title: RNA-seq in NPC 72 wild type

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-2


title: NY_KO

status: Public on Nov 21 2017

type: SRA

city: Cincinnati

first: Jeff

last: Kuerbitz

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

country: USA

institute: Cincinnati Childrens Hospital

description:
rsem_expected_count_matrix.csv
rsem_TPM_matrix.csv

library_source: transcriptomic

data_processing:
Illumina HiSeq Control Software used for base calling
Sequenced reads were trimmed for Nextera adaptor sequence and low quality regions using Trimmomatic-0.33 with the parameters:2:30:10:1:keepBothReads SLIDINGWINDOW:4:20
Reads were mapped to the genome and transcripts per million transcripts (TPM) and expected counts were calculated using rsem-1.2.22  with the --bowtie2 parameter
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Amygdalar Intercalated Cells

extract_protocol:
E16.5 Embryos were harvested and stored on ice while tail tissue samples were used for genotyping.  Brains from Tshz1GFP/+ or Tshz1GFP/RA embryos were dissected, quickly embedded in low melting agarose at 36°C, and hardened on ice.  Brains were cut into 700µm coronal sections using a vibratome.  The ventro-lateral portions of caudal telencephalic sections containing the amygdala were dissected as depicted in Figure 6A.  Tissue from embryos of the same genotype was pooled in PBS and dissociated.  Cell suspensions were diluted to a concentration of approximately 1.5x106 cells/mL and GFP expressing cells were isolated by FACS sorting.  Sorted cells were collected in 350µL in buffer RLT with 1% (v/v) 2-mercaptoethanol and RNA was isolated using the Qiagen RNeasy Micro Kit.
Double stranded cDNA was generated and amplified with the NuGEN Ovation RNA-Seq System v2. The Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool, and the concentration of the pool was optimized to acquire at least 30-35 million reads per sample.

treatment_protocol: Animal protocols were conducted in accordance with guidelines set forth by the Cincinnati Children’s Hospital Medical Center Institutional Animal Care and Use Committee and the National Institutes of Health.  All mice used in this study were maintained on an outbred background. For staging of embryos, the day of vaginal plug detection was considered embryonic day 0.5 (E0.5)

tag: cell type

value: amygdala intercalated cells

tag: age

tag: genotype


title: RNA-seq in NPC 75 wild type

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-3

data_processing:
RNA-seq alignment. Tuxedo-suite was used for the entire RNA-seq analyses (Trapnell et al. 2012). Specifically, TopHat2 (v2.1.0) was used to align RNA-seq reads to the mouse genome (mm10). To ensure correct alignment especially for assigning the spliced reads to the correct transcripts, we supplied the software with an existing transcript reference annotations from RefSeq with option --GTF. The RefSeq annotation is available as the iGenome project at the TopHat website (https://ccb.jhu.edu/software/tophat/igenomes.shtml). Other settings of the aligner were left to the default.
Transcript assembly. We then supplied the alignment BAM files from TopHat2 to Cufflinks to perform transcript assembly and expression estimation. The assembly was guided by the above RefSeq annotations with option --GTF-guide. We also turn on the multi-read correction (--multi-read-correct) and fragment bias correction options (--frag-bias-correct $genome) to correct for the sequencing biases. Other settings of the assembler were left to the default.
Differential analysis. We assembled transcripts in each sample library and biological replicate separately. In the end, we ran Cuffmerge to combine all assembled transcripts into a merged custom annotation file (merged.gtf) for the differential expression analysis. In particular, we ran Cuffdiff to compare between M14 knockout mutant and wild-type libraries using the read alignment files from TopHat2 as input and the above custom annotation file as reference. The 3 biological replicates per condition were used to estimate the dispersion in the negative binomial likelihood function modeled by Cuffdiff. We also enabled --multi-read-correct and --frag-bias-correct to improve estimation. The main output from Cuffdiff that were used for downstream analysis in this paper were the “gene_exp.diff” and “genes.read_group_tracking” (default output names from the software), which provide the differential expression statistical results and the actual expression estimate in terms of FPKM, respectively. Significant fold-change was determined based on FDR < 0.05 (as the default threshold of the Cuffdiff program).
ChIP-seq analysis. To align ChIP-seq DNA reads to the reference mm10 genome, we used Bowtie2 (v2.3.1) (Langmead and Salzberg 2012) with the default options except that “--broad” was turned on for calling broad peaks. Each ChIP library in each biological replicate was compared against the DNA input background library in the corresponding cell type + condition. Specifically, histone marks H3K4me1, H3K4me3, H3K27ac, and H3K27me3 in wild-type and M14 knockout (KO) mutant of mouse neural progenitor cell (NPC) were compared with the DNA input in wild-type and M14 KO NPC, respectively. Default cutoff of FDR < 0.05 were used to determine ChIP-seq peaks relative to the input libraries. The main outputs from MACS2 were the broadPeak files in BED format, which we used for downstream comparison among the experimental conditions and with other cognate genome-wide results (i.e., RNA-seq and RIP-seq).
For RIP-seq, we used Tophat2 to align reads to the mouse reference mm10 genome with default setting and RefSeq annotations as guide (i.e., the same method as in the RNA-seq analysis). To call RIP-seq peaks, we used MACS2 with default settings except for enabling the --broad option (i.e., the same as in the ChIP-seq analysis).
Genome_build: mm10
Supplementary_files_format_and_content: text or peak (bed) format

source_name: WT

extract_protocol:
Positive ES clones were used for injection into c57 blastocysts and generation of chimerical mice. To produce Mettl14 f/+ mice, the chimeras were crossed wild-type c57 for germ line transmission and then crossed with Atcb-Flpe transgenic mice (The Jackson Laboratory, # 003800) to remove FRT flanked selection cassette. Male Mettl14 f/+ were crossed to female EIIa-Cre transgenic mice (The Jackson Laboratory, # 003724) to obtain Mettl14 +/- and Mettl14 +/- mice were intercrossed to obtain Mettl14 conventional knockout mice. To conditional knockout Mettl14 in brain, floxed Mettl14 mice were bred with nestin-Cre transgenic mice (The Jackson Laboratory, # 003771) to generate Mettl14 f/f;nes-cre. Mice were maintained at the SANFORD BURNHAM PREBYS Medical Discovery Institute Institutional animal facility, and experiments were performed in accordance with experimental protocols approved by local Institutional Animal Care and Use Committees (IACUC).
Total RNA was isolated using TRIZOL (Invitrogen) and treated with DNaseI (Roche). Polyadenylated mRNA was purified using GenElute™ mRNA Miniprep Kit (Sigma-Aldrich) and residual ribosomal RNA was depleted with RiboMinus™ Eukaryote System v2 (Life Technologies). m6A protocol: Purified polyA+ RNA was blotted to a nylon membrane (Millipore) using Bio-Dot Microfiltration Apparatus (Bio-Rad). After crosslinking with a UV crosslinker (Spectroline), the membrane was blocked with non-fat milk in TBST and then incubated with antibody against m6A (Synaptic Systems, Cat. # 202 003, 1:1,000) then an HRP-conjugated antibody against rabbit IgG. After incubation with the Immobilon Western Chemiluminescent HRP Substrate (Millipore), the membrane was exposed to autoradiography film (Kodak). ChIP-seq: Histones were extracted from NSCs cultured for 7 days in vitro using Histone Extraction Kit (Abcam) following manufacturer’s protocols. Histone lysates were separated on SDS-PAGE gel, blotted onto Immobilon-FL PVDF membrane (Millipore, Cat. # IPFL00010) and incubated with primary antibodies including rat anti-H3 (Active Motif, Cat. # 61647; 1:2000), rabbit anti- H3K4me3 (Abcam, Cat. # Ab8580; 1:2000), rabbit anti-H3K27ac (Active Motif, Cat. # Ab8580; 1:2000), rabbit anti-H3K27me3 (Millipore, Cat. # 07-449; 1:2000), rabbit anti-H3K9me3 (Active Motif, Cat. # Ab8898; 1:2000) and rabbit anti-H3ac (Active Motif, Cat. # 39133; 1:2000). Secondary antibodies were conjugates of IRDye 680RD and 800CW (LI-COR Biosciences). Membranes were scanned by Odyssey Imager (LI-COR Biosciences) and quantified using Image Studio Lite (LI-COR Biosciences).

treatment_protocol: Mettl14 gene targeting vector was created by E. coli bacterial recombination as described1. NotI-ApaI fragment including intron 1 to 5 of Mettl14 in the fosmid WI1-205L1 (CHORI) was cloned into pGEM11-DTA2L vector2, yielding pGEM-Mettl14(1-5)-DTA. Two primer pairs (M14-L50F and M14-L50R, the left arm for bacterial recombination; LoxP-LF and LoxP-LR) were annealed and cloned into XhoI/HindIII of pBS-2xFRT-Zeo, derivative of pBS- 2xF5-Zeo3. The PCR fragment including Mettl14 intron 1 to 2 with LoxP site (primer pair, M14- ex2F and M14-ex2R-LoxP) digested by BstBI-MluI and right arm adaptor (annealed primer pair, Mettl14-R50F and Mettl14-R50R) were cloned into the vector with the left arm. The splice acceptor (SA)-internal ribosomal entry site (Ires)-hygromycin resistance gene (Hyg)-tandem polyadenylation signals (tpA) cassette of pGEM-SA-Ires-Hyg-tpA was cloned into NheI-PmlI of the vector with left and right arms 3. The bacterial targeting vector was digested by AgeI- NotI to remove vector backbone and was transfected into E.coli strain SW106 containing pGEM472 Mettl14(1-5)-DTA for bacterial recombination, yielding Mettl14 targeting vector for mouse ES cells. Mettl14 ES targeting vector was linearized by NotI and transfected into G4 male ES cells as described4, 5. 24 hours after transfection, 150 μg/ml Hygromycin was added to the ES medium. Hygromycin-resistant ES colonies were picked 10 days after transfection. Targeting of Mettl14 was confirmed by genomic PCR analysis using primer pairs: M14cF and SA-R for 5′-end; UptpA-F and M14-cR for 3′-end.

value: neural progenitor cell

tag: developmental stage

value: embryo

tag: strain

value: WT


title: RNA-seq in NPC 43 wild type

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-1


title: P38_T

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

country: France

institute: Univ. Bordeaux

data_processing:
Real time analysis (RTA) software used for basecalling.The reads were demultiplexed with bcl2fastq and quality checked with FastQC.
Reads were mapped to the human genome (GRCh38) with CRAC (version 2.5.0 with options "-k 22”, “--no-ambiguity” and “--stranded") (18) and the biological events including SNPs, indels and splice junctions were extracted using cractools (version 1.24 and command “extract”). Reads for each gene were summarized by featureCounts (19) using the annotation from Ensembl (version 82).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts per Sample

organism: Homo sapiens

source_name: Hepatoblastoma

extract_protocol:
Total RNA from 50 frozen patient tissues constituting the tumoral and adjacent NT and 2 cell lines was extracted using the mirVana kit (Thermo Fisher Scientific) according to the supplier’s protocol. The RNA integrity number (RIN) was evaluated by Agilent 2100 Bioanalyzer.
The total of 4 μg was used for generation of each poly-A library with an Illumina TruSeq Stranded mRNA Sample Preparation kit according to standard protocol. Paired-end 125 nt sequencing was performed by MGX-Montpellier GenomiX platform on an Illumina HiSeq 2500.

value: tumour

tag: tissue

value: Hepatoblastoma


title: P38_NT

source_name: Normal liver

value: normal

value: Normal liver


title: QT_Ctrl


title: RNA-seq in NPC 50 Mettl14 heterozogous

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-9

source_name: Het

value: Mettl14 Het


title: NY_Ctrl


title: P36_T


title: P36_NT


title: NX_KO


title: RNA-seq in NPC 78 Mettl14 homozygous knockout

description:
batch1 (Jun-15)
Processed data files: genes.read_group_tracking1, merged1.gtf
YW-6

source_name: KO

value: Mettl14 KO


title: P35_NT


title: P34_T


title: NX_Ctrl


title: SLIRP_WT_RNase_T1

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description:
mitochondrial RNA
processed data files:
SLIRP_WT.CPM.fwd.Cscore.wig
SLIRP_WT.CPM.rev.Cscore.wig
SLIRP_WT.A_TI.fwd.Rscore.wig
SLIRP_WT.A_TI.rev.Rscore.wig

data_processing:
Technical replicates were pooled and sequenced reads were trimmed of adapter sequences with cutadapt v1.10, using default parameters, and aligned to the mouse genome (mm10) with Bowtie239 v2.2.9 with a seed length of 10 and reporting up to 20 alignments per read (-L10 -k 20).
Paired alignments with multiply mapping reads that aligned once to the mitochondrial genome and at least once to a NUMT region were rescued.
All properly paired alignments to the mitochondrial genome with an observed template length of 15 to 35 nt were retained and a subtractive alignment against nuclear tRNA and Illumina contaminant sequences was performed.
Strand-specific fragment BED files were created and 5′ coverage profiles normalised to sequenced library size were produced with bedtools40 v2.26.0.
Footprints were identified as previously described (Liu et al., Cell Reports, 2013) with some modifications reported here. The RNase accessibility of each base, i, in the mitochondrial genome was quantified according to its C score, defined as:  Cscorei = log10( max[Ai+1,T1i+1,Ifi+1] +1 / Untreatedi+1 +1 )  where Ai+1, T1i+1, Ifi+1 and Untreatedi+1 represent the normalised 5′ coverage of the nucleotide immediately downstream of the inspected position in RNase A-, T1-, and If-treated and untreated samples, respectively. The footprint detection algorithm searches for a span of between 8 and 40 nucleotides with an average C score lower than the flanking left and right three nucleotides, the central footprinting region, and calculates its F score:  Fscore = 10C/10L + 10C/10R  where C, L and R are the average C score of the central, left flanking and right flanking regions, respectively. We initially searched for footprints in the control data and for each footprint we calculated its F score(control) and the F score of the equivalent region in the knockout sample, F score(knockout), and the log2-transformed fold change of F scores (knockout/control). We also searched for novel RBP interactions or sites of decreased RNase accessibility by searching for footprints in the experimental data initially, before calculating F scores and extracting the data from the equivalent region in the control sample. To estimate if the F score fold change of a footprint is significant, we built an empirical null model by shuffling the C score of both samples within the mitochondrial genome 1,000 times and for each locus, calculating an F score fold change from each pair of shuffled data sets. For the candidate footprint loci, the central footprint region was required to have a C score(knockout) greater than its C score(control), and the F score fold change was filtered to achieve an expected 5% false discovery rate (FDR) relative to a score obtained from random shuffling 1,000 times, as previously described (Chen et al., Bioinformatics, 2010). The propensity for secondary structure was quantified according to the ratio of double-stranded RNase cleavage over single-stranded, its R score:  Rscorei = log2( Ai+1 +1 / T1i+1 +1 )
Genome_build: mm10
Supplementary_files_format_and_content: WIG files containing per-base Cscore and Rscore values, and BED files containing significant footprint sites

source_name: Heart mitochondria

growth_protocol: Knockout transgenic mice on a C57BL/6N background were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity and fed a normal chow diet and water were provided ad libitum.

extract_protocol:
Mitochondria were isolated from homogenized hearts and isolated by differential centrifugation as described previously (Lagouge et al., PLoS Genetics, 2015; Mourier et al., Human Molecular Genetics, 2014), with some modifications. Hearts or livers were cut and washed three times with ice cold PBS, and once with mitochondrial isolation buffer (MIB) containing 310 mM sucrose, 10 mM Tris-HCl and 0.05 % BSA (w/v) by centrifugation at 4,500 g for 1 min at 4°C. Heart pieces were homogenized in 5 ml of fresh MIB using a Potter S pestle (Sartorius). The homogenate was centrifuged at 1,000 g for 10 min at 4˚C and the supernatant was centrifuged at 4,500 g for 15 min at 4°C to isolate mitochondria. Crude mitochondrial pellets were suspended in MIB supplemented with 1x Complete EDTA-free protease inhibitor cocktail (Roche). Protein concentration was determined by the Bradford or BCA method using BSA as a standard. Mitochondria (2 mg.ml-1) were lysed by addition of 200 µl of lysis buffer (100mM Tris-HCl, 100mM NaCl, 40mM MnCl2, 2mM dithiothreitol pH 7.5, 0.1% TritonX-100). The concentration of the RNase A (10 U/µl), RNase T1 (0.1 U/µl) or RNase If (0.01 U/µl) were optimized and added to each mitochondrial lysate or purified RNA to generate 15-55 nt size fragments. All incubations were carried out at 37˚C for up to 30 minutes and reactions were ended by addition of 700 µl Qiazol, followed by RNA isolation using the miRNeasy Mini Kit (Qiagen). We used mitochondria lysed and mock treated as controls for the footprinting assay.
The libraries were constructed using the Illumina TruSeq Small RNA Sample Prep Kit and deep sequencing of the mitochondrial small RNAs was performed by Australian Genomic Research Facility (Melbourne, Australia) on an Illumina GAII (Illumina, CA) according to the manufacturer’s instructions with one modification, sample isolation from the PAGE gel after adaptor ligation was performed with a modified set of size markers to facilitate capture of small RNAs between 15-55 nt.

value: heart

tag: cell compartment

value: mitochondria


title: P35_T


title: SLIRP_WT_RNase_If


title: SLIRP_WT_RNase_A


title: P34_NT


title: SLIRP_KO_RNase_Untreated

description:
mitochondrial RNA
processed data files:
SLIRP_KO.CPM.fwd.Cscore.wig
SLIRP_KO.CPM.rev.Cscore.wig
SLIRP_KO.A_TI.fwd.Rscore.wig
SLIRP_KO.A_TI.rev.Rscore.wig


title: P33_T


title: SLIRP_KO_RNase_If


title: P33_NT


title: SLIRP_KO_RNase_T1


title: P32_T_rep2


title: SLIRP_KO_RNase_A


title: LRPPRC_WT_RNase_If

description:
mitochondrial RNA
processed data files:
LRPPRC_WT.CPM.fwd.Cscore.wig
LRPPRC_WT.CPM.rev.Cscore.wig
LRPPRC_WT_A-T1.fwd.Rscore.wig
LRPPRC_WT_A-T1.rev.Rscore.wig
LRPPRC.KO_called.sig_footprints.bed
LRPPRC.WT_called.sig_footprints.bed


title: LRPPRC_WT_RNase_T1


title: P32_NT_rep1


title: SLIRP_WT_RNase_Untreated


title: P29_T


title: LRPPRC_WT_RNase_Untreated


title: P32_T_rep1


title: LRPPRC_KO_RNase_If

description:
mitochondrial RNA
processed data files:
LRPPRC_KO.CPM.fwd.Cscore.wig
LRPPRC_KO.CPM.rev.Cscore.wig
LRPPRC_KO_A-T1.fwd.Rscore.wig
LRPPRC_KO_A-T1.rev.Rscore.wig
LRPPRC.KO_called.sig_footprints.bed
LRPPRC.WT_called.sig_footprints.bed


title: P28_NT


title: LRPPRC_WT_RNase_A


title: LRPPRC_KO_RNase_Untreated


title: P27_T


title: LRPPRC_KO_RNase_T1


title: P32_NT_rep2


title: LRPPRC_KO_RNase_A


title: P26_b_T


title: P28_T


title: P26_b_NT


title: P27_NT


title: P29_NT


title: P24_NT


title: P24_T


title: 1MP+cMoP

city: Los Angeles

first: Helen

middle: S

last: Goodridge

state: CA

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

description: MP + cMoP

data_processing:
RNA-Seq was aligned with STAR-2.5.1b to mm10 with gencode vM4 gene models
bams were passed through a picard pipeline of CleanSam, Sort, and MarkDups
Reads were counted with featureCounts from Rsubread version 1.22 against gencode vM4 gene models
Genes that had at least 1 cpm in at least 2 samples were retained for normalization via TMM limma/voom pipeline
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.txt contains read counts from featureCounts. Rows are genes, columns are samples.

source_name: bone marrow (femurs and tibias)

extract_protocol: GP and MP + cMoPs were isolated from the pooled bone marrow of 20 mice. RNA was extracted from using an RNeasy mini kit (Qiagen).  Each sample was subjected to library preparation with a KAPA kit (Kapa Biosystems) and multiplexed across 4 lanes to yield a mean of 32.9 million 75 bp single-end reads per sample (standard deviation 1.7 million reads).

tag: differentiation

value: In vivo

value: Wild-type

tag: gating/cell markers

value: :Lin- c-Kit+ CD34+ FcgRhi Ly6C+ Flt3- CD115hi


title: 2GP

description: GP

value: :Lin- c-Kit+ CD34+ FcgRhi Ly6C+ Flt3- CD115lo


title: 1GP

description: GP


title: WT VSV

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

country: China

institute: Peking university health science center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: peritoneal macrophages

extract_protocol:
Peritoneal macrophages and 293T cells were prepared, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type


title: P23_T_rep1


title: MEFs-control

data_processing:
Adapter sequences were removed from PAR-CLIP reads with cutadapt v1.10, requiring a minimum length after trimming of 14 nt.
Trimmed reads were aligned to the Numts-masked genome sequence with Bowtie v1.12 (-k 1 -n 2 -M 100 --chunkmbs 512 --best --strata).
Cross-linked regions were identified with BMix v1.0, using default parameters (minimum coverage of 5, refinement coverage of 1, a minimum posterior probability of crosslinking of 95% and strand-specific parameter calculation).
Genome_build: mm10
Supplementary_files_format_and_content: BED file containing binding sites identified by BMix

source_name: Mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts from Lrpprc–FLAG transgenic mice generated as previously described (Ruzzenente et al., EMBO J, 2012), were maintained in DMEM medium (Thermo Fisher Scientific) supplemented with GlutaMAX-I, 10% fetal bovine serum, 1% penicillin-streptomycin and 1X MEM non-essential amino acids.

extract_protocol:
PAR-CLIP was performed according to Spitzer et al., 2013, with the exception that cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.5), 260 mM sucrose, 100 mM KCl, 20 mM MgCl2, 1% digitonin) in the presence of RNase inhibitor (New England Biolabs) and protease inhibitors (Roche). Lysates were clarified by centrifugation and diluted in lysis buffer without digitonin until the final digitonin concentration was 0.2%. Diluted lysates were incubated with anti-FLAG M2 magnetic beads (Sigma, Cat. No. M8823) for 2.5 h at 4°C. Beads were washed in lysis buffer with 0.1% digitonin and then in lysis buffer without digitonin.
RNA library preparation and sequencing was performed by Vertis Biotechnologie (Freising, Germany) using unique molecular identifiers to identify PCR duplicates according to Kivioja et al., 2011.

treatment_protocol: Induction of LRPPRC-FLAG expression was achieved by addition of 2 μg/ml doxycycline to the incubation medium for 72 h.

value: Mouse embryonic fibroblasts (MEF)


title: MEFs-experimental


title: P23_NT_rep3


title: ELF4 KO VSV


title: WT_rep2

data_processing:
A transcriptome assembly was performed with RSEM v1.2.31 (--bowtie2 --strandedness reverse --paired-end) against the GENCODE vM13 transcript set combined with custom mitochondrial rRNA/mRNA sequences with an additional 50 adenine residues added to the 3′ ends to allow mapping of polyA tails.
RSEM generated gene counts were imported and analysed for differential expression with tximport v1.4.0 and DESeq2 v1.16.1.
Coverage profiles for each mitochondrial transcript were generated with bedtools v2.26.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files containing RSEM abundances are available on the samples record. DESeq normalized values and results are available on the series record.

source_name: wildtype

growth_protocol: Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-hr light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 ± 2°C and 50 + 10% relative humidity and fed a normal chow diet (Rat & Mouse Chow, Specialty Foods) and water were provided ad libitum.

extract_protocol:
RNA was isolated from total hearts using the miRNeasy Mini kit (QIAGEN) incorporating an on-column RNase-free DNase digestion to remove all DNA.
RNA sequencing was performed on total RNA from four control and four Lrpprc knockout mice using the Illumina HiSeq platform, according to the Illumina Tru-Seq protocol.

value: wildtype


title: WT_rep3


title: P23_T_rep2


title: WT_rep1


title: WT_rep4


title: KO_rep3

source_name: Lrpprc knockout

value: Lrpprc knockout


title: P23_NT_rep2


title: KO_rep4


title: KO_rep1


title: 2MP+cMoP

description: MP + cMoP


title: KO_rep2


title: KO rep3

city: Stanford

first: Devin

middle: Aalpoel

last: King

address: 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Raw sequencing reads (FASTQ) were generated at the Stanford Center for Genomics and Personalized Medicine (SCGPM)
Read quality was assessed using FastQC
76bp paired-end reads were mapped to genome GRCm38 (mm10) using STAR (v2.4.2a), with gene annotations from GENCODE's evidence-based annotation of the mouse genome (GRCm38), version 6 (Ensembl 81)
Reads aligning to annotated transcripts were counted using the summarizeOverlaps() function from the GenomicAlignments R package
Significance results and log2-fold-change values were generated using the DESeq2 package on untransformed count data
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: comma-delimited text file includes default DESeq2 output: baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, symbol

source_name: Heart

growth_protocol: The mouse colony was housed in and cared for by the Stanford Veterinary Service Center in accordance to protocols approved by Stanford’s Institutional Animal Care and Use Committee (IACUC). The mouse colony consisted of approximately 10 cages containing a total of up to 50 mice for propagation. The population consisted of approximately 20% males and 80% females with ages ranging from newborn to six months old.

extract_protocol:
Crosses between male and female mice commenced at 6 to 8 weeks of age in order to obtain progeny. To obtain embryos of a given embryonic stage, timed pregnancy was verified by checking for the presence of a vaginal plug, which was designated as embryonic day 0.5. Female mice 13.5 days after impregnation were euthanized by CO2 followed by cervical dislocation in accordance with guidelines for euthanasia from the American Veterinarian Medical Association (AVMA). The embryos were harvested and the heart dissected out. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). We recovered approximately 40 ng/uL of RNA from each embryonic heart. We used the NEB Next Ultra RNA Library Prep Kit for Illumina for mRNA library preparation.
RNA libraries were prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Whole Heart

value: Embryonic day 13.5

value: Tie2Cre INO80 flox/flox


title: P22_T

value: tumour

value: Hepatoblastoma


title: KO rep2


title: KO rep1


title: P23_T_rep3


title: P23_NT_rep1

value: normal

value: Normal liver


title: WT rep3

value: wild-type


title: 4C_cortical astrocytes_digested_and_ligated_2

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Digested and ligated 4C library (technical replicate 2)

library_source: genomic

data_processing:
Library strategy: Circular Chromosome Conformation Capture (4C)
Computational analyses were performed on single end sequences. Sequences were sorted according to their bait (M1-M5), trimmed at the restriction site, size selected (>50 bp after trimming) and positioned onto the Mus musculus reference genome (mus_musculus.ensemble.release-74) and the E.coli control sequence (Supplementary Table S5) using bowtie aligner (version 1.0.0) with parameters “bowtie -v0 -k 1“ (Langmead et al. 2009). No mismatches were allowed during positioning
Significant interactions between mitochondrial and nuclear DNA were selected based on the consideration that the pairings are independent and therefore the number of times one specific pairing occurs is a binomially distributed random variable (Rodley et al. 2009). Only the reads in the cut-ligated replicates were considered in this step. The FDR rate was <2% for all pairs tested. Interactions were subsequently removed if they were present in both the cut and cut-ligated samples, or if they overlapped known coordinates for nuclear mitochondrial sequences
Genome_build: mus_musculus.ensemble.release-74
Supplementary_files_format_and_content: Raw genome coordinates containing the chromosomal coordinates of the nuclear loci interacting with each of the five mitochondrial baits across the three samples before correction for signficance. M1 - coordinates of nucler loci intreacting with mt bait 1; M2 - coordinates of nucler loci intreacting with mt bait 2; M3 - coordinates of nucler loci intreacting with mt bait 3, M4 - coordinates of nucler loci intreacting with mt bait 4; M5 - coordinates of nucler loci intreacting with mt bait 5

molecule: genomic DNA

source_name: genomic DNA

growth_protocol: Cortices were isolated from one and two day old postnatal mice and incubated with 0.25% trypsin/0.02% EDTA (10 min, 37°C). Trypsin was inactivated with culture medium (D-MEM/F12 medium supplemented with glutamine, 1% penicillin-streptomycin, 10% fetal bovine serum (FBS)). Cells were dissociated by gentle pipetting in 7-8 mL culture medium before being plated in 75mm2 flasks (two cortices per flask) and incubated (5% CO2, 37°C). The culture medium was changed every 3-4 days. After 10-12 days, cultures were shaken for 24-36 h (180 rpm) and treated with 10 mM leucine methyl ester (12 hrs, 5% CO2, 37°C) to remove oligodendrocyte precursors and microglia. Secondary astrocyte cultures were then established by trypsinizing the primary cultures, and sub-plating 1x106 cells onto 100 mm dishes. Confluent secondary astrocyte cultures were fixed (2% (final conc.) paraformaldehyde, 10 min, RT). Unreacted formaldehyde was quenched by addition of glycine (125 mM final conc., 5 min, RT), cells were scraped off the dishes, sedimented (400g, 8 min, 4°C), suspended in PBS (320g, 8 min, 4°C), divided into three aliquots and collected by centrifugation (320g, 8 min, 4°C). Cells were stored in aliquots of 4x106 cells at -80oC until use

extract_protocol:
Chromatin was prepared as described (Splinter et al. 2004) with minor modifications. Briefly, astrocytes (4 x 106) were pelleted by centrifugation (320g, 8 min, 4°C) and lysed (10 min) with ice cold lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitor cocktail-EDTA-free (Roche)). Cell nuclei were collected by centrifugation (600g, 5 min, 4°C). Nuclei were incubated with SDS (0.3% final conc., 1 hr, 37oC, with shaking). Triton-X-100 (1.8% final conc.) was added and the chromatin solution incubated (1 hr, 37oC, with shaking). Restriction buffer (NEB) was added (1x final concentration) before the chromatin was digested with MspI (C^CGG; 160U, New England Biolabs, 37oC, o/n, with shaking). MspI was inactivated (SDS [1.3% final conc.], 20 min, 65oC) and the chromatin solution diluted (10-fold) in water. Triton-X-100 (1% final conc.) was added and the digested chromatin incubated (1 hr, 37oC, with shaking) to sequester the unreacted SDS. A MspI digested E. coli amplicon (Supplementary Table S5 and Supplementary Fig. S1) was added at the same concentration as a diploid mouse locus, to control for random inter-molecular ligation events. T4 DNA ligase (40U, Invitrogen) was added and the chromatin ligated (4.5 hr, 16oC). Following ligation, crosslinks were reversed (3.56U Proteinase K (Fermentas), overnight, 65oC), before removal of RNA by incubation with DNase free RNAase A (0.06 mg, 45 min, 37oC). DNA was purified by three rounds of Chloroform:Phenol (1:1) extraction, addition of 12 µl LPA (10 mg/ml), 0.1x volume 3M Sodium Acetate and 2x volume absolute ethanol and precipitated (-20oC, 2 hr). DNA was pelleted by centrifugation (25 min, 13000rpm, RT) and subjected to two 70% ethanol washes (15 min, 13000rpm, RT). DNA was suspended in 100µl water
A region spanning ~1/3 of the mtDNA genome (NC_010339, 3361-8410) encoding the ND1, ND2, CO1, CO2, ATPase8, ATPase 6 genes was digested in silico with MspI to produce five 4C baits. Inverted PCR primer pairs (Supplementary Table S4) were designed (Primer3 (v. 0.4.0);(Untergasser et al. 2012; Koressaar & Remm 2007)) to amplify out of each individual bait. Blocker primers (Karkare & Bhatnagar 2006; Vestheim & Jarman 2008) were designed (Supplementary Table S5) to hybridise to the adjacent baits. Blocker primers were modified with three carbons on their 5’ and 3’ ends to prevent amplification of the sequences to which they anneal by blocking polymerase activity. PCR reactions contained bait-specific combinations of primers and blockers, and KAPA long range polymerase (Supplementary Table S6). PCR reaction conditions for baits 1, 3, 4, and 5 were (94 °C, 3:00 min; 35x [94°C, 0:25 sec; 55°C, 0:15 sec; 72°C, 5:00 min]; 72°C, 7:00min). PCR conditions for bait 2 were (94°C, 3:00 min; 35x [94°C, 0:25 sec; 41°C, 0:15 sec; 72°C, 5:00 min]; 72°C, 7:00min). Four 20µl PCR reactions were completed for each of the 4C baits. PCR products (10µl) were visualized following separation on a 1.5% agarose gel (Supplementary Fig. S3). Following amplification, PCR products (M1 to M5 for each replicate) were pooled and column purified (QIAquick PCR Purification Kit). Purified libraries (cut library, 3µg; CL1 & 2 libraries, 6µg) were sequenced on a HiSeq 2000 (Beijing Genomics Institute, Hong Kong. Between 29 and 56 million paired-end 100 bp sequences were obtained for each library

treatment_protocol: Confluent secondary astrocyte cultures were fixed (2% (final conc.) paraformaldehyde, 10 min, RT). Unreacted formaldehyde was quenched by addition of glycine (125 mM final conc., 5 min, RT), cells were scraped off the dishes, sedimented (400g, 8 min, 4°C), suspended in PBS (320g, 8 min, 4°C), divided into three aliquots and collected by centrifugation (320g, 8 min, 4°C). Cells were stored in aliquots of 4x106 cells at -80oC until use.

value: Mouse cortical astrocytes

value: postnatal day 1-2


title: 4C_cortical astrocytes_digested

description: Digested but not ligated 4C library


title: P22_NT


title: WT rep2


title: P20_T


title: P20_NT


title: WT rep1


title: CLIP_BMDM_KO2

city: New York

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

description: Sample 5

data_processing:
library strategy: HITS-CLIP
HITS-CLIP reads were filtered by quality (the first 5 nucleotides had a minimum quality score of 15 and the next 45 had a minimum mean score of 15) and exact sequences were collapsed. The 5’ linker was stripped off and Illumina adapter sequences were clipped from the 3’ end (Fastx Toolkit).
Reads were then parsed by size into mRNA (³25nt) and miRNA(³ 17nt and £ 24nt) fractions using a custom python script.
miRNA reads were aligned to mm9 using bowtie (v0.12.8) with the following specifications: “-l 17 -v 2 --best --strata -m 12”.
Read counts were quantified with SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) using miRNA intervals defined by miRBase (v18). miRNAs mapping to multiple positions in the genome were then collapsed.
mRNA reads were uniquely aligned to mm9 using bowtie (v0.12.8) with the following options: “-v 2 --best --strata -m 1”.
A second step of PCR duplicate removal was performed as previously described (Chi et al., 2012) in which reads with the same 5’ 5nt degenerate linker and the same coordinates were removed. This step eliminates true PCR duplicates, in which sequencing errors were also introduced, and would therefore be missed by an exact sequence collapser.
Clusters were defined in SeqMonk as regions with ≥ 8 reads that overlapped by at least 5 nucleotides. The peaks of the clusters were identified as previously described (Chi et al., 2009).
The read depth of each footprint from HITS-CLIP and RNA-Seq was calculated using SeqMonk and CLIP depth was normalized to transcript expression (RNA-Seq read depth; WT/GSM1419282 used for WT CLIP and KO/GSM1419283 used for KO CLIP) to define the “Ago occupancy” (reads per million mapped CLIP/reads per million mapped RNA-Seq).
Ago footprints were filtered to 17,477 that were contained within “expressed” regions, defined as an RPM of greater than or equal to 1, as this provided reasonable coverage of these regions, and would eliminate the any problems with artifactually increasing Ago footprint occupancy values by normalizing to a value less than 1.
The biological complexity (the number of replicates contributing to each Ago Footprint) was calculated based on the replicate contributing ≥2 reads to the footprint. “High-confidence” footprints (14,781) were defined as having a biological complexity of ≥ 2
As all APOBEC1 editing and most miRNA targeting happening within the 3′UTR of a given transcript, we narrowed our search to only 3′UTRs. We generated a permissive 3′UTR database from RefSeq by merging (Bedtools, mergeBed) overlapping 3′UTR regions, thereby defining a region as a 3′UTR if it was catalogued as such in any transcript isoform. 6,270 high-confidence footprints were contained within these merged 3′UTRs.
Genome_build: mm9
Supplementary_files_format_and_content: Final list of filter AGO footprints in 3'UTRs with locations, Ago occupancy values and biological complexity indicated. Tab delimited text file.

source_name: bone marrow derived macrophages

growth_protocol: 3 pairs of C57BL/6 littermate mice were used at 6-12 weeks of age. Apobec1-/- mice were generated as previously described (Hirano et al., 1996) and provided by N. Davidson (Washington University School of Medicine, St. Louis, MO). To isolate BMDMs, mice were euthanized by cervical dislocation and the hind leg removed and cleaned of hair, skin and muscle. The bare bone was cleaned with a 70% EtOH. The two ends of the femurs were cut and the marrow was flushed with 22G needle with cold PBS onto a cell strainer. The cells were pelleted and resuspended in macrophage media (DMEM, 10% FBS, 1% Non-essential amino acids (Invitrogen), 0.1% BME, 20ng/mL M-CSF (Peprotech)) and plated onto one untreated 10cm and incubated in a Precursor cells were plated onto untreated 10cm dishes and incubated in humidified 37°C/5% CO2 incubator overnight. On day 2, cells were counted and re-plated at a concentration of 2 million cells per 10mL macrophage media onto untreated 10cm dishes. Cells were matured for 7 days in, replacing half of the media (with macrophage media supplemented with 40ng/mL M-CSF) every 3 days. Macrophage surface markers: F4/80 (Invitrogen) and Cd11b (BD biosciences) were confirmed via flow cytometry on a FACS Calibur flow cytometer after the 7-day maturation.

extract_protocol:
BMDMs were scrapped off the plates, flash-frozen and stored at -80C. Frozen cells were thawed and lysed in 1mL PXL lysis buffer (1x PBS, 0.1% SDS, 0.5% Na-DOC, 0.5% NP-40) with complete protease inhibitor. After lysing on ice with occasional vortexing, the cells were subjected to DNAse treatment with RQ1 RNAse-free DNAse (Promega) for 5 minutes at 37°C shaking in a Thermomixer. RNAse treatment performed with high (1:100) or low (1:10,000) RNAse A solutions and incubated for 5 minutes shaking at 37°C. Lysates were spun down (14,000RPM, 30minutes at 4°C) and the supernatant transferred to a new tube. Protein A beads were pre-loaded with rabbit anti-mouse IgG bridging antibody (Jackson ImmunoResearch, at 2.3 mg/mL), incubated for 35 minutes at room temperature. Beads were washed (in 0.02% Tween) and then loaded with 3 uL Ago antibody (2A8 ascites provided by Dr. Zissimos Mourelatos- (Nelson et al., 2007)) per 400 uL of beads and rotated for 3 hours at 4°C. Cleared lysates were incubated with primary antibody-loaded beads for 2 hours at 4°C and washed in a series of washes: 1) 2x 1x PXL buffer; 2) 2x 5x PXL (5xPBS 0.1 % SDS, 0.5% Na-DOC, 0.5% NP-40); 3) 2x with high stringency buffer (15mM Tris-HCl, pH 7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Na-DOC, 0.1% SDS, 120mM NaCl, 25mM KCl); 4) 1x with high salt buffer (15mM Tris-HCl, pH 7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Na-DOC, 0.1% SDS, 1M NaCl); 5) 2x with low salt buffer (15mM Tris-HCl, pH 7.5, 5mM EDTA); 6) 2x NT-2 buffer (50mM Tris-HCl pH 7.4, 150mM NaCl, 1mM MgCl2, 0.05% NP-40); 7) 2x PNK buffer (50mM Tris-HCl, pH 7.5, 10mM MgCl2, 0.5% NP-40).
Dephosphorylation of the 5’ phosphate was performed with calf intestinal phosphatase (Roche) with RNAsin Plus RNAse Inhibitor (Promega) at 37°C for 20 minutes, shaking at 1000rpm for 15s every 2 min. Beads were then washed 1) 1x PNK buffer 2) 2x PNK buffer supplemented with 20mM EGTA 3) 2x PNK buffer. The puromycin blocked linker was radio-labeled with T4 PNK (New England Biolabs) and 32P-γ-ATP for 30 min at 37°C. Radiolabeled linker was spun through a G-25 column to remove free-ATP. Labeled 3’RNA linker was ligated to the 3’ end of the RNA with T4 RNA ligase (Fermentas) incubated at 16°C for 1 hour, shaking at 1000rpm for 15s every 4 min. After 1 hour, 80 pmole of cold L32 RNA linker with 5’ phosophate was added. Sampels were incubated overnight and washed 3x with PNK buffer. 5’ ends were re-phosphorylated with with T4 PNK for 20 min at 37°C shaking at 1000rpm for 15s every 4 min. Protein:RNA complexes were eluted off the beads in NuPAGE loading buffer (Invitrogen) at 70°C for 10 min shaking at 1000rpm. Supernatants were run on Novex NuPAGE 8% Bis-Tris gels (Invitrogen) in MOPS running buffer (Invitrogen) for 2hr at 175V and transferred onto Protran BA85 nitrocellulose (Whatman) and exposed to Biomax MR film (Kodak). Regions that corresponded to Ago:mRNA and Ago:miRNA complexes were excised from the membrane, diced and treated with proteinase K (4mg/mL Roche) for 20 min at 37°C shaking at 1100rpm. RNA was then extracted via phenol-chloroform extraction and ethanol precipitation. 5’ linkers with a degenerate nucleotide end were ligated to the extracted RNA with T4 RNA ligase (Fermentas) at 16°C for 5 hours. The ligated reaction was then subjected to DNAse treatement with RQ1 DNAse (Promega) for 20min at 37°C and extracted with phenol-chloroform and subjected to ethanol precipitation. Precipitated RNA was reverse transcribed with Superscript III (Invitrogen) and PCR amplified with Accuprime Pfx Supermix (Invitrogen) for 20-35 cycles. PCR products were run on a 10% denaturing polacrylamide gel and visualized with SYBR Gold (Molecular Probes) staining. 60-100nt products were excised from the lowest cycle number with visual product and gel extracted. Additional PCR amplification followed by gel extraction was performed as described with fusion primers to provide the platform for Illumina sequencing. 10-30uL of 10nM DNA was submitted for sequencing on Illumina HiSeq.

value: BMDM

tag: genotype/variation

value: APOBEC1 KO

tag: antibody


title: P19_T


title: 4C_cortical astrocytes_digested_and_ligated_1

description: Digested and ligated 4C library (technical replicate 1)


title: CLIP_BMDM_WT3

description: Sample 3

value: WT

value: Ago antibody (2A8 ascites provided by Dr. Zissimos Mourelatos- (Nelson et al., 2007)


title: P17_T


title: CLIP_BMDM_KO1

description: Sample 4


title: 2M-mono

description: MDP-derived Ly6Chi monocytes

extract_protocol:
GMPs and MDPs were isolated from the pooled bone marrow of 20 mice and cultured in vitro in media (RPMI with 10% FCS and 1% penicillin-streptomycin) supplemented with M-CSF (50 ng/ml; Peprotech). On days 2, 3 and 4 of culture, cells were harvested and FACS sorted for monocyte progenitors (Ly6G− CD11b− c-Kit+ Ly6C+ CD115+) and Ly6Chi monocytes (Ly6G− CD11b+ c-Kit− Ly6Chi CD115+ F4/80−). Whole cell lysates of cells isolated at the three timepoints were pooled for each cell type, and RNA was extracted from using an RNeasy mini kit (Qiagen).
Each sample was subjected to library preparation with a KAPA kit (Kapa Biosystems) and multiplexed across 4 lanes to yield a mean of 32.9 million 75 bp single-end reads per sample (standard deviation 1.7 million reads).

value: Wild-type C57BL/6 mice (CD45.2)

value: bone marrow

value: MDP-derived Ly6Chi monocytes

value: In vitro

value: c-Kit- CD11b+ Ly6G- CD115+ Ly6Chi F4/80-


title: 2cMoP

description: cMoP (MDP-derived)

value: cMoP (MDP-derived)

value: c-Kit+ CD11b- Ly6C+ CD115hi


title: 1MDP

description: MDP

value: MDP

value: In vivo

value: Lin- c-Kit+ CD34+ FcgRlo Flt3+ CD115hi


title: 2MDP

description: MDP


title: P15_T

value: tumour

value: Hepatoblastoma


title: 1cMoP

description: cMoP (MDP-derived)


title: 1M-mono

description: MDP-derived Ly6Chi monocytes


title: CLIP_BMDM_WT1

description: Sample 1


title: P17_NT

value: normal

value: Normal liver


title: CLIP_BMDM_WT2

description: Sample 2

value: BMDM


title: P16_NT


title: P16_T


title: P15_NT


title: 2MP

description: MP (GMP-derived)

value: MP (GMP-derived)


title: 2GMP

description: GMP

value: GMP

value: Lin- c-Kit+ CD34+ FcgRhi Ly6C- Flt3- CD115lo


title: 1MP

description: MP (GMP-derived)

value: Wild-type C57BL/6 mice (CD45.2)

value: bone marrow


title: CLIP_BMDM_KO3

description: Sample 6

value: APOBEC1 KO

value: Ago antibody (2A8 ascites provided by Dr. Zissimos Mourelatos- (Nelson et al., 2007)


title: P19_NT


title: 2G-mono

description: GMP-derived Ly6Chi monocytes

value: GMP-derived Ly6Chi monocytes

value: In vitro

value: c-Kit- CD11b+ Ly6G- CD115+ Ly6Chi F4/80-


title: 1G-mono

description: GMP-derived Ly6Chi monocytes


title: P11_NT


title: HeLa-control

data_processing:
Adapter sequences were removed from PAR-CLIP reads with cutadapt v1.10, requiring a minimum length after trimming of 14 nt.
Trimmed reads were aligned to the Numts-masked genome sequence with Bowtie v1.12 (-k 1 -n 2 -M 100 --chunkmbs 512 --best --strata).
Strand-specific coverage profiles were generated with bedtools v2.26.0
Genome_build: hg38
Supplementary_files_format_and_content: Strand-specific bedGraph files of mitochondrial read coverage

source_name: HeLa cells

growth_protocol: HeLa Tet-On cells stably transformed with pTRE-hLRPPRC-FLAG were generated as previously described (Ruzzenente et al., EMBO J, 2012) and maintained in DMEM medium supplemented with GlutaMAX-I, 10% fetal bovine serum, 1% penicillin-streptomycin and 200 μg/ml hygromycin (Harmel et al., J Biol Chem, 2013).

tag: cell line

value: HeLa


title: P09_T


title: P10_NT


title: P04_c_T_rep2


title: P04_c_NT_rep3


title: P04_c_T_rep1


title: P05_T


title: P02_T


title: HuH6

source_name: Hepatoblastoma cell line (10-15 passages)

value: cell line

value: Hepatoblastoma cell line


title: P02_NT


title: P09_NT


title: P05_NT


title: P11_T

value: tumour

value: Hepatoblastoma


title: P04_c_T_rep3


title: Sample90_B10.D2_SNI_M

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

description:
Ribozero RNA
B10.D2_SNI
toc_ENS_genes_mouse_DRG.csv
LncRNAs_toc_mouse_DRG.csv
lncs_res_SNI_vs_sham_B10.D2.csv
ens_genes_res_SNI_vs_sham_B10.D2.csv
Novel_lncRNAs_mouse_DRG.gtf
SJ_regs_mouse_DRG.gtf

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version 3.3.52 and Illumina HiSeq2000 analysis software version 2.0.12.0
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14 and BcltoFastq 1.8.4
Reads were mapped to mm10 genome (Mus_musculus.GRCm38.dna.primary_assembly.fa, Mus_musculus.GRCm38.87.chr.gtf) or rn6 genome (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa, Rattus_norvegicus.Rnor_6.0.90.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with Intersection not empty strategy
All reads overlapping annotations:  RefSeq (Pruitt et al., 2014), XenoRefSeq, ENSEMBL genes (Harrow et al., 2012) were discarded. We then used the remaining subset of RNA-seq reads in order to identify islands of expression outside known gene models (continuously expressed regions) using a coverage window approach. Workflow generally described in (Cabili et al., 2011; Gerstein et al., 2014; Ilott and Ponting, 2013) with modifications to produce annotations at the gene level. Doing this we get a non-redundant annotation of unique genes of LncRNAs suitable for count based DE analysis (Anders et al., 2015; Love et al., 2014). The concept of islands of expression (I.o.E) is described in (Gerstein et al., 2014). Coverage cut-off has been set as in (Cabili et al., 2011)  Only properly paired and uniquely mapped reads were selected. We selected splicing junctions covered with > 2 reads. We discarded all reads overlapping know gene models. We then used the remaining subset of RNA-seq reads to identify I.o.E outside known gene models using a coverage window approach.  We selected continuous regions above the coverage threshold of more than a read-mate length to ensure that overlapping read-mates would not artificially increase coverage. I.o.E were collapsed and clustered as co-overlapping features connected by splicing junctions. In each cluster consensus introns were calculated by the relative frequency of each discrete segment of a set of splicing junctions. We then subtracted the genomic intervals of these consensus introns from the genomic intervals of the grouped (I.o.E) to reconstruct full length putative LncRNAs.   We included putative LncRNAs in this novel annotation only if they were present in all replicates a biological condition or strain. Annotations were exported in the Gene Transfer Format (GTF). Subsequently we filtered out transcripts with length < 200 bp and we used CPAT (Wang et al., 2013) to assess coding potential. The pipeline was scripted in R using bioconductor (Gentleman et al., 2004) packages and custom scripts.
Genome_build: mm10 for mouse, rn6 for rat
Supplementary_files_format_and_content: CSV files *res*.csv include DESeq2 results for both ENSEMBL genes (ens_genes_res) and novel LncRNAs (lncs_res). CSV files *toc*.csv include read-pairs counts calculated using HTSeq. GTF files Novel_LncRNAs_*.gtf included gene models of novel LncRNAs.

source_name: DRG L3 and L4

extract_protocol:
RNA was extracted according to the hybrid method of combined phenol extraction (TriPure, Roche) and column purification (High Pure RNA tissue Kit, Roche) (Bartus et al., 2016). The concentration of RNA in the samples was measured using a nanodrop and proved sufficient for sequencing. According to the hybrid method, DRG tissue was first homogenized in TriPure and then mixed with chloroform, following the phenol extraction method. After centrifuging the aqueous liquid, which stays on the top of the tube and contains the nucleic acids, was removed. This solution was then subjected to the column purification method. Following this protocol, the clear aqueous liquid was placed in Roche High Pure RNA tissue Kit columns and washed several times in order to purify the RNA. RNA was then extracted with the mRNeasy kit and all samples were subjected to on-column DNAse digestion in order to prevent genomic contamination i.e. presence of DNA in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols. Second strand cDNA  synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing over eight lanes of a flow cell.

value: DRG L3 and L4

tag: pooled

value: NO

tag: Sex

value: Male

tag: condition

value: SNI surgery


title: HeLa-experimental


title: P04_c_NT_rep1

value: normal

value: Normal liver


title: 1GMP

description: GMP

value: Wild-type C57BL/6 mice (CD45.2)

value: bone marrow

value: GMP

value: In vivo

value: Lin- c-Kit+ CD34+ FcgRhi Ly6C- Flt3- CD115lo


title: HepG2


title: P04_a_NT


title: P10_T


title: P04_a_T


title: Sample69_B10.D2_SNI_F

value: Female


title: Sample78_B10.D2_SNI_F


title: Sample70_BALB.c_SNI_M

description:
Ribozero RNA
BALB.c_SNI
toc_ENS_genes_mouse_DRG.csv
LncRNAs_toc_mouse_DRG.csv
lncs_res_SNI_vs_sham_BALB.c.csv
ens_genes_res_SNI_vs_sham_BALB.c.csv
Novel_lncRNAs_mouse_DRG.gtf
SJ_regs_mouse_DRG.gtf

value: BALB/c


title: Sample89_B10.D2_SNI_M


title: Sample76_B10.D2_SNI_F


title: Sample65_BALB.c_SNI_F


title: P04_c_NT_rep2


title: Sample49_BALB.c_SNI_M


title: Sample77_B10.D2_SHAM_F

description:
Ribozero RNA
B10.D2_SHAM
toc_ENS_genes_mouse_DRG.csv
LncRNAs_toc_mouse_DRG.csv
lncs_res_SNI_vs_sham_B10.D2.csv
ens_genes_res_SNI_vs_sham_B10.D2.csv
Novel_lncRNAs_mouse_DRG.gtf
SJ_regs_mouse_DRG.gtf

value: Sham surgery


title: Sample88_B10.D2_SHAM_M


title: Sample71_BALB.c_SHAM_M

description:
Ribozero RNA
BALB.c_SHAM
toc_ENS_genes_mouse_DRG.csv
LncRNAs_toc_mouse_DRG.csv
lncs_res_SNI_vs_sham_BALB.c.csv
ens_genes_res_SNI_vs_sham_BALB.c.csv
Novel_lncRNAs_mouse_DRG.gtf
SJ_regs_mouse_DRG.gtf


title: Sample67_B10.D2_SHAM_F


title: Sample60_B10.D2_SHAM_M


title: Sample64_BALB.c_SNI_F


title: Sample58_B10.D2_SHAM_M


title: Sample56_BALB.c_SHAM_F


title: Sample51_BALB.c_SHAM_M


title: Sample50_BALB.c_SHAM_M


title: ctl_day_20 (RNA-Seq)

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v2.2.3
Fragments Per Kilobase Million (FPKM) were calculated using systemPipeR
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

growth_protocol: Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.

extract_protocol:
Cells harvested by trypsinization.  Total RNA isolated from cells using Qiagen Rneasy Micro Kit.
Standard TruSeq v2 for mRNA

treatment_protocol: Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.

value: immortalized mouse embryonic fibroblast cell line

tag: time

value: day 20


title: ctl_day_16_rep_3 (RNA-Seq)

value: day 16


title: ctl_day_12 (RNA-Seq)

value: day 12


title: ctl_day_16_rep_1 (RNA-Seq)


title: ctl_day_16_rep_2 (RNA-Seq)


title: ctl_day_9 (RNA-Seq)

value: day 9


title: ctl_day_5 (RNA-Seq)

value: day 5


title: ctl_day_0 (RNA-Seq)

value: day 0


title: exp_day_16_rep_1 (RNA-Seq)


title: exp_day_16_rep_3 (RNA-Seq)


title: exp_day_16_rep_2 (RNA-Seq)


title: exp_day_5 (RNA-Seq)


title: exp_day_12 (RNA-Seq)


title: ctl_day_20 (RRBS)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using the Bismark bisulfite read aligner
Methylation calling was performed in Bismark
Genome_build: mm10

source_name: immortalized mouse embryonic fibroblast cell line

extract_protocol:
Cells harvested by trypsinization.  Genomic DNA was purified using the Qiagen Blood and Tissue kit.
Lib RRBS


title: exp_day_9 (RNA-Seq)


title: exp_day_0 (RNA-Seq)


title: ctl_day_9 (RRBS)


title: ctl_day_16 (RRBS)


title: exp_day_20 (RRBS)


title: Sample55_BALB.c_SHAM_F

value: DRG L3 and L4

value: NO


title: ctl_day_12 (RRBS)


title: exp_day_12 (RRBS)


title: ctl_day_0 (RRBS)


title: exp_day_9 (RRBS)


title: exp_day_0 (RRBS)


title: exp_day_20 (RNA-Seq)


title: exp_day_5 (RRBS)


title: NHDF_NEURONS_C2

description:
Ribozero RNA
toc_ENS_genes_ips_neurons.csv
LncRNAs_toc_ips_neurons.csv
lnc_res_NEURONS_vs_IPS_AD2.csv
ens_genes_res_NEURONS_vs_IPS_AD2.csv
Novel_lncRNAs_ips_neurons.gtf
SJ_regs_ips.gtf

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version HD 3.4.0.38
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14
Reads were mapped to GRCh38 human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.88.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with the intersection not empty strategy
All reads overlapping annotations:  RefSeq (Pruitt et al., 2014), XenoRefSeq, ENSEMBL genes (Harrow et al., 2012) were discarded. We then used the remaining subset of RNA-seq reads in order to identify islands of expression outside known gene models (continuously expressed regions) using a coverage window approach. Workflow generally described in (Cabili et al., 2011; Gerstein et al., 2014; Ilott and Ponting, 2013) with modifications to produce annotations at the gene level. Doing this we get a non-redundant annotation of unique genes of LncRNAs suitable for count based DE analysis (Anders et al., 2015; Love et al., 2014). The concept of islands of expression (I.o.E) is described in (Gerstein et al., 2014). Coverage cut-off has been set as in (Cabili et al., 2011)  Only properly paired and uniquely mapped reads were selected. We selected splicing junctions covered with > 2 reads. We discarded all reads overlapping know gene models. We then used the remaining subset of RNA-seq reads to identify I.o.E outside known gene models using a coverage window approach.  We selected continuous regions above the coverage threshold of more than a read-mate length to ensure that overlapping read-mates would not artificially increase coverage. I.o.E were collapsed and clustered as co-overlapping features connected by splicing junctions. In each cluster consensus introns were calculated by the relative frequency of each discrete segment of a set of splicing junctions. We then subtracted the genomic intervals of these consensus introns from the genomic intervals of the grouped (I.o.E) to reconstruct full length putative LncRNAs.   We included putative LncRNAs in this novel annotation only if they were present in all replicates a biological condition or strain. Annotations were exported in the Gene Transfer Format (GTF). Subsequently we filtered out transcripts with length < 200 bp and we used CPAT (Wang et al., 2013) to assess coding potential. The pipeline was scripted in R using bioconductor (Gentleman et al., 2004) packages and custom scripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files *res*.csv include DESeq2 results for both ENSEMBL genes (ens_genes_res) and novel LncRNAs (lncs_res). CSV files *toc*.csv include read-pairs counts calculated using HTSeq. GTF files Novel_LncRNAs_*.gtf included gene models of novel LncRNAs.

source_name: SENSORY NEURONS

growth_protocol: Induced pluripotent stem cell generation  NHDF1 (from 44-year-old female) was reprogrammed with Yamanaka retroviruses SOX2, KLF4, OCT3/4, c-MYC and NANOG (Takahashi et al., 2006), and has previously been described (Hartfield et al., 2014). AD2-01 (from 51-year-old male) (Buskin et al., in preparation) and AD4-01 (from 68-year-old male) (Melguzo et al, in preparation) were reprogrammed using the CytoTune™-iPS Reprogramming Kit (ThermoFisher). The fibroblasts to generate AD2-01 and AD4-01 were obtained from a commercial source (Lonza, CC-2511).   CytoTune-iPS reprogramming was performed as directed by the manufacturer’s instructions (ThermoFisher). The CytoTune reprogramming kit contains four Sendai virus-based reprogramming vectors each capable of expressing one of the four Yamanaka factors (KLF4, OCT3/4, SOX2 and c-MYC). Briefly, after fibroblast transduction with the four Sendai virus-based reprogramming vectors, cells are cultured for 5-6 days, with medium changes every other day (DMEM, high glucose (Sigma), 10% FBS (ThermoFisher), 1% Pen/Strep (100x, ThermoFisher), 200mM L-glutamine (Sigma), 1% non-essential amino acids (ThermoFisher)). The transduced fibroblasts are then passaged using 0.05% Trpsin-EDTA onto pre-prepared feeder layer plates containing mitotically inactivated mouse embryonic fibroblasts (MEF). 3-4 weeks after transduction, colonies should have grown to an appropriate size to allow for manual picking. Using an inverted microscope, a single colony displaying iPSC morphology is cut into 5-6 pieces using a 25 gauge needle, transferred into iPS media (KO-DMEM (ThermoFisher), 25% Knock Serum Replacement (ThermoFisher), 1% nonessential amino acids (100x, ThermoFisher), 200mM L- glutamine (Sigma), 1% Pen/Strep (100x, ThermoFisher), 8 ng/ml human FGF2 (Miltenyi Biotec)) and plated onto pre-prepared MEF plates. Colonies are allowed to attach for 48 hours, and thereafter medium changes are performed daily. iPSCs were adapted to feeder-free conditions onto Matrigel (Scientific Laboratory Supplies)-coated plates in mTeSR1 medium (ScienCell). Bulk passaging was by 0.5 mM ethylenediaminetetraacetic acid (EDTA) to make large-scale, quality-controlled stocks that were cryopreserved in liquid nitrogen. The number of feeder-free passages was kept to a minimum. When selecting iPSCs from frozen stocks for differentiation, vials with the same passage number were selected for each cell line throughout all experiments performed in this study.  The iPSC lines AD2-01 and AD4-01 were obtained through the IMI/EU sponsored StemBANCC consortium via the Human Biomaterials Resource Centre, University of Birmingham, UK (http://www.birmingham.ac.uk/facilities/hbrc).  All iPSC lines were subject to strict quality control checks before the initiation of differentiation. Quality control checks of this line included: tests for Sendai virus clearance, fluorescence-activated cell sorting (FACS) for pluripotency markers, genomic integrity checks and embryoid body tri-lineage differentiation experiments. Cells are also confirmed as negative for Mycoplasma before cryopreservation.  Sensory neuron differentiation  For neuronal differentiation, iPSCs were passaged onto Matrigel®-coated six-well plates using TrypLE express (ThermoFisher Scientific) and maintained in mTeSR1 supplemented with 10 μM ROCK inhibitor (ScienCell). Twenty-four hours after plating, the medium was exchanged to mouse embryonic fibroblast (MEF) conditioned medium (ScienCell) supplemented with 10 ng/ml human recombinant FGF2. Cells were allowed to expand on MEF-conditioned medium until ∼50% confluent, at which time differentiation was started according to Chambers et al. (2012). Briefly, medium was exchanged to knockout serum replacement (KSR) medium containing; knockout-DMEM, 15% knockout-serum replacement, 1% GlutaMAX™, 1% non-essential amino acids, 100 μM β-mercaptoethanol, 1% antibiotic/antimycotic (ThermoFisher Scientific), supplemented with the SMAD inhibitors SB431542 (Sigma, 10 μM) and LDN-193189 (Stratech, 100 nM). The medium was gradually transitioned from KSR medium to N2 medium (Neurobasal® medium, 2% B27 supplement, 1% N2 supplement, 1% GlutaMAX™, 1% antibiotic/antimycotic) (ThermoFisher Scientific) over an 11-day period. On Day 2, the small molecules CHIR99021 (Apollo Scientific, 3 μM), SU5402 (R&D Systems, 10 μM) and DAPT (Sigma, 10 μM) were also added. SMAD inhibitors were removed from the media from Day 6 onwards. On Day 11, the now immature neurons were replated onto Matrigel®-coated coverslips (25 000 cells per 13 mm coverslip) in 100% N2 medium containing human recombinant NGF, GDNF, BDNF, NT3 (all at 25 ng/ml, PeproTech) and 10 μM ROCK inhibitor. CHIR99021 (3 μM) was included in the medium until Day 14, and laminin (1 μg/ml, ThermoFisher Scientific) was supplemented into the medium from Day 20 onwards. Medium changes were performed twice weekly after replating. Cytosine β-D-arabinofuranoside (AraC, 2 μM, Sigma) was included in the medium for 24 h following replating to remove the few non-neuronal dividing cells remaining in the culture. This differentiation resulted in a completely pure neuronal culture with extensive arborized neurites by 3 weeks after the end of the small inhibitor stage.  Ethics statement   Human iPSC lines used in this study were derived from human skin biopsy fibroblasts, following signed informed consent. Three control cells lines were used in this study – AD2-01, AD4-01 and NHDF1. NHDF1 were reprogrammed with approval from research ethics committee: National Health Service, Health Research Authority, NRES Committee South Central, Berkshire, UK (REC 10/H0505/71).

value: Differentiated sensory neurons


title: Sample57_BALB.c_SHAM_F


title: AD4_IPS_A

source_name: AD4 IPSC from 68-year-old male

value: IPSC


title: AD2_IPS_B

source_name: AD2 IPSC from 51-year-old male


title: AD4_NEURONS_D


title: NHDF_NEURONS_C1


title: AD2_IPS_A


title: NHDF_IPS_B

source_name: NHDF IPSC from 44-year-old female


title: ctl_day_5 (RRBS)


title: AD2_NEURONS_C1


title: AD2_NEURONS_C2


title: AD4_NEURONS_C


title: AD4_IPS_B


title: NHDF_IPS_A


title: 3'-seq, alpha-amanitin +TEX, rep 3

status: Public on Nov 20 2017

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: To inhibit RNA polymerase II transcription activity, U2Os cells were incubated with α-amanitin (10 µg/ml; Sigma) for 6h or 9h at 37°C

data_processing:
U2OS samples: Raw reads (fastq files) were inspected for quality issues with FastQC v0.11.2. Reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32
U2OS samples:  adapter sequences were removed with Trim Galore v0.3.7, with parameters: -length 15
U2OS samples: filtered to remove very low quality reads, using the fastq_quality_filter program of the FASTX v0.0.14, with a quality threshold of 20 at 90 percent or more of the read's positions
U2OS samples: Sequences were mapped to hg19 using tophat (v2.0.13), with parameters: -N 2 --read-gap-length 5 --read-edit-dist 7 --segment-length 18 --read-realign-edit-dist 3 --no-coverage-search -r 270 --mate-std-dev 100
Remaining reads were re-paired
293 samples:  both R1 and R2 reads were quality trimmed at both ends with a threshold of 32
293 samples: adapter sequences were removed with cutadapt v1.7.1
293 samples: reads were filtered by overall quality with a threshold of 20 over 90 percent of the read
293 samples: Remaining reads were re-paired
YMC samples: reads were quality trimmed at both ends with a threshold of 32
YMC samples:adapters were removed with cutadapt
YMC samples: poly-A sequences were trimmed with cutadapt
YMC samples: reads were filtered by overall quality with a threshold of 20 over 90 percent of the read
Genome_build: hg19
Supplementary_files_format_and_content: Supp_Table1_U2OS_TEX_fit_hmm.tsv, Supp_Table2_U2OS_5prime_fit_hmm.tsv, Supp_Table3_U2OS_3prime_fit_hmm.tsv, Supp_Table4_293_TEX_fit_hmm.tsv: These files include HMM predictions of 3'UTR cleavage points, by comparing mRNA-seq data following three different treatments (TEX, 5prime-pulldown and 3prime-pulldown) with the untreated data, for either U2OS or 293 cells.
Supplementary_files_format_and_content: Supp_Table5_3end_RNA-seq_peaks_prox+dist.tsv: Matching proximal and distal peaks in 3'-end RNA-seq data, with and without alpha-amanitin treatments.
Supplementary_files_format_and_content: Supp_Table6_293_Mir92_fit_hmm.tsv, Supp_Table7_293_Let7_fit_hmm.tsv: HMM analysis (as in supp. tables 1-4) for RNA-seq data following miR-92a (table 6) or let-7a (table 7) transfection in 293 cells.

growth_protocol: U2OS, HEK293 and HEK293T cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100units/ml penicillin and 100μg/ml streptomycin at 37 °C

extract_protocol:
RNA was extracted from cells using QIAzol Reagent (Qiagen 79306) and treated with DNase I (NEB-M0303S). 5Μg of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB, E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep kit (NEB, E7420S) or 3‘ mRNA-Seq Library Prep Kit (lexogen 015UG009V0211).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: 3'-seq, alpha-amanitin +TEX,


title: 3'-seq, Alpha-amanitin, rep 3

value: 3'-seq, Alpha-amanitin,


title: exp_day_16 (RRBS)


title: 3'-seq, Control, rep 3

value: 3'-seq, Control,


title: 3'-seq, TEX, rep 2

value: 3'-seq, TEX,


title: 3'-seq, alpha-amanitin +TEX, rep 2


title: 3'-seq, Control, rep 2


title: 3'-seq, TEX, rep 3


title: 3'-seq, alpha-amanitin +TEX, rep 1


title: 3'-seq, TEX, rep 1


title: 3'-seq, Alpha-amanitin, rep 2


title: mRNA with TEX in 293 cells, rep 3

description: Transfection of miRNA, synthetic mir92a-3p, mirlet7 or negative control dsRNA performed using TransIT-X2TM Dynamic Delivery System according to manufacturer's instructions. Cells were collected for analysis 40h after transfection

value: mRNA with TEX in 293 cells,


title: mRNA with TEX in 293 cells, rep 2


title: mRNA with TEX in 293 cells, rep 1


title: mRNA 293 cell rep 3

value: mRNA 293 cell


title: 3'-seq, Control, rep 1


title: mRNA with let7 MIR after TEX 293 cell rep 1

value: mRNA with let7 MIR after TEX 293 cell


title: mRNA 293 cell rep 2


title: mRNA with mir92a MIR after TEX 293 cell rep 2

value: mRNA with mir92a MIR after TEX 293 cell


title: mRNA with mir92a MIR after TEX 293 cell rep 1


title: mRNA with mir92a MIR after TEX 293 cell rep 3


title: mRNA with let7 MIR after TEX 293 cell rep 2


title: mRNA with let7 MIR after TEX 293 cell rep 3


title: 3'-seq, Alpha-amanitin, rep 1


title: mRNA 293 cell rep 1


title: mRNA after 3prime-pulldown U2OS cell rep 1

value: mRNA after 3prime-pulldown U2OS cell


title: mRNA after 3prime-pulldown U2OS cell rep 2


title: mRNA after 5prime-pulldown U2OS cell rep 3

value: mRNA after 5prime-pulldown U2OS cell


title: mRNA after TEX U2OS cell rep 3

value: mRNA after TEX U2OS cell


title: mRNA after TEX U2OS cell rep 2


title: mRNA after 5prime-pulldown U2OS cell rep 2


title: mRNA after 5prime-pulldown U2OS cell rep 1


title: mRNA U2OS cell rep 3

value: mRNA U2OS cell


title: mRNA after TEX U2OS cell rep 1


title: mRNA U2OS cell rep 1


title: Adult basal cell 204

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were aligned to the mouse genome by Subread version 1.5.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rusbread's in-built NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Mammary gland

extract_protocol:
Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Nextseq 500 using standard Illumina protocols.

value: FVB/NJ

value: Adult

tag: cell source

value: Basal


title: Adult basal cell 207

tag: age


title: Adult basal cell 199


title: Adult basal cell 201


title: Adult basal cell 196


title: Adult basal cell 193


title: Adult basal cell 206


title: Adult basal cell 194


title: Adult basal cell 202


title: Adult basal cell 205


title: Adult basal cell 197


title: Adult basal cell 203


title: Adult basal cell 208


title: Adult basal cell 195


title: Adult basal cell 192


title: Adult basal cell 188


title: mRNA U2OS cell rep 2


title: Adult basal cell 187


title: Adult basal cell 191


title: Adult basal cell 185


title: Adult basal cell 184


title: Adult basal cell 183


title: Adult basal cell 200


title: Adult basal cell 182


title: Adult basal cell 190


title: Adult basal cell 189


title: Adult basal cell 176


title: Adult basal cell 177


title: Adult basal cell 181


title: Adult basal cell 173


title: Adult basal cell 168


title: Adult basal cell 172


title: Adult basal cell 175


title: Adult basal cell 180


title: Adult basal cell 174


title: Adult basal cell 170


title: Adult basal cell 179


title: Adult basal cell 169


title: Adult basal cell 186


title: Adult basal cell 158


title: Adult basal cell 164


title: Adult basal cell 159


title: Adult basal cell 161


title: Adult basal cell 163


title: Adult basal cell 162


title: Adult basal cell 166


title: Adult basal cell 160


title: mRNA after 3prime-pulldown U2OS cell rep 3


title: Adult basal cell 165


title: Adult basal cell 157


title: Adult basal cell 178


title: Adult basal cell 167


title: Adult basal cell 152


title: Adult basal cell 153


title: Adult basal cell 151


title: Adult basal cell 171


title: Adult basal cell 156


title: Adult basal cell 147


title: Adult basal cell 150


title: Adult basal cell 198


title: Adult basal cell 146


title: Adult basal cell 148


title: Adult basal cell 144


title: Adult basal cell 138


title: Adult basal cell 136


title: Adult basal cell 142


title: Adult basal cell 133


title: Adult basal cell 140


title: Adult basal cell 134


title: Adult basal cell 145


title: Adult basal cell 154


title: Adult basal cell 132


title: Adult basal cell 149


title: Adult basal cell 139


title: Adult basal cell 143


title: Adult basal cell 131


title: Adult basal cell 128


title: Adult basal cell 130


title: Adult basal cell 129


title: Adult basal cell 127


title: Adult basal cell 125


title: Adult basal cell 126


title: Adult basal cell 122


title: Adult basal cell 120


title: Adult basal cell 123


title: Adult basal cell 121


title: Adult basal cell 119


title: Adult basal cell 141


title: Adult basal cell 135


title: Adult basal cell (2) 112


title: Adult basal cell 114


title: Adult basal cell 116


title: Adult basal cell 113


title: Adult basal cell 115


title: Adult basal cell 117


title: Adult basal cell (2) 110


title: Adult basal cell (2) 108


title: Adult basal cell (2) 111


title: Adult basal cell (2) 104


title: Adult basal cell (2) 109


title: Adult basal cell 124


title: Adult basal cell (2) 107


title: Adult basal cell (2) 99


title: Adult basal cell (2) 101


title: Adult basal cell (2) 97


title: Adult basal cell (2) 105


title: Adult basal cell (2) 106


title: Adult basal cell 137


title: Adult basal cell (2) 94


title: Adult basal cell (2) 103


title: Adult basal cell (2) 102


title: Adult basal cell 155


title: Adult basal cell (2) 93


title: Adult basal cell (2) 88


title: Adult basal cell (2) 89


title: Adult basal cell (2) 84


title: Adult basal cell (2) 86


title: Adult basal cell (2) 81


title: Adult basal cell (2) 100


title: Adult basal cell (2) 80


title: Adult basal cell (2) 98


title: Adult basal cell (2) 96


title: Adult basal cell (2) 95


title: Adult basal cell 118


title: Adult basal cell (2) 71


title: Adult basal cell (2) 70


title: Adult basal cell (2) 90


title: Adult basal cell (2) 92


title: Adult basal cell (2) 91


title: Adult basal cell (2) 67


title: Adult basal cell (2) 68


title: Adult basal cell (2) 66


title: Adult basal cell (2) 65


title: Adult basal cell (2) 87


title: Adult basal cell (2) 85


title: Adult basal cell (2) 63


title: Adult basal cell (2) 83


title: Adult basal cell (2) 64


title: Adult basal cell (2) 59


title: Adult basal cell (2) 58


title: Adult basal cell (2) 56


title: Adult basal cell (2) 82


title: Adult basal cell (2) 79


title: Adult basal cell (2) 78


title: Adult basal cell (2) 77


title: Adult basal cell (2) 53


title: Adult basal cell (2) 76


title: Adult basal cell (2) 75


title: Adult basal cell (2) 47


title: Adult basal cell (2) 74


title: Adult basal cell (2) 44


title: Adult basal cell (2) 48


title: Adult basal cell (2) 73


title: Adult basal cell (2) 72


title: Adult basal cell (2) 42


title: Adult basal cell (2) 69


title: Adult basal cell (2) 62


title: Adult basal cell (2) 61


title: Adult basal cell (2) 38


title: Adult basal cell (2) 57


title: Adult basal cell (2) 36


title: Adult basal cell (2) 37


title: Adult basal cell (2) 51


title: Adult basal cell (2) 52


title: Adult basal cell (2) 34


title: Adult basal cell (2) 54


title: Adult basal cell (2) 50


title: Adult basal cell (2) 49


title: Adult basal cell (2) 46


title: Adult basal cell (2) 29


title: Adult basal cell (2) 45


title: Adult basal cell (2) 60


title: Adult basal cell (2) 28


title: Adult basal cell (2) 40


title: Adult basal cell (2) 27


title: Adult basal cell (2) 43


title: Adult basal cell (2) 41


title: Adult basal cell (2) 39


title: Adult basal cell (2) 35


title: Adult basal cell (2) 32


title: Adult basal cell (2) 25


title: Adult basal cell (2) 31


title: Adult basal cell (2) 18


title: Adult basal cell (2) 30


title: Adult basal cell (2) 26


title: Adult basal cell (2) 23


title: Adult basal cell (2) 33


title: Adult basal cell (2) 19


title: Adult basal cell (2) 16


title: Adult basal cell (2) 15


title: Adult basal cell (2) 14


title: Adult basal cell (2) 17


title: Adult basal cell (2) 13


title: Adult basal cell (2) 20


title: Adult basal cell (2) 12


title: Adult basal cell (2) 11


title: Adult basal cell (2) 5


title: Adult basal cell (2) 10


title: Adult basal cell (2) 7


title: Adult basal cell (2) 8


title: Adult basal cell (2) 6


title: Adult basal cell (2) 55


title: Adult basal cell (2) 24


title: Adult basal cell (2) 4


title: Adult basal cell (2) 22


title: Adult basal cell (2) 2


title: Adult basal cell (2) 1


title: Adult epithelial cell 213

data_processing:
Reads were aligned to the mouse genome by Rsubread version 1.23.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's in-built NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

tag: time stage

value: Total epithelium


title: Adult epithelial cell 221


title: Adult epithelial cell 222


title: Adult epithelial cell 220


title: Adult epithelial cell 217


title: Adult epithelial cell 223


title: Adult epithelial cell 215


title: Adult epithelial cell 212


title: Adult epithelial cell 219


title: Adult epithelial cell 216


title: Adult epithelial cell 211


title: Adult epithelial cell 210


title: Adult basal cell (2) 9


title: Adult epithelial cell 209


title: Adult epithelial cell 207


title: Adult epithelial cell 208


title: Adult epithelial cell 206


title: Adult epithelial cell 202


title: Adult epithelial cell 205


title: Adult epithelial cell 214


title: Adult basal cell (2) 21


title: Adult epithelial cell 200


title: Adult epithelial cell 199


title: Adult epithelial cell 198


title: Adult basal cell (2) 3


title: Adult epithelial cell 203


title: Adult epithelial cell 197


title: Adult epithelial cell 196


title: Adult epithelial cell 195


title: Adult epithelial cell 192


title: Adult epithelial cell 204


title: Adult epithelial cell 191


title: Adult epithelial cell 193


title: Adult epithelial cell 186


title: Adult epithelial cell 185


title: Adult epithelial cell 194


title: Adult epithelial cell 189


title: Adult epithelial cell 201


title: Adult epithelial cell 188


title: Adult epithelial cell 181


title: Adult epithelial cell 184


title: Adult epithelial cell 178


title: Adult epithelial cell 183


title: Adult epithelial cell 182


title: Adult epithelial cell 177


title: Adult epithelial cell 180


title: Adult epithelial cell 175


title: Adult epithelial cell 176


title: Adult epithelial cell 174


title: Adult epithelial cell 173


title: Adult epithelial cell 172


title: Adult epithelial cell 187


title: Adult epithelial cell 171


title: Adult epithelial cell 169


title: Adult epithelial cell 165


title: Adult epithelial cell 166


title: Adult epithelial cell 167


title: Adult epithelial cell 158


title: Adult epithelial cell 161


title: Adult epithelial cell 157


title: Adult epithelial cell 160


title: Adult epithelial cell 162


title: Adult epithelial cell 163


title: Adult epithelial cell 155


title: Adult epithelial cell 153


title: Adult epithelial cell 154


title: Adult epithelial cell 152


title: Adult epithelial cell 168


title: Adult epithelial cell 156


title: Adult epithelial cell 150


title: Adult epithelial cell 179


title: Adult epithelial cell 149


title: Adult epithelial cell 190


title: Adult epithelial cell 148


title: Adult epithelial cell 147


title: Adult epithelial cell 170


title: Adult epithelial cell 146


title: Adult epithelial cell 145


title: Adult epithelial cell 144


title: Adult epithelial cell 159


title: Adult epithelial cell 142


title: Adult epithelial cell 218


title: Adult epithelial cell 151


title: Adult epithelial cell 164


title: Adult epithelial cell 141


title: Adult epithelial cell 138


title: Adult epithelial cell 139


title: Adult epithelial cell 137


title: Adult epithelial cell 140


title: Adult epithelial cell 136


title: Adult epithelial cell 131


title: Adult epithelial cell 130


title: Adult epithelial cell 133


title: Adult epithelial cell 135


title: Adult epithelial cell 127


title: Adult epithelial cell 126


title: Adult epithelial cell 128


title: Adult epithelial cell 134


title: Adult epithelial cell 125


title: Adult epithelial cell 124


title: Adult epithelial cell 123


title: Adult epithelial cell 122


title: Adult epithelial cell 143


title: Adult epithelial cell 121


title: Adult epithelial cell 120


title: Adult epithelial cell 118


title: Adult epithelial cell 113


title: Adult epithelial cell 129


title: Adult epithelial cell 115


title: Adult epithelial cell 116


title: Adult epithelial cell 132


title: Adult epithelial cell 114


title: Adult epithelial cell 112


title: Adult epithelial cell 110


title: Adult epithelial cell 108


title: Adult epithelial cell 109


title: Adult epithelial cell 106


title: Adult epithelial cell 117


title: Adult epithelial cell 107


title: Adult epithelial cell 101


title: Adult epithelial cell 104


title: Adult epithelial cell 103


title: Adult epithelial cell 99


title: Adult epithelial cell 97


title: Adult epithelial cell 98


title: Adult epithelial cell 100


title: Adult epithelial cell 95


title: Adult epithelial cell 96


title: Adult epithelial cell 119


title: Adult epithelial cell 111


title: Adult epithelial cell 92


title: Adult epithelial cell 89


title: Adult epithelial cell 88


title: Adult epithelial cell 91


title: Adult epithelial cell 87


title: Adult epithelial cell 94


title: Adult epithelial cell 105


title: Adult epithelial cell 102


title: Adult epithelial cell 84


title: Adult epithelial cell 83


title: Adult epithelial cell 86


title: Adult epithelial cell 82


title: Adult epithelial cell 90


title: Adult epithelial cell 79


title: Adult epithelial cell 74


title: Adult epithelial cell 76


title: Adult epithelial cell 77


title: Adult epithelial cell 75


title: Adult epithelial cell 72


title: Adult epithelial cell 73


title: Adult epithelial cell 78


title: Adult epithelial cell 69


title: Adult epithelial cell 81


title: Adult epithelial cell 70


title: Adult epithelial cell 93


title: Adult epithelial cell 68


title: Adult epithelial cell 66


title: Adult epithelial cell 85


title: Adult epithelial cell 65


title: Adult epithelial cell 64


title: Adult epithelial cell 63


title: Adult epithelial cell 67


title: Adult epithelial cell 61


title: Adult epithelial cell 80


title: Adult epithelial cell 60


title: Adult epithelial cell 59


title: Adult epithelial cell 55


title: Adult epithelial cell 58


title: Adult epithelial cell 57


title: Adult epithelial cell 54


title: Adult epithelial cell 52


title: Adult epithelial cell 62


title: Adult epithelial cell 48


title: Adult epithelial cell 49


title: Adult epithelial cell 46


title: Adult epithelial cell 47


title: Adult epithelial cell 51


title: Adult epithelial cell 43


title: Adult epithelial cell 44


title: Adult epithelial cell 40


title: Adult epithelial cell 53


title: Adult epithelial cell 39


title: Adult epithelial cell 41


title: Adult epithelial cell 38


title: Adult epithelial cell 56


title: Adult epithelial cell 36


title: Adult epithelial cell 33


title: Adult epithelial cell 34


title: Adult epithelial cell 37


title: Adult epithelial cell 32


title: Adult epithelial cell 71


title: Adult epithelial cell 35


title: Adult epithelial cell 31


title: Adult epithelial cell 50


title: Adult epithelial cell 28


title: Adult epithelial cell 24


title: Adult epithelial cell 45


title: Adult epithelial cell 25


title: Adult epithelial cell 22


title: Adult epithelial cell 23


title: Adult epithelial cell 20


title: Adult epithelial cell 26


title: Adult epithelial cell 21


title: Adult epithelial cell 18


title: Adult epithelial cell 14


title: Adult epithelial cell 19


title: Adult epithelial cell 17


title: Adult epithelial cell 15


title: Adult epithelial cell 16


title: Adult epithelial cell 12


title: Adult epithelial cell 9


title: Adult epithelial cell 10


title: Adult epithelial cell 8


title: Adult epithelial cell 7


title: Adult epithelial cell 30


title: Adult epithelial cell 11


title: Adult epithelial cell 5


title: Adult epithelial cell 27


title: Adult epithelial cell 13


title: Adult epithelial cell 29


title: Adult epithelial cell 42


title: Adult epithelial cell 4


title: Adult epithelial cell 3


title: Adult epithelial cell 1


title: Puberty epithelial cell 219

value: Puberty


title: Adult epithelial cell 2


title: Puberty epithelial cell 218


title: Puberty epithelial cell 221


title: Puberty epithelial cell 217


title: Puberty epithelial cell 220


title: Puberty epithelial cell 212


title: Puberty epithelial cell 216


title: Puberty epithelial cell 215


title: Puberty epithelial cell 211


title: Puberty epithelial cell 213


title: Puberty epithelial cell 210


title: Puberty epithelial cell 209


title: Puberty epithelial cell 214


title: Puberty epithelial cell 208


title: Puberty epithelial cell 206


title: Puberty epithelial cell 204


title: Puberty epithelial cell 205


title: Puberty epithelial cell 207


title: Puberty epithelial cell 202


title: Puberty epithelial cell 203


title: Puberty epithelial cell 200


title: Puberty epithelial cell 199


title: Puberty epithelial cell 201


title: Adult epithelial cell 6


title: Puberty epithelial cell 196


title: Puberty epithelial cell 198


title: Puberty epithelial cell 197


title: Puberty epithelial cell 194


title: Puberty epithelial cell 195


title: Puberty epithelial cell 191


title: Puberty epithelial cell 190


title: Puberty epithelial cell 192


title: Puberty epithelial cell 189


title: Puberty epithelial cell 185


title: Puberty epithelial cell 184


title: Puberty epithelial cell 187


title: Puberty epithelial cell 186


title: Puberty epithelial cell 182


title: Puberty epithelial cell 183


title: Puberty epithelial cell 181


title: Puberty epithelial cell 180


title: Puberty epithelial cell 177


title: Puberty epithelial cell 176


title: Puberty epithelial cell 175


title: Puberty epithelial cell 179


title: Puberty epithelial cell 178


title: Puberty epithelial cell 173


title: Puberty epithelial cell 174


title: Puberty epithelial cell 172


title: Puberty epithelial cell 171


title: Puberty epithelial cell 193


title: Puberty epithelial cell 168


title: Puberty epithelial cell 170


title: Puberty epithelial cell 167


title: Puberty epithelial cell 188


title: Puberty epithelial cell 166


title: Puberty epithelial cell 165


title: Puberty epithelial cell 162


title: Puberty epithelial cell 163


title: Puberty epithelial cell 164


title: Puberty epithelial cell 159


title: Puberty epithelial cell 160


title: Puberty epithelial cell 155


title: Puberty epithelial cell 154


title: Puberty epithelial cell 157


title: Puberty epithelial cell 158


title: Puberty epithelial cell 152


title: Puberty epithelial cell 151


title: Puberty epithelial cell 153


title: Puberty epithelial cell 147


title: Puberty epithelial cell 169


title: Puberty epithelial cell 146


title: Puberty epithelial cell 145


title: Puberty epithelial cell 149


title: Puberty epithelial cell 150


title: Puberty epithelial cell 144


title: Puberty epithelial cell 143


title: Puberty epithelial cell 161


title: Puberty epithelial cell 141


title: Puberty epithelial cell 142


title: Puberty epithelial cell 140


title: Puberty epithelial cell 156


title: Puberty epithelial cell 136


title: Puberty epithelial cell 139


title: Puberty epithelial cell 137


title: Puberty epithelial cell 138


title: Puberty epithelial cell 133


title: Puberty epithelial cell 148


title: Puberty epithelial cell 132


title: Puberty epithelial cell 129


title: Puberty epithelial cell 131


title: Puberty epithelial cell 127


title: Puberty epithelial cell 125


title: Puberty epithelial cell 124


title: Puberty epithelial cell 123


title: Puberty epithelial cell 121


title: Puberty epithelial cell 122


title: Puberty epithelial cell 126


title: Puberty epithelial cell 119


title: Puberty epithelial cell 118


title: Puberty epithelial cell 116


title: Puberty epithelial cell 114


title: Puberty epithelial cell 113


title: Puberty epithelial cell 112


title: Puberty epithelial cell 115


title: Puberty epithelial cell 117


title: Puberty epithelial cell 134


title: Puberty epithelial cell 111


title: Puberty epithelial cell 110


title: Puberty epithelial cell 106


title: Puberty epithelial cell 107


title: Puberty epithelial cell 109


title: Puberty epithelial cell 108


title: Puberty epithelial cell 130


title: Puberty epithelial cell 104


title: Puberty epithelial cell 105


title: Puberty epithelial cell 102


title: Puberty epithelial cell 120


title: Puberty epithelial cell 101


title: Puberty epithelial cell 135


title: Puberty epithelial cell 100


title: Puberty epithelial cell 128


title: Puberty epithelial cell 98


title: Puberty epithelial cell 99


title: Puberty epithelial cell 96


title: Puberty epithelial cell 95


title: Puberty epithelial cell 97


title: Puberty epithelial cell 94


title: Puberty epithelial cell 93


title: Puberty epithelial cell 91


title: Puberty epithelial cell 92


title: Puberty epithelial cell 89


title: Puberty epithelial cell 86


title: Puberty epithelial cell 87


title: Puberty epithelial cell 84


title: Puberty epithelial cell 88


title: Puberty epithelial cell 103


title: Puberty epithelial cell 81


title: Puberty epithelial cell 80


title: Puberty epithelial cell 90


title: Puberty epithelial cell 85


title: Puberty epithelial cell 79


title: Puberty epithelial cell 77


title: Puberty epithelial cell 82


title: Puberty epithelial cell 76


title: Puberty epithelial cell 73


title: Puberty epithelial cell 75


title: Puberty epithelial cell 72


title: Puberty epithelial cell 74


title: Puberty epithelial cell 71


title: Puberty epithelial cell 70


title: Puberty epithelial cell 69


title: Puberty epithelial cell 67


title: Puberty epithelial cell 68


title: Puberty epithelial cell 64


title: Puberty epithelial cell 83


title: Puberty epithelial cell 66


title: Puberty epithelial cell 65


title: Puberty epithelial cell 63


title: Puberty epithelial cell 61


title: Puberty epithelial cell 55


title: Puberty epithelial cell 78


title: Puberty epithelial cell 58


title: Puberty epithelial cell 56


title: Puberty epithelial cell 57


title: Puberty epithelial cell 62


title: Puberty epithelial cell 50


title: Puberty epithelial cell 52


title: Puberty epithelial cell 51


title: Puberty epithelial cell 49


title: Puberty epithelial cell 59


title: Puberty epithelial cell 53


title: Puberty epithelial cell 44


title: Puberty epithelial cell 43


title: Puberty epithelial cell 48


title: Puberty epithelial cell 46


title: Puberty epithelial cell 60


title: Puberty epithelial cell 42


title: Puberty epithelial cell 41


title: Puberty epithelial cell 38


title: Puberty epithelial cell 35


title: Puberty epithelial cell 37


title: Puberty epithelial cell 36


title: Puberty epithelial cell 34


title: Puberty epithelial cell 31


title: Puberty epithelial cell 33


title: Puberty epithelial cell 28


title: Puberty epithelial cell 39


title: Puberty epithelial cell 47


title: Puberty epithelial cell 27


title: Puberty epithelial cell 26


title: Puberty epithelial cell 54


title: Puberty epithelial cell 32


title: Puberty epithelial cell 29


title: Puberty epithelial cell 24


title: Puberty epithelial cell 23


title: Puberty epithelial cell 19


title: Puberty epithelial cell 20


title: Puberty epithelial cell 18


title: Puberty epithelial cell 40


title: Puberty epithelial cell 21


title: Puberty epithelial cell 22


title: Puberty epithelial cell 45


title: Puberty epithelial cell 17


title: Puberty epithelial cell 16


title: Puberty epithelial cell 14


title: Puberty epithelial cell 30


title: Puberty epithelial cell 12


title: Puberty epithelial cell 13


title: Puberty epithelial cell 7


title: Puberty epithelial cell 8


title: Puberty epithelial cell 25


title: Puberty epithelial cell 11


title: Puberty epithelial cell 9


title: Puberty epithelial cell 6


title: Puberty epithelial cell 4


title: Puberty epithelial cell 5


title: Pregnancy total epithelial cell 121

data_processing:
Reads were aligned to the mouse genome using Subread version 1.4.6
Read counts were summarized by Entrez Gene ID using Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: mammary gland

tag: animal status

value: Pregnancy


title: Puberty epithelial cell 2

tag: strain


title: Puberty epithelial cell 1


title: Puberty epithelial cell 15


title: Pregnancy total epithelial cell 120


title: Pregnancy total epithelial cell 123


title: Pregnancy total epithelial cell 122


title: Pregnancy total epithelial cell 118


title: Pregnancy total epithelial cell 115


title: Pregnancy total epithelial cell 119


title: Pregnancy total epithelial cell 116


title: Pregnancy total epithelial cell 113


title: Pregnancy total epithelial cell 114


title: Pregnancy total epithelial cell 117


title: Pregnancy total epithelial cell 111


title: Pregnancy total epithelial cell 110


title: Pregnancy total epithelial cell 109


title: Puberty epithelial cell 10


title: Pregnancy total epithelial cell 104


title: Pregnancy total epithelial cell 103


title: Pregnancy total epithelial cell 105


title: Pregnancy total epithelial cell 106


title: Pregnancy total epithelial cell 100


title: Puberty epithelial cell 3


title: Pregnancy total epithelial cell 101


title: Pregnancy total epithelial cell 102


title: Pregnancy total epithelial cell 112


title: Pregnancy total epithelial cell 90


title: Pregnancy total epithelial cell 96


title: Pregnancy total epithelial cell 98


title: Pregnancy total epithelial cell 99


title: Pregnancy total epithelial cell 91


title: Pregnancy total epithelial cell 94


title: Pregnancy total epithelial cell 93


title: Pregnancy total epithelial cell 97


title: Pregnancy total epithelial cell 88


title: Pregnancy total epithelial cell 92


title: Pregnancy total epithelial cell 87


title: Pregnancy total epithelial cell 86


title: Pregnancy total epithelial cell 108


title: Pregnancy total epithelial cell 85


title: Pregnancy total epithelial cell 89


title: Pregnancy total epithelial cell 84


title: Pregnancy total epithelial cell 107


title: Pregnancy total epithelial cell 83


title: Pregnancy total epithelial cell 82


title: Pregnancy total epithelial cell 80


title: Pregnancy total epithelial cell 79


title: Pregnancy total epithelial cell 81


title: Pregnancy total epithelial cell 78


title: Pregnancy total epithelial cell 95


title: Pregnancy total epithelial cell 77


title: Pregnancy total epithelial cell 76


title: Pregnancy total epithelial cell 73


title: Pregnancy total epithelial cell 71


title: Pregnancy total epithelial cell 70


title: Pregnancy total epithelial cell 72


title: Pregnancy total epithelial cell 69


title: Pregnancy total epithelial cell 64


title: Pregnancy total epithelial cell 67


title: Pregnancy total epithelial cell 65


title: Pregnancy total epithelial cell 62


title: Pregnancy total epithelial cell 63


title: Pregnancy total epithelial cell 68