: Boston

first: Matthew

middle: Robert

last: Jones

address: 72 East Concord Street

department: Medicine

institute: Boston University School of Medicine

data_processing:
Quality assessment using Fastqc and subsequent trimming with Cutadapt 1.7.1
STAR 2.4.2a alignment to the GRCm38.p4 genome with appended tdTomato marker cassette
Indexed bam files were converted to raw counts using HTseq with Gencode M10 gene annotation reference
DESeq2 was used for normalization, statistical comparisons and expression differences
Genome_build: mm10

source_name: tdTomato-negative multiciliated cells 3

extract_protocol:
Lungs from Miwi2tdTomato mice were enzymatically digested to achieve a single cell suspension which was then subject to FACS using CD45-EpCAM+tdTomato-/+ gates.
Total RNA was isolated using Trizol, cleaned with Qiagen RNAeasy mini kit, amplified with Ovation RNA-Seq System V2, and used to prepare TruSeq Nano DNA libraries.

value: tdTomato-negative multiciliated cells

tag: individual

value: Mouse 2

value: lung


title: TOM5

source_name: tdTomato-negative multiciliated cells 5

value: Mouse 3