title: M_rep2


title: IL1-1-3 rep1

status: Public on Jan 01 2018

type: SRA

city: Davis

first: Siobhan

middle: M

last: Brady

state: CA

address: 1 Shields Ave

department: Plant Biology

country: USA

institute: UC Davis

library_source: transcriptomic

data_processing:
Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.
Demultiplexed data and filtered and trimmed bad base calls.  Note that FASTQ files provided to GEO have been demultiplexed but not trimmed.
A chimeric reference was created for each IL by combining parental matched references (SlCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa and SpCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa) using the latter pennellii reference in the introgression region obtained from (Chitwood et al. 2013) or if not there then using introgression coordinates obtained by using the sequence data to locate the introgression.
Reads were mapped to chimeric references using BWA with parameters “aln -t 4 -k 1 -l 25 -n 0.1 -e 15 -i 10” and mapped read counts extracted with samtools.
Custom R code was used to combine count files, normalized using R edgeR package function calcNormFactors() method TMM, differentially expressed genes (DEG) called using edgeR.  Custom R code tested DEG for GO and other biological category enrichments and special gene set enrichments and looked for common enrichments in ILs exhibiting QTLs for various root traits.  Gene-gene and gene-trait correlations were done. Co-expression networks were built using partial correlation R package SPACE and using a probabilistic graphical model with bootstrap aggregation with R package DAGBAG.
Genome_build: Matched references from (Koenig et al. 2013) and chimeric references described above, based on International Tomato Annotation Group SL2.40 ITAG 2.3 genome at SolGenomics.net.

molecule: total RNA

organism: Solanum lycopersicum x Solanum pennellii

source_name: Root

growth_protocol: Seedlings of S. lycopersicum (cv. M82), S. pennellii (LA0716), and 75 introgression lines between those parents were grown according to (Ron et al., 2013). Plates were placed vertically in a rack in a randomized block design.

extract_protocol:
The  germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Four replicates of each of the 77 genotypes were grown. Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Between 7 and 14 root tips (1 cm), 3 to 4 days post-germination, from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation.
Libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer.

treatment_protocol: The experiments were carried out in a growth chamber with a 16:8 light:dark cycle at 22ºC and 50-75% humidity with a light intensity of 100μE.

tag: solanum pennellii introgression line

tag: tissue

value: Root

tag: solanum lycopersicum cultivar


title: M_rep3

city: Marburg

first: Pengfei

last: liu

department: Department of Biogeochemistry

country: Germany

institute: Max-Planck-Institute for terrestrial microbiology

description:
mRNA were enriched for sequencing
processed data file: Raw_reads_counts_M.txt

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, Reads were aligned to reference genomes (CP003243 for M. conradii and AP009389 for P. thermopropionicum) using the function BWA-MEM of program bwa version 0.7.5a-r405 (Li and Durbin, 2009) with parameters: -t 4. Unique mapped reads were filtered by using samtools-0.1.19 (Li et al., 2009), with parameters: -f 0×2, -q 30, -F 0×100, NM≤5. Reads belonging to 16S/23S rRNA, reads that matched more than one segment of a genome, and reads with more than 5 mismatches were discarded. To exclude reads that may align ambiguously (that is, to either genome), we did a cross reference alignment by using the parameter described above (Fig. S3). Briefly, we firstly aligned reads from M and P to the opposing genome.
Unique mapped reads were analyzed and assigned to individual CDSs by HTSeq (Anders et al., 2014) according to the genome annotation provided by GenBank (M. conradii: NC_017034 and P. thermopropionicum: NC_009454).
Genome_build: CP003243 for M. conradii and AP009389 for P. thermopropionicum
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each samples calculated by HTSeq

organism: Methanocella conradii

source_name: M. conradii_anaerobic_monocultures

growth_protocol:
Methanocella conradii strain HZ254 was grown in monoculture (abbreviated as M) in strictly anaerobic medium with H2:CO2 (4:1, 1.7 atm ) as previously described (Liu et al., 2014, Appl Environ Microbiol, 80:4668-4676; Lü and Lu, 2012, PLoS One, 7:e35279 )
Pelotomaculum thermopropionicum strain SI was grown in monoculture (abbreviated as P) in the same strictly anaerobic medium as M. conradii with N2:CO2 (4:1, 1.7 atm) and 20 mM pyruvate as previously described (Liu et al., 2014, Appl Environ Microbiol 80:4668-4676& Imachi et al., 2002, Int J Syst Evol Microbiol 52:1729-1735 )
Methanocella conradii and Pelotomaculum thermopropionicum coculture (abbreviated as MP) were grown in the same strictly anaerobic medium as M. conradii with N2:CO2 (4:1, 1.7 atm) and 20 mM propionate as previously described (Liu et al., 2014, Appl Environ Microbiol 80:4668-4676 )

extract_protocol:
Total RNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacture’s instruction. RLT plus buffer was supplemented with 2% v/v 2 M DTT (Sangon Biotech, China). 600 µl RLT Plus buffer was added to each cell pellet. Cell pellets of P and MP were homogenized for 120 s in total (5.0 m/s, 3×40 s with 2 min intervals on ice) in a FastPrep-24 (MP Biomedicals, USA) with 0.5 g RNase free beating beads (0.1 mm, Sigma, USA). Cell pellets of M were homogenized at 5.0 m/s for 20 s without beating beads. Residue DNA digestion, verification of DNA absence and RNA purification were carried out as previously described (Liu et al., 2014, Applied and environmental microbiology 80:4668-4676;). RNA was finally dissolved in 75 µl RNase free H2O. RNA integrity values (RIN) were determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) according to the manufacturer’s instruction
mRNA enrichment was carried out by using the Ribo-Zero™ Magnetic Kit for Bacteria (Epicenter, USA) and RNA libraries were prepared for strand specific sequencing using protocols as previously described (Parkhomchuk et al., 2009, Nucleic Acids Res, 37:e123)

treatment_protocol: Cultivation was carried out at 55 °C in the dark without agitation and all cultures were harvested for transcriptomic analysis at the middle to late exponential-growth phases

tag: strain

tag: growth stage

value: middle exponential-growth phases


title: O_K_2_sRNA

city: Shanghai

first: jianfei

last: lu

address: No.999, Huchenghuan Rd

department: Freshwater Fishery Germplasm Resources

country: China

institute: Shanghai Ocean University

data_processing:
For the miRNA analyze, data processing followed the procedures as described in a previous study (Li. M, 2010) provided by LC Sciences Service. Brieﬂy, the raw reads were subjected to the Illumina pipeline ﬁlter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-26 nucleotide were mapped to speciﬁc species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3. and 5. ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to speciﬁc species mature miRNAs in hairpin arms were identiﬁed as known miRNAs. The unique sequences mapping to the other arm of known speciﬁc species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of speciﬁc species) in miRBase 20.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the speciﬁc species genomes to determine their genomic locations. The above two we deﬁned as known miRNAs. The unmapped sequences were BLASTed against the speciﬁc genomes, and the hairpin RNA structures containing sequences were predicated from the ﬂank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12) (2) number of base pairs in the stem region of the predicted hairpin =16) (3) cutoﬀ of free energy (kCal/mol <=15) (4) length of hairpin (up and down stems + terminal loop >=50) (5) length of hairpin loop (<=20). (6) number of nucleotides in one bulge in mature region (<=8) (7) number of biased errors in one bulge in mature region(<=4) (8) number of biased bulges in mature region (<=2) (9) number of errors in mature region (<=7) (10) number of base pairs in the mature region of the predicted hairpin (>=12) (11) percent of mature in stem (>=80).
Genome_build: none de novo sequencing
Supplementary_files_format_and_content: 1_Expressed_miRNA.xlsx, 2_gene_expression.xlsx,3_Trinity_gene.fasta, format and content :fasta,xlsx, assembly sequences and expression data.

organism: Carassius gibelio

source_name: control sample, were injected with PBS at the same dosage as treated sample.

growth_protocol: Healthy silver crucian carp for the present experiment (approximately 10 cm in body length) were obtained from the SHOU experimental fish breeding farm. Initially, fish were temporarily reared in at 23 °C for adaptation.

extract_protocol: RNA preparation, library construction and high-throughput sequencing were performed by LC Sciences (Houston, TX, USA). The experimental procedure is introduced as follows: total RNAs were extracted using Trizol reagent (Invitrogen, CA, USA) following the instruction of the product manual. The total RNA quantity and purity were analyzed by using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number higher than 7.0. The total RNA with lowest quality was not used for further study from the pre-receptive endometrium samples and receptive endometrium samples, respectively. For sRNA-seq experiment, approximately 1 μ g of total RNA was subjected to construct sRNA library according to the protocol of TruSeq™ Small RNA Sample Prep Kits (Illumina, San Diego, USA). Then, single-end sequencing (50 bp) was performed on the Illumina Hiseq2500 platform following the vendor’s recommended protocol. For RNA-seq experiment, approximately 10 μ g of total RNA was used to enrichment of poly (A)-tailed mRNAs with poly-Toligo attached magnetic beads (Invitrogen, MA, USA). Following purification, the mRNAs were fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to produce the final cDNA library according to the protocol of the mRNA-seq sample preparation kit (Illumina, San Diego, USA). Each PE and RE library was constructed by pooling 9 homogenized total RNAs from the endometrium samples. Then, paired-end sequencing of the PE and RE libraries was performed on the Illumina Hiseq2500 (LC Sciences, USA) following the vendor’s recommended protocol. The length of the reads was 100 bp, and the average insert size for the paired-end libraries was 179 bp (the length of the adapter was 121 bp). Pre-treatment of the sRNA-seq. First, the sequencing adapters were removed and the short reads containing ambiguous base “N” were discarded. Then, in order to allow cross-library comparison, read count normalization was performed. Specifically, the normalized read count (in RPM, reads per million) of a short sequence from a sequencing library was calculated by dividing the raw count of this sequence by the total counts of the library, and then multiplied by 10^6.

treatment_protocol: After seven days of acclimation, fish were inoculated by intraperitoneal injection with Cyhv-2 suspended in PBSat a dose of 1 ×106 TCID50/g which was applied and verified by previous challenge experiments5. As control, fish were injected with PBS at the same dosage. After the injection, all the fish were fostered under the same and suitable condition, fed with a diet according to standard feeding scheme, and continuously observed for collecting moribund animals.

value: kidney

tag: development

value: one year old


title: IL1-1-2 rep3


title: IL1-1-2 rep4


title: O_K_1_sRNA


title: IL1-1-2 rep2


title: T5_D3_K_mRNA

data_processing:
For the mRNA analyze, the raw paired end (PE) reads were cleaned by removing adapter sequences, empty reads, and low quality sequences (reads with over 10% unknown base pairs ‘N’). The reads obtained were randomly decomposed into overlapping k-mers (default k = 25) for assembly by using Trinity software69. To identify transcripts homologous to those in the other species, a locally installed BLAST all program70 was utilized to search the assembled transcripts against the sequences in NCBI NR protein database (http://www.ncbi.nlm.nih.gov/protein/)71 and the Swissprot database (http://www.uniprot.org/)72 with E-values lower than 1e-10. Genes were tentatively annotated according to the best hits against known sequences. COG73 and KEGG74 annotation systems were employed to analyze the biological pathways that the assembled transcripts were involved in. For expression level calculation, Bowtie (version 0.12.7)75 was utilized to map RNA-seq reads to all the assembled transcripts by using the “single-end” method and the parameter “-v 3 -a – phred 64-quals” (allowing one read to be mapped to multiple transcripts). The perfectly mapped reads counts were retained for expression level calculation by using the following formula: Expression level of a transcript (RPKM; reads per kilobase of exon model per million mapped reads) = Number of the reads mapped to the transcript / [Total number of the reads mapped to all the transcripts (in million) × the length of the transcript (in kilobases)]
Genome_build: none de novo sequencing
Supplementary_files_format_and_content: 1_Expressed_miRNA.xlsx, 2_gene_expression.xlsx,3_Trinity_gene.fasta, format and content :fasta,xlsx, assembly sequences and expression data.

source_name: treated sample,were inoculated by intraperitoneal injection with Cyhv-2 suspended in PBS at a dose of 1 ×106 TCID50/g which was applied and verified by previous challenge experiments after seven days of acclimation, fish


title: T4_D3_K_mRNA


title: IL1-1-2 rep1


title: P_rep4

description:
mRNA were enriched for sequencing
processed data file: Raw_reads_counts_P.txt

organism: Pelotomaculum thermopropionicum

value: SI


title: T6_D3_K_mRNA


title: T3_0_K_mRNA


title: WG001

city: Wuxi

first: Yunfei

last: Gao

address: Binhu district, Lihu Avenue 1800

institute: Jiangnan University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean reads were aligned to reference sequences with SOAPaligner/SOAP2
Reads per kilobase transcriptome per million mapped reads(RPKM) were calculated
Results of gene expression include gene expression levels and differential expression analysis.
Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis were performed.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Corynebacterium glutamicum

source_name: WG001_planktonic culture

growth_protocol: For transcriptome analysis, overnight cultures of C.glutamicum ATCC13869 and WG001 were inoculated as initial OD562 of 0.1 into 50 ml BHI medium and grown at 30°C to the exponential phase with OD562 around 7.0 and 2.5.

extract_protocol:
Total RNA was prepared using the Qiagen RNeasy Total RNA kit.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000

treatment_protocol: Cells from cultures were harvested by addition of the same volume of RNA-protect buffer and centrifugation.

tag: background strain

tag: genotype

value: pks13 mutant (strain WG001)

tag: cell density


title: ATCC13869

source_name: ATCC13869_planktonic culture

value: wild type


title: T1_0_K_mRNA


title: D3_K_1_sRNA


title: P_rep2


title: P_rep3


title: Trichuris muris

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: Bisulfite sequencing

library_source: genomic

data_processing:
Processing and alignment to genome was performed using Bismark using non-directional mode to generate bam files
CG methylation extracted from bam files using MethylExtract with default parameters
Genome_build: P. sambesii: BioSample SAMN07227113; R. culicivorax, T. spiralis and T. muris all from Wormbase Parasite release 4 (WBPS4)
Supplementary_files_format_and_content: All CG sequences genome-wide with >10 total reads.  Bed files tab delimited: chr, start, stop, methyl C reads, total reads

molecule: genomic DNA

organism: Trichuris muris

source_name: Tmuris

extract_protocol:
DNA extracted using Qiagen blood/tissue kit according to manufacturer's instructions
Pico-methylseq kit (Zymo) according to manufacturer's instructions

tag: developmental stage

value: Adult


title: P_rep1


title: PEP1_R3_apex

city: Buenos Aires

first: Julieta

middle: L

last: Mateos

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads in the raw data (FASTQ files) were filtered out and reads kept were then mapped to the Arabis alpina reference assembly V3 (Willing et al, 2015) using TopHat with the GTF file used in (6) (--min-anchor-length 10; --max-multihits 5; library-type fr-unstranded)
Count tables for raw counts were obtained from bam files using coverageBed.
Differential gene expression was estimated using DESeq2 package 1.10.0 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
Genome_build: Arabis alpina (version from Willing et al 2015, Nature Plants, 1), see http://arabis-alpina.org/refseq.html (Version 3)
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

organism: Arabis alpina

source_name: apices

growth_protocol: Seeds were sown on soil and grown at 22°C for 2 weeks in a long day photoperiod

extract_protocol:
Total RNA was extracted with Rneasy Plant Moni Kit (Qiagen) following manufacture´s protocol. To estimate the quality of the RNA, samples were measured with the Agilent 2100 Bioanalyzer using Agilent RNA high sensitivity CHIP
Libraries were prepared following the TruSeq RNA Sample preparation guideline (Illumina)
4µg of total RNA were polyA-purified, fragmented and first-strand cDNA synthesized by reverse transcriptase (SuperScript II-Invitrogen) and random hexamers. This was followed by RNA degradation and second strand cDNA synthesis. End repair process and adittion of a single ‘A’ nucleotide to the 3’ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included quality control and quantification. All libraries were pooled before sequencing

treatment_protocol: Apices or leaves from wild type or pep1-1 mutant were collected after two weeks at ZT8.

tag: cultivar

value: Pajares

tag: age

value: 2 weeks-old under long-day photoperiod

tag: genotype/variation

value: pep1-1 mutant

value: apices


title: PEP1_R2_apex


title: M_rep1


title: pKM033_3

city: Lausanne

first: Karin

middle: Lederballe

last: Meibom

state: Vaud

address: EPFL ENAC IIE EML  CE 1 543 (Centre Est)  Station 6

country: Switzerland

institute: EPFL

description:
replicate 3
chr_megaplasmid_counts_fC.txt
chr_megaplasmid_normalized.txt

data_processing:
RNA fastq files were aligned to the genome with TopHat2 v.2.0.11. Parameters: --library-type fr-firststrand -p  6 -g 2 -G
Reads were counted using featureCounts, included in the SourceForge Subread v.1.5.1 package
Raw counts were normalized with edgeR package.
Only those genes having more than 10 counts per million mapped reads (CPM) in at least 3 of all the samples were kept.
Genome_build: Chromosome: NC_004347.2, Plasmid: NC_004349.1
Supplementary_files_format_and_content: Tab delimited text files. chr_megaplasmid_counts_fC.txt: number of reads assigned to each gene. chr_megaplasmid_normalized.txt: normalized and filtered reads assigned to each gene

organism: Shewanella oneidensis

source_name: Bacterial culture

growth_protocol: Bacteria were grown in LB medium to OD600~0.7 (mutant strains) and harvested. Strains with plasmids (empty or containing ryhB) were grown to OD600~ 0.2, expression induced with IPTG and bacteria harvested after 60min.

extract_protocol:
RNA was extracted using Trizol, combined with cleaning on a QIAGEN RNeasy column. Samples were DNase treated and re-purified on a RNeasy column. Quality of RNA was assessed using a Fragment Analyzer (Advanched Analytical Technologies)
RNA sequencing libraries were constructed after rRNA depletion (with the Illumina Ribo-Zero rRNA removal kit) using the Truseq stranded mRNA library prep kit (without polyA selection using the strand-specific kit (Illumina, San Diego, CA, USA)). Library construction and RNA sequencing was performed at the Lausanne Genomic Technologies Facility at the University of Lausanne, Switzerland.

value: ryhB mutant w. empty plasmid


title: pKM033_2

description:
replicate 2
chr_megaplasmid_counts_fC.txt
chr_megaplasmid_normalized.txt


title: pRyhB_3

value: ryhB mutant w. RyhB expresssing plasmid


title: pRyhB_2


title: pKM033_1

description:
replicate 1
chr_megaplasmid_counts_fC.txt
chr_megaplasmid_normalized.txt


title: WT_R2_apex


title: WT_R3_apex


title: T2_0_K_mRNA


title: WT_R1_apex


title: PEP1_R1_apex


title: pRyhB_1


title: PEP1_R3_leaf

source_name: leaves

value: leaves


title: wt2

value: wild-type


title: PEP1_R1_leaf


title: cerevisiae upf1D untreated replicate B

city: Santa Cruz

first: Jason

last: Talkish

address: 1156 High St.

department: Molecular, Cellular, and Developmental Biology

institute: University of California, Santa Cruz

data_processing:
RNAseq 1a: the 100x100bp pairedEnd reads for cerevisiae samples were not trimmed.
RNAseq 1b: the 51x51bp pairedEnd reads for mikatae and bayanus samples were not trimmed.
RNAseq 2: reads mapping (by bowtie2) to cerevisiae rRNA, tRNA elements defined by Ensembl,  or to Ty elements defined in SGD, were discarded.
RNAseq 3a: cerevisiae reads were mapped to sacCer3 by STAR 2.4.1d, with "twopass" mode.
RNAseq 3b: mikatae reads were mapped to sacMik2 by STAR 2.4.0h with "twopass" mode
RNAseq 3c: bayanus reads were mapped to sacBay2 by STAR 2.4.0h with "twopass" mode
RNAseq 4: duplicate read mappings of the same start and end position were discarded
Ratios involving three coverage numbers were generated for each of the samples and each splice junction. A splice junction coverage was the number of reads that contained the splice junction. The intron coverage was generated from the coverage data using the average across the whole intron. When introns overlapped, a minimal length intron was used such that start of the intron was the maximal start of any of the overlapping introns and the end of the minimal length intron was the minimal end of any overlapping intron. Exon2 coverage was the average coverage for 100 bases of the following exon. Log2-transformed ratios were calculated for the three comparisons: intron/exon2, junction/exon2, intron/junction. Final scores were generated by subtracting the timepoint zero score for each timepoint. Separately intron splice sites and branch points are classified. Given an intron position the splice sites are extracted with conservation scores and a most likely branch point is found using several heuristics. The likely branch points are prioritized 1.)ACTAA, 2.)PYTPAYP, 3.)YTPAY. It must be 45 or more bases away from the 5' splice site and the one closest to the 3' splice site is chosen. Conservation is then calculated around the adenosine branch point. Details and scripts are at: http://exon.ucsc.edu/intron_bp_generator/
Genome_build: sacCer3 (UCSC Apr 2011 )
Genome_build: sacMik2 (sequences obtained in Feb 2015 from the Saccharomyces sensu stricto database)
Genome_build: sacBay2 (sequences obtained in Feb 2015 from the Saccharomyces sensu stricto database)
Supplementary_files_format_and_content: Intron_master_list.xls: junction coordinates and counts, splice site identification and conservation, bp prediciton,  intron and exon2 coverage and log2 ratios, change in log2 ratios after rapamycin treatment, splicing efficiency
Supplementary_files_format_and_content: Deseq_Log2_0vs60.xls: DEseq log2 ratios of expression changes in s. cerevisiae after treatment with rapamycin.

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Yeast were grown in YEPD to early log phase (OD600 about 0.25 to 0.3) at 30°C (S. cerevisiae) or 26°C (S. mikatae, S. bayanus)

extract_protocol:
RNA was isolated as described in Rio et al. (RNA: A Laboratory Manual, CSH Press)
RNA was treated using the RiboZero kit to remove ribosomal RNAs and then RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated cells were harvested by centrifugation after growth, or after growth plus 1 hour treatment with 200 uM rapamycin as per Munding et al. (2013) Mol. Cell 51: 338-48.

tag: cell type

value: haploid, vegetative

value: BY4741, upf1::KanMX4


title: cerevisiae upf1D rapa-treated replicate A


title: PEP1_R2_leaf


title: cerevisiae upf1D untreated replicate A


title: fur3

value: fur mutant


title: WT_R3_leaf


title: WT_R2_leaf


title: fur2


title: WT_R1_leaf


title: cerevisiae upf1D rapa-treated replicate B


title: wt1


title: fur1


title: PEP1 ChIP-Seq control rep2

city: Cologne

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

data_processing:
For both species, low quality and duplicated reads in the raw sequencing data were filtered out using Parallel-QC v1.0 (Zhou et al., 2013; PLoS ONE). Low quality reads were considered those not having Phred quality scores≥13 in at least 90% of the bases called. Duplicated reads were also removed to achieve a better specificity (fewer false positive peaks) during the peak-calling step at each individual replicate as recommended in Bailey et al. (2013), PLoS Comput. Biol.
Reads kept were then mapped either to the Arabis alpina reference assembly V3 (Willing et al., 2015; Nature Plants) or to the Arabidopsis thaliana TAIR10 using Bowtie v2.0.2 (Langmead et al., 2019; Genome Biol.), reporting alignments under default mode parameters.
The software PeakRanger (Feng et al., 2011; BMC Bioinformatics) was used to identify read-enriched genomic regions (P-value <1e-6, q-value (FDR) < 0.01, rest of parameters default).
Using MULTOVL v1.2 with parameters '-L 1 -u-m 2 -M 0 -s multovl -f BED' (Aszodi A, 2012; Bioinformatics), a total of 222 peak regions present in at least two replicates of PEP1 ChIP-seq or 377peak regions present in the two replicates of FLC ChIP-seq were retained for further processing (the union of overlapping regions was reported, minimum overlap required 1bp). After filtering by peak length (peaks shorter than 1.5kb were kept), we obtained the final peak set for both species, namely 204 peaks in Arabis alpina and 297 peaks in Arabidopsis thaliana.
Genome_build: TAIR10 (A.thaliana); A_alpina_V3 (A.alpina, http://arabis-alpina.org/refseq.html)

source_name: pep1-1 above-ground

growth_protocol: For ChIP experiments plants were grown in LD for 2 weeks and above-ground tissue was collected at ZT8.

extract_protocol:
After crosslinking, the ChIP and the ChIP-seq was done as in Mateos et al. (2015) Genome Biol 16:31, for both species.
For ChIP-seq, 10 μl from the eluted chromatin was then used for library preparation using Ovation Ultralow DR Multi- plex System (NuGen, Leek, The Netherlands). Libraries were sequenced using an Illumina Hi-Seq2500 instrument.

treatment_protocol: For ChIP on PEP1 we used Pajares and pep1-1 mutant with 1 µl of PEP1 antiserum raised against the C-terminal domain of PEP1 protein. For ChIP on FLC we analysed the Arabidopsis genotypes Col FRI and flc-3 FRI and 2 µl of FLC antiserum was used. Three independent biological replicates were performed for PEP1 ChIP-seq assays and two for FLC ChIP-seq. For ChIP on PEP1 the Pajares and pep1-1 genotypes were used.

value: above-ground tissue


title: DD2

value: fur ryhB mutant


title: PEP1 ChIP-Seq control rep3


title: DD3


title: PEP1 ChIP-Seq control rep1


title: DD1


title: Romanomermis culicivorax

description: Bisulfite sequencing

organism: Romanomermis culicivorax

source_name: Rculicivorax


title: PEP1 ChIP-Seq WT rep2

source_name: Pajares above-ground


title: PEP1 ChIP-Seq WT rep1


title: Nbenthamiana_smallRNA_library

city: Edmonton

first: Juan

last: Jovel

state: Alberta

address: 7-142 KATZ Group Centre for Pharmacy & Health Research

country: Canada

institute: University of Alberta

description: NGS Small RNA library from Nicotiana benthamiana leaves.

data_processing:
Trimming of adapters with in-house Perl scripts
Assembly of small RNAs into contigs was performed with MetaVelvet
Alignment of contigs to NR database was done with BLASTx
Parsing of BLASTx reports was with in-house Perl scripts
Genome_build: de novo assembly of virus genome. The FASTA of the contigs and a text file with the BLAST results are available on the series record.
Supplementary_files_format_and_content: text file containing count of small RNA sequences aligning to virus genome.

organism: unclassified viruses

source_name: Nicotiana benthamiana leaves

extract_protocol:
Total RNA was extracted with TRIzol
NEB Small RNA construction kit, according to manufacturer's protocol

tag: host organism

value: Nicotiana benthamiana

tag: host tissue

value: leaf


title: Trichinella spiralis

description: Bisulfite sequencing

organism: Trichinella spiralis

source_name: Tspiralis


title: Jasmine1_smallRNA_library

description: NGS Small RNA library from Jasmine leaves.

source_name: Jasminum sambac-1 leaves

value: Jasminum sambac


title: androgen biological replicate 1

status: Public on Dec 31 2017

city: São Paulo

first: Lucas

middle: Ferreira

last: daSilva

state: São Paulo

address: Av. Vital Brasil 1500

department: Parasitology

country: Brazil

institute: Instituto Butantan

data_processing:
All RNA-seq data were trimmed of low-quality reads and clipped of sequencing adaptors with Trimmomatic (Bolger, Lohse et al. 2014). Trimmed reads were aligned to hg19 version of the human genome with TopHat2 (Kim, Pertea et al. 2013), followed by an assembly using the Cufflinks 2.2 tool (Trapnell, Hendrickson et al. 2013) with the default parameters.
We used as reference for the alignment and assembly a custom GTF with the human lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013). This file is availble on the series record.
We generated transcriptome assemblies for each of these samples  separately and then used Cuffmerge (Trapnell, Hendrickson et al. 2013) to combine this assemblies from LNCaP treated with androgen and those assemblies generated by using LNCaP treated with etanol vehicle (GSE79301).
For differential expression analysis we performed count-based analysis as described in (Anders, McCarthy et al. 2013). In summary we calculated the sum of exon read count per gene with HTSeq (Anders, Pyl et al. 2015) and differential expression (DE) was calculated with DESeq2 (Love, Huber et al. 2014).
Genome_build: hg19
Supplementary_files_format_and_content: GTF file containing an extended repertory of lincRNAs (Harrow, Frankish et al.2012, Cabili, Trapnell et al. 2011;Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013).
Supplementary_files_format_and_content: HTSeq Transcripts count table

organism: Homo sapiens

source_name: LNCaP cell line_presence of androgen

growth_protocol: LNCaP cell line (ATCC) was cultured in RPMI-1640 medium (Gibco) supplemented with 1x Pen-Strep (Vitrocell Embriolife), 10 mM HEPES (Gibco), and 10 % FBS (Vitrocell Embriolife); the latter was substituted with 10 % charcoal stripped FBS (Sigma) 24 h. Subsequently the samples were kept in charcoal stripped FBS and cultured for 24h in the presence of 1 nM of the synthetic androgen R1881 with  prior to RNA extraction.

extract_protocol:
LNCaP poly(A)+ RNA was extracted with FastTrack MAG Maxi mRNA Isolation Kit (Invitrogen), as per manufacturer’s protocol, treated with 25 U of DNase I, Amplification Grade (Invitrogen) for 1 h at room temperature, quantified using Quant-iT RiboGreen RNA Reagent (Invitrogen) and assessed for integrity on 2100 Bioanalyzer (Agilent).
RNA samples from two biological replicates were processed and sequenced on Illumina HiSeq 2000.  Approximately 1 µg of this RNA was prepared for Next Generation Sequencing using a modified version of the Illumina protocol, Directional_mRNA-Seq_SamplePrep_Guide_15018460_A.pdf, in which 12 cycles of PCR were performed instead of 15 and standard Truseq adapters and Truseq barcoded primers were used instead of the v1.5 adapters and primers described in the guide.  A final size selection was performed using agarose gel to capture library with insert sizes ranging from 150 – 250 bases in length suitable for 2 x 75 base paired end sequencing. Library product was purified from agarose using standard oligo purification columns. The prepared library was then loaded onto an Illumina HiSeq v2 single-read flowcell, standard cluster generation was performed on a Cbot followed by paired-end sequenced of 2 x 75 bases of the insert and 7 bases of the index read using standard HiSeq sequencing reagents except for the use of an alternative read-2 sequencing primer which was designed as the reverse complement of the indexing read sequencing primer. Strand-oriented paired-end RNA-seq

tag: cell line

value: LNCaP


title: wt3


title: untreated biological replicate 1

source_name: LNCaP cell line_absence of androgen


title: Jasmine2_smallRNA_library

description: NGS Small RNA library from Jasmine leaves (repeat).

source_name: Jasminum sambac-2 leaves


title: androgen biological replicate 2


title: 11_synectin_shRNA_PDGF

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: liver

growth_protocol: Human primary HSCs (ScienCell Research Laboratories, CA, USA) were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.  Synectin short hairpin RNAs (shRNA) were purchased from Sigma-Aldrich (NM_005716.2-1083s1c1, NM_005716.2-1045s1c1, St. Louis, MO).  HSCs lentiviral transduction of shRNA was carried out by incubation with viral particles for 48 hours in DMEM with 10% FBS and polybrene, followed by selection with puromycin for 24 hours.

extract_protocol:
RNA was harvested using Trizol reagent and RNeasy kit (Qiagen, Netherlands) and 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HSCs transduced with control shRNA or synectin shRNA for 24-48 hours  were serum starved overnight and were treated with PDGF-bb (10 ng/ml) for 2 hours and were then harvested for RNA isolation, mRNAseq experiment.

value: human liver stellate cells

value: synectin knock down


title: 16_synectin_shRNA_vehicle

value: wild type


title: 8_ctrl_shRNA_PDGF


title: 2_ctrl_shRNA_PDGF


title: 7_ctrl_shRNA_vehicle


title: 5_ctrl_shRNA_PDGF


title: 4_ctrl_shRNA_vehicle


title: 14_synectin_shRNA_PDGF


title: PEP1 ChIP-Seq WT rep3

value: Pajares


title: 10_synectin_shRNA_vehicle


title: 1_ctrl_shRNA_vehicle


title: human upf1 depletion replicate 3

first: Manuel

last: Ares

address: 1156 High Street

department: MCDB

institute: UC Santa Cruz

data_processing:
RNAseq 1a: the 100x100bp pairedEnd reads for 6 of the samples were trimmed at the 3' ends to 95x58
RNAseq 1b: the 100x58bp pairedEnd reads for the remaining samples were trimmed at the 3' ends to 95x58
RNAseq 2: reads mapping (by bowtie2) to repeatMasker elements in mouse (mouse samples) or human (human samples) were discarded.
RNAseq 3:  reads were mapped by tophat2 to mm9 (mouse samples) or hg19 (human samples) assisted by gtf files of UCSC Known Genes for the appropriate assembly.
RNAseq 4: The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
RNAseq 5: The coverage summed over all exonic positions of a gene was divided by 153 (95+58) to determine the read per gene for a sample. This was done for all mm9/hg19 UCSC KnownGenes.
RNAseq 6: For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: Excel Workbook with DESEQ output, refined through multiple tables to identify genes with significantly increased expression level upon depletion of Staufen or  Upf1 in mouse and human myoblasts

source_name: myoblast

growth_protocol: Adult human skeletal-muscle (hSkMc) myoblasts (Cell Applications) were propagated in SkMc cell-growth medium (PromoCell), mouse skeletal-muscle C2C12 myoblasts were propagated in DMEM (GIBCO-BRL) containing 15% fetal bovine serum (FBS), and HeLa cells (ATCC) were propagated in DMEM (GIBCO-BRL) containing 10% FBS.

extract_protocol:
RNA was purified from total cell-lysates using TRIzol (Invitrogen)
All  samples polyA selected and libraries prepared according to Jacobs et al. Nature 516:242-245, except polyA selected rather than rRNA depleted RNA was used: StrandSpecific, Rd1 is antisense to coding strand (Rd2 is sense)

treatment_protocol: Where specified, cells were transiently transfected with siRNA using Lipofectamine RNAiMAX (Invitrogen) and/or plasmids using Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions.

value: SkMc


title: human upf1 depletion replicate 1


title: human upf1 depletion replicate 2


title: human stau depletion replicate 3


title: 17_synectin_shRNA_PDGF


title: human stau depletion replicate 2


title: human control replicate 2


title: MNase-seq_Snail2-1

city: Camperdown

first: Guy

last: Lyons

state: NSW

address: Room W350 Blackburn Bldg D06

department: Dermatology

country: Australia

institute: University of Sydney

description: chromatin digested with MNase

data_processing:
Base calls and de-multiplexing done using Illumina Casava
Groomed using Galaxy FASTQ Groomer v1.0.4
Mapped to hg19 using Galaxy Bowtie for Illumina v1.1.2
Converted to BAM format using Galaxy SAM-to-BAM v1.1.3
Technical and biological replicates merged using Galaxy Picard Merge BAM Files v1.1.2
Indexed the BAM files using GenePattern Picard.SortSAM v4
Genome_build: hg19
Supplementary_files_format_and_content: Indexed BAM files for merged biological replicates
Supplementary_files_format_and_content: The indexed BAM files enable users who download the processed data to process it using NSeq

source_name: HN13(TVA) Snail2-expressing cells

growth_protocol: sub-confluent cells grown in DMEM+10% fetal bovine serum

extract_protocol:
The cells were fixed with 4% paraformaldehyde in PBS to immobilize the nucleosomes by cross-linking them to the DNA. MNase digestion and DNA purification were performed by the method of Kouskouti A, Kyrmizi I. Chromatin Immunoprecipitation (ChIP) Assay (PROT11). http://www.epigenesys.eu/en/protocols/chromatin-immunoprecipitation-chip/163-chromatin-immunoprecipitation-chip-assay. Updated 27 July 2005 Accessed 2 September 2014.
Samples were prepared with the ChIP-seq DNA Sample Prep kit from Illumina (#IP-102-1001), using ~10ng of input for each sample. To index the libraries for multiplexing, the PE adapters from the Multiplexing Sample Preparation Oligonucleotide kit (#PE-400-1001) were ligated onto the DNA.The material was size selected on a 2% Pippin gel (Sage Science) for a 280-420bp insert range. PCR was performed with the index primers from the Oligonucleotide kit (the one above) using 18 cycles. The libraries were run as 50bp Single-read (SR) using Illuminas SBS reagents on the HiSeq2000.

value: keratinocyte

tag: organ

value: tongue


title: MNase-seq_Snail2-2

description: chromatin digested with MNase


title: human control replicate 1


title: human control replicate 3


title: MNase-seq_Control-1

description: chromatin digested with MNase

source_name: HN13(TVA) Control cells


title: MNase-seq_Control-2

description: chromatin digested with MNase


title: 13_synectin_shRNA_vehicle


title: Scale E9 input

city: Los Angeles

first: Ping

last: Wu

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

data_processing:
Alignment of reads (Bowtie2, UCSC galGal4) was done in Partek Flow.
Only unique reads are used for peak calling.
MACS was used for peak calling.
The replicates of each sample group are combined to perform peak calling.
BigWig files were generated using deepTools.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: BigWig files

organism: Gallus gallus

source_name: tarsometatarsal skin, E9, input

growth_protocol: Fertilized eggs.

extract_protocol:
ChIP; see the supplementary file 'Chip_protocol_Chuong_lab.pdf'.
NEBNext® Ultra™ DNA Library Prep Kit.

treatment_protocol: Untreated

tag: breed

value: White Leghorn

tag: tissue

value: tarsometatarsal skin

tag: chip antibody


title: Scale E11 input

source_name: tarsometatarsal skin, E11, input


title: H3K4me3_ChIPSeq

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg18 genome assembly using Novoalign version 2.07.11 with the default configuration and the output written in SAM format
The aligned reads were subjected to quality control by omitting reads with 0 mapping quality and removing the redundant reads using samtools
peaks were called using SICER version 1.1 with the following settings: Fragment size=150bp, window size=200 for K4me1 and K4me3 while 500 for K27me3, FDR=1E-5
Genome_build: hg18
Supplementary_files_format_and_content: wig files were generated in variable step with a span size of 200bp for K4me1 and K4me3 and 500bp for K27me3. The wig files were then converted to bigWig format using “WigToBigWig” utility from UCSC tools. These files contain amplitude of the ChIP-seq signal as number of reads without normalizing to tags per million reads.

source_name: airway smooth muscle

growth_protocol: ASM cells were generated by re-plating confluent cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic I

extract_protocol:
Lysates were prepared from Mnase-treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: airway smooth muscle

tag: passages

value: H3K4me3 (Millipore, CS200 580)


title: Feather dorsal E9 input

source_name: dorsal skin, E9, input

value: dorsal skin


title: H3K4me1_ChIPSeq

value: H3K4me1 (Abcam ab8895)


title: H3K27me3_ChIPseq


title: MC3T3-E1 cells_Ctcf_day0_ChIP-Seq

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: Sample 1

data_processing:
Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version 0.12.8) with seed length of 28 base, allowing upto 2 mismatches in the seed.
Read densities and regions of statistically significant enrichment (“peaks”) were determined using MACS (Model-Based Analysis of ChIP-Seq, version 1.4.1) [2] using default settings. Peaks of ChIP-seq enrichment with p < 10-10, relative to input, were considered significant and included in subsequent analyses.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using MACS (version 1.4.1) and wigToBigWig (version 4); Scores represent reads per 10 million reads. The bed files report read densities and regions of statistically significant enrichment (“peaks”).

organism: Mus musculus

source_name: proliferating preosteoblast MC3T3-E1 subclone 4 cells at day 0

growth_protocol: The calvaria-derived preosteoblast cell line MC3T3-E1 (Subclone 4) was obtained from ATCC and maintained in ascorbic acid-free alpha-MEM (Hyclone) supplemented with 10% fetal bovine serum (FBS; Hyclone), 2 mM L-glutamine, 100 U/ml of penicillin and 100 µg/ml streptomycin (Pen/Strep, Invitrogen). To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid and 10 mM beta-glycerophosphate (Sigma Aldrich). Cells were maintained at 37C in a humidified 5% CO2 environment and media replaced every 2-3 days for the duration of all experiments.

extract_protocol:
For ChIP-Seq, nuclear lysates were sonicated and Ctcf-DNA complexes were isolated with Ctcf antibody (Millipore, 07-729).
Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II.

tag: time

value: preosteoblast

tag: strain

value: Ctcf antibody (Millipore, catalog#07-729, lot#DAM1772428)


title: MC3T3-E1 cells_Input DNA (for ChIP-Seq)

description: Sample 4

source_name: matrix-depositing MC3T3-E1 subclone 4 cells

value: matrix-depositing osteoblast


title: Feather dorsal E9 ChIP

description: This GEO Sample represents 2 replicates.

source_name: dorsal skin, E9, H3K27ac ChIP

value: H3K27ac (Abcam ab4729)


title: MC3T3-E1 cells_Ctcf_day28_ChIP-Seq

description: Sample 3

source_name: mineralizing MC3T3-E1 subclone 4 cells at day 28

value: mineralizing osteoblast


title: Feather dorsal E7 input

source_name: dorsal skin, E7, input


title: MC3T3-E1 cells_Ctcf_day9_ChIP-Seq

description: Sample 2

source_name: matrix-depositing MC3T3-E1 subclone 4 cells at day 9


title: Scale E11 ChIP

source_name: tarsometatarsal skin, E11, H3K27ac ChIP


title: untreated biological replicate 2

source_name: LNCaP cell line_absence of androgen

value: LNCaP


title: Feather dorsal E7 ChIP

source_name: dorsal skin, E7, H3K27ac ChIP


title: Scale dermis E9, rep2

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/QC were done in Partek Flow.
HTSeq-count was used for quantification.
TMM in edgeR was used for normalization.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: Feather-scale_CPM_E7-E11.xlsx: Tab-delimited text file includes CPM value for each sample.

source_name: tarsometatarsal skin, E9

extract_protocol:
Dissected tissue was extracted in Trizol reagent.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2.


title: Scale dermis E11, rep1

source_name: tarsometatarsal skin, E11


title: Scale dermis E11, rep2


title: Scale dermis E9, rep1


title: Feather dermis thigh E9, rep2

source_name: thigh skin, E9

value: thigh skin


title: Feather dermis wing E9, rep1

source_name: wing skin, E9

value: wing skin


title: Feather dermis dorsal E9, rep2

source_name: dorsal skin, E9


title: Feather dermis wing E9, rep2


title: Feather dermis dorsal E7, rep2

source_name: dorsal skin, E7


title: Feather dermis dorsal E7, rep1


title: Feather dermis thigh E9, rep1


title: Scale E9 ChIP

source_name: tarsometatarsal skin, E9, H3K27ac ChIP


title: NTSE5_RG_bulk

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description:
Bulk RNA-Seq library from sorted Ntsr1+ adult mouse corticothalamic neurons
cummeRbund_diffTable.txt

data_processing:
paired-end reads were aligned to the mouse reference genome (mm10) using Hisat2 with the default parameters except: -p 8.
Aligned reads from individual samples were quantified against a reference transcriptome (GENCODE vM8; Mudge and Harrow, 2015) supplemented with additional lncRNA genes described previously (File S1; Molyneaux et al., 2015) with cuffquant (Trapnell et al., 2013) using default parameters with the following exceptions: --no-update-check –p 8.
For bulk RNA-Seq, pre-processed expression estimates were used as input for cuffdiff using default parameters except: -p 16, and the output of cuffdiff was analyzed using the cummeRbund R/Bioconductor package (Trapnell et al., 2012).
For single-cell experiments, normalized expression estimates across all samples were obtained using cuffnorm with default parameters.
The normalized FPKM matrix from cuffnorm was used as input for the Monocle2 single-cell RNA-seq framework (Trapnell et al., 2014) in R/Bioconductor (Huber et al., 2015). Relative FPKM values for each cell were converted to estimates of absolute mRNA counts per cell (RPC) using the Monocle2 census utility.
Genome_build: mm10
Supplementary_files_format_and_content: count_table.txt:  A tab-delimited text file containing CENSUS estimated RNA copies per cell for each single cell RNA-Seq library across all genes.
Supplementary_files_format_and_content: cummeRbund_diffTable.txt:  A tab-delimited text file containing quantifications (FPKM) and differential test results for the bulk RNA-Seq samples.

source_name: Bulk Ntsr1+ L6 Corticothalamic Projection Neurons from adult mice somatosensory cortex

growth_protocol: All procedures were approved by the Johns Hopkins Animal Care and Use Committee and followed the guidelines of the Society for Neuroscience and the National Institutes of Health. Animals used for single cell RNA-seq ranged from postnatal day 23 (P23) to P28, animals used for immunohistochemistry and in situ hybridization ranged from P23 to P32. Both males and females were used in this study (gender indicated for each replicate in methods below). All animals were kept on a 12h light/dark cycle, housed with at least two mice per cage and provided with unlimited water and food. All animals were healthy and we observed no obvious behavioral impairments. Information about the generation and genotyping of the transgenic lines used in this study can be found in the corresponding original studies: Ntsr1-Cre (Gong et al., 2007), lox-STOP-lox-tdTomato (Ai9 and Ai14; Madisen et al., 2010), lox-STOP-lox-YFP (Ai3; Madisen et al., 2010) and Pantr1-Lacz (Sauvageau et al., 2013). Mice were maintained on mixed backgrounds including C57BL/6 and CD-1.

extract_protocol:
For bulk samples, RNA was extracted with a Qiagen RNeasy Micro Kit. RNA quality was assessed with the Bioanalyzer Pico RNA kit and samples had RIN scores of 8.2-8.8.
For bulk samples, library preparation and amplification were performed according to the Smart-Seq2 protocol (Picelli et al., 2014) with some modifications. Principally, all primer and adapter sequences were synthesized with a 5’-biotin to minimize primer dimerization. Briefly, 200 pg of RNA per sample were used as input for template switching cDNA synthesis. Full-length cDNA was amplified by KAPA HiFi mediated PCR for 20 cycles using a 5’-biotinylated ISPCR primer. Then, 500 pg of Ampure XP bead cleaned (1:1) cDNA was used as input for a standard Nextera XT tagmentation reaction, and amplification of adapter-ligated fragments was carried out for 12 cycles during which individual index sequences were added to each distinct sample. Library concentration was assessed with Qubit and library fragment size distribution was assessed on the Agilent Bioanalyzer. Pooled, indexed bulk RNA-seq samples were initially sequenced on the Illumina MiSeq 500 platform, and subsequently the same pool was sequenced on one lane of the Illumina HiSeq 2500 platform to produce 50 bp paired-end reads. Libraries were sequenced to an average depth of 4.2x107 fragments each. Reads from both runs were aggregated by index prior to mapping.  Library preparation and amplification of single-cell samples was performed using a modified version of the Smart-Seq2 protocol. Briefly, 96-well plates of single-cell lysates were thawed to 4°C, heated to 72°C for 3 minutes, and then immediately placed on ice. Template switching first-strand cDNA synthesis was performed as described above using a 5’-biotinylated TSO oligo. cDNAs were amplified using 18 cycles of KAPA HiFi PCR and 5’-biotinylated ISPCR primer. Amplified cDNA was cleaned with a 1:1 ratio of Ampure XP beads and 300 pg was used for a one-half standard-sized Nextera XT tagmentation reaction. Tagmented fragments were amplified for 12 cycles and dual indexes were added to each well to uniquely label each library. Concentrations were assessed with Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and samples were diluted to ~2 nM and pooled. Pooled libraries were sequenced on the Illumina HiSeq 2500 platform to a target mean depth of ~8.0 x 105 50 bp paired end fragments per cell (Mudge and Harrow, 2015) at the Hopkins Genetics Research Core Facility to generate 50 bp paired-end reads.

treatment_protocol: Mice P18 to P23 were anesthetized with ketamine (50 mg/kg), dexmedetomidine (25 µg/kg) and the inhalation anesthetic, isoflurane. Animals were placed in a custom-built stereotactic frame and anesthesia was maintained with isoflurane (1-2.5%). A small craniotomy was performed, and a glass pipette (10–25 µm tip diameter) was lowered into the thalamus. To identify L6CThNs that project to the ventral posterior medial nucleus (VPM) of the thalamus, Ntsr1-Cre;tdTomato mice were injected in VPM (1.1 mm posterior, 1.7 mm lateral , 3.4 mm ventral from bregma) with either Alexa 488 Cholera toxin B (CTB488, ThermoFisher) or green Retrobeads IX (Lumafluor), and Ntsr1-Cre;YFP mice were injected with Alexa 555 Cholera toxin B (CTB555, ThermoFisher). To identify L6CThNs that project to both VPM and to the posterior medial nucleus of the thalamus (POm), Ntsr1-Cre;tdTomato mice were injected in POm (1.35 mm posterior, 1.23 mm lateral , 3.3 mm ventral from bregma) with green Retrobeads IX, and Ntsr1-Cre;YFP mice were injected with either CTB555 or red Retrobeads (Lumafluor). Between 30 and 100 nl of tracer were pressure-injected, and the pipette was kept in position for 5-10 minutes before removal. Following the injection, the incision was sutured and buprenorphine (0.05 mg/kg) was administered to all animals postoperatively. Quantification of the colocalization between retrogradely labeled neurons and Cre expression in Ntsr1-Cre mice (Figure 1E,J) was performed on mice injected with either CTB or Retrobeads.  For bulk sequencing experiments (bulk RNA-seq), POm was injected with green Retrobeads in three Ntsr1-cre;tdTomato mice. For single-cell sequencing experiments (scRNA-seq), POm was injected with red or green Retrobeads in Ntsr1-Cre;YFP mice or in Ntsr1-Cre;tdTomato mice, respectively. Mice were sacrificed 5-7 days after surgery (Bulk RNA-seq: Replicate 1: P23 female; Replicate 2: P23 female; Replicate 3: P26 male; scRNA-seq baseline: Replicate 1: P27 male, Replicate 2: P28 female; scRNA-seq Day 1: Replicate 1: P24 female, Replicate 2: P24 female; scRNA-seq Day 7: Replicate 1: P29 female, Replicate 2: P27 female). Brains were rapidly removed and 300 µm thick somatosensory thalamocortical (Agmon and Connors, 1991) or coronal slices were sectioned (VT-1200s, Leica) in ice-cold sucrose solution containing the following (in mM): 76 NaCl, 25 NaHCO3, 25 glucose, 75 sucrose, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgSO4, pH 7.3, 310 mOsm continuously bubbled with 95% O2/5% CO2. The slices were then placed in a submersion chamber on an upright microscope in ice-cold sucrose solution continuously bubbled with 95% O2/5% CO2. The barrel cortex was identified using differential interference contrast (DIC) and epifluorescence microscopy (Axioskop2 FsPLus, Zeiss) using 4x (0.1 NA) and 40x (water immersion, 0.75 NA) objectives. The location of the retrograde tracer in the lower half of layer 6 was visually confirmed, and then regions of cortex below barrels with appropriate labeling were microdissected and immediately dropped into 2.6 mL equilibrated Papain DNase-I solution. For all experiments, at least three consecutive slices confirmed as clearly labeled were microdissected.  The dissociation protocol was adapted from the trehalose-enhanced neuronal isolation protocol described in Saxena et al., 2012 which is based on the Worthington Papain Dissociation System (Worthington Biochemical Corporation). Briefly, tissue pieces were dropped into a 5 ml tube containing 2.6 mL of a trehalose-Papain-DNase1 solution which included RNase inhibitor, incubated 30-45 min at 37°C with gentle trituration at the half way point using a p1000 pipetter. The reaction was stopped by adding a protease inhibitor solution (for solution compositions, see Saxena et al., 2012). The tissue was then further dissociated and washed by sequential pipetting and low-speed centrifugations. The final pellet was resuspended in 200 µL of media (DMEM, 5% trehalose (w/v), 25 µM AP-V, 0.4 mM kynurenic acid, 6 µL of 40 U/µl RNase inhibitor) at room temperature and introduced into a FACS machine (Beckman Coulter MoFlo Cell Sorter). Neurons were sorted based on their fluorescence (either tdTomato-positive (red) and Retrobead-positive (green) versus tdTomato-positive only or YFP-positive (green) and Retrobead-positive (red) versus YFP-positive only) directly into lysis buffer either in eppendorf tubes for bulk sequencing (350 µL lysis buffer, Qiagen RNeasy Micro Kit; Replicate 1: tdTomato-only: 1943 cells, tdTomato and tracer: 2287 cells; Replicate 2: tdTomato-only: 386, tdTomato and tracer: 782; Replicate 3: tdTomato-only: 604, tdTomato and tracer: 934) or into individual wells of 96-well plates for single-cell sequencing (2 µL Smart-Seq2 lysis buffer + RNAase inhibitor, 1 µL oligo-dT primer, and 1 µL dNTPs according to Picelli et al., 2014. Upon completion of a sort, the plates were briefly spun in a tabletop microcentrifuge and immediately placed on dry ice. Single-cell lysates were subsequently kept at -80°C until cDNA conversion.

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: double

tag: retro-labeled from pom

value: TRUE

value: FALSE

tag: hemisphere

value: Unk

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

value: not determined

tag: plate

tag: well

tag: sort date

tag: size factor

tag: total mrnas

tag: celltype

value: mixed

tag: pseudotime

tag: state

value: bulk


title: NTSE4_RG_bulk

tag: strain


title: 131194_TDPQ6_3_H07

description:
Single cell RNA-Seq library from sorted Ntsr1+ adult mouse corticothalamic neuron
count_table.txt

source_name: Single Ntsr1+ L6 Corticothalamic Projection Neurons from adult mice somatosensory cortex

tag: days post whisker manipulation

value: R

value: L

value: Contralateral

value: F

value: VPM/POm

value: VPM-only enriched

value: single cell


title: NTSB3_R_bulk

tag: label (ntsr1 or ntsr1+retrobead)

value: single


title: 131194_TDPQ6_3_H12

tag: retro-labeled from pom


title: 131194_TDPQ6_3_H06

tag: hemisphere

value: Ipsilateral

value: VPM-only

value: Root


title: 131194_TDPQ6_3_H02

value: Mixed (including C57BL/6 and CD1)

value: TRUE

tag: animal id


title: 131194_TDPQ6_3_H03

value: FALSE

tag: whiskers pulled

value: Unk


title: Feather dermis dorsal E9, rep1

tag: breed

value: White Leghorn

tag: tissue

value: dorsal skin

tag: developmental stage


title: NTSE4_R_bulk

tag: hemisphere (wrt whisker pull)

tag: Sex

value: not determined

tag: plate

tag: well

value: mixed

value: bulk


title: 131194_TDPQ6_3_H05

value: L

value: F

tag: sort date

tag: size factor

tag: total mrnas

tag: celltype


title: human stau depletion replicate 1

source_name: myoblast

tag: cell type

value: SkMc


title: 131194_TDPQ6_3_G09

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: double

value: R

value: Contralateral

value: VPM/POm

tag: pseudotime

tag: state

value: single cell


title: 131194_TDPQ6_3_G11

value: Mixed (including C57BL/6 and CD1)

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

tag: whiskers pulled

value: Root


title: 131194_TDPQ6_3_H01

value: single

value: FALSE

value: TRUE

tag: hemisphere (wrt whisker pull)

value: Ipsilateral

tag: Sex

value: VPM-only enriched


title: 131194_TDPQ6_3_G06

tag: plate

tag: well

value: Unk

value: VPM-only


title: 131194_TDPQ6_3_G07

value: L

tag: sort date

tag: size factor


title: 131194_TDPQ6_3_H04

value: F

tag: total mrnas

tag: celltype


title: NTSB3_RG_bulk

tag: strain

value: not determined

value: mixed

value: bulk


title: 131194_TDPQ6_3_G03

tag: days post whisker manipulation


title: 131194_TDPQ6_3_G02

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ6_3_G01

tag: pseudotime


title: 131194_TDPQ6_3_H11

value: double

value: R

value: Contralateral

tag: state


title: 131194_TDPQ6_3_H10

value: Mixed (including C57BL/6 and CD1)

tag: retro-labeled from pom

value: VPM/POm

value: single cell


title: 131194_TDPQ6_3_G12

tag: hemisphere


title: 131194_TDPQ6_3_G10

tag: animal id

value: VPM/POM enriched


title: NTSE5_R_bulk

value: single

value: FALSE

tag: whiskers pulled


title: 131194_TDPQ6_3_F12

value: TRUE

tag: hemisphere (wrt whisker pull)

value: Root


title: 131194_TDPQ6_3_F08

tag: Sex

value: Unk


title: 131194_TDPQ6_3_F09

value: L

tag: plate


title: 131194_TDPQ6_3_F06

value: Ipsilateral

value: F

tag: well

value: VPM-only

value: VPM-only enriched


title: 131194_TDPQ6_3_F07

value: double

tag: sort date


title: 131194_TDPQ6_3_F11

value: R

tag: size factor


title: 131194_TDPQ6_3_F10

value: Contralateral

tag: total mrnas


title: 131194_TDPQ6_3_F04

value: Mixed (including C57BL/6 and CD1)

tag: celltype


title: 131194_TDPQ6_3_F05

tag: strain


title: 131194_TDPQ6_3_F03

tag: days post whisker manipulation

value: VPM/POm


title: 131194_TDPQ6_3_E09

tag: label (ntsr1 or ntsr1+retrobead)

value: single cell


title: 131194_TDPQ6_3_E05

tag: pseudotime


title: 131194_TDPQ6_3_E12

tag: state


title: 131194_TDPQ6_3_E04

tag: retro-labeled from pom


title: 131194_TDPQ6_3_H08

tag: hemisphere


title: 131194_TDPQ6_3_E07

tag: animal id


title: 131194_TDPQ6_3_F01

tag: whiskers pulled


title: 131194_TDPQ6_3_E06

tag: hemisphere (wrt whisker pull)


title: 131194_TDPQ6_3_E08

tag: Sex


title: 131194_TDPQ6_3_F02

tag: plate


title: 131194_TDPQ6_3_E10

tag: well


title: 131194_TDPQ6_3_E01

tag: sort date


title: 131194_TDPQ6_3_D11

tag: size factor


title: 131194_TDPQ6_3_E11

tag: total mrnas


title: 131194_TDPQ6_3_D06

tag: celltype


title: 131194_TDPQ6_3_E03

tag: strain


title: 131194_TDPQ6_3_C06

tag: days post whisker manipulation


title: 131194_TDPQ6_3_D05

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ6_3_D02

tag: pseudotime


title: 131194_TDPQ6_3_C04

tag: state


title: 131194_TDPQ6_3_C05

tag: retro-labeled from pom


title: 131194_TDPQ6_3_D01

tag: hemisphere


title: 131194_TDPQ6_3_D04

tag: animal id


title: 131194_TDPQ6_3_C03

tag: whiskers pulled


title: 131194_TDPQ6_3_C02

tag: hemisphere (wrt whisker pull)


title: 131194_TDPQ6_3_C01

tag: Sex


title: 131194_TDPQ6_3_B02

tag: plate


title: 131194_TDPQ6_3_B03

tag: well


title: 131194_TDPQ6_3_B04

tag: sort date


title: 131194_TDPQ6_3_B05

tag: size factor


title: 131194_TDPQ6_3_A05

tag: total mrnas


title: 131194_TDPQ6_3_A04

tag: celltype


title: 131194_TDPQ6_3_A03

tag: strain


title: 131194_TDPQ6_3_A06

tag: days post whisker manipulation


title: 131194_TDPQ6_3_E02

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ6_3_A02

tag: pseudotime


title: 131194_TDPQ2_3_D08

tag: state


title: 131194_TDPQ2_3_D09

tag: retro-labeled from pom


title: 131194_TDPQ6_3_D03

tag: hemisphere


title: 131194_TDPQ6_3_H09

tag: animal id


title: 131194_TDPQ6_3_B01

tag: whiskers pulled


title: 131194_TDPQ2_3_C12

tag: hemisphere (wrt whisker pull)

value: VPM/POM enriched


title: 131194_TDPQ2_3_D07

tag: Sex


title: 131194_TDPQ6_3_A01

value: single

tag: plate


title: 131194_TDPQ2_3_C11

tag: well


title: 131194_TDPQ2_3_C10

tag: sort date


title: 131194_TDPQ2_3_D10

tag: size factor


title: 131194_TDPQ2_3_B11

tag: total mrnas


title: 131194_TDPQ2_3_B10

tag: celltype


title: 131194_TDPQ2_3_B08

tag: strain


title: 131194_TDPQ2_3_C07

tag: days post whisker manipulation


title: 131194_TDPQ2_3_B12

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ2_3_B07

tag: pseudotime


title: 131194_TDPQ6_3_B06

value: FALSE

tag: state


title: 131194_TDPQ2_3_A11

tag: retro-labeled from pom

value: TRUE


title: 131194_TDPQ2_3_A10

tag: hemisphere


title: 131194_TDPQ2_3_A09

tag: animal id

value: Root


title: 131194_TDPQ2_2_H12

tag: whiskers pulled

value: Unk


title: 131194_TDPQ2_2_H10

value: L

tag: hemisphere (wrt whisker pull)


title: 131194_TDPQ2_3_A07

tag: Sex


title: 131194_TDPQ2_3_A08

tag: plate


title: 131194_TDPQ2_2_H09

tag: well


title: 131194_TDPQ2_2_H05

value: Ipsilateral

tag: sort date


title: 131194_TDPQ2_2_H04

value: F

tag: size factor


title: 131194_TDPQ2_3_C09

tag: total mrnas

value: VPM-only


title: 131194_TDPQ2_2_H02

tag: celltype

value: VPM-only enriched


title: 131194_TDPQ2_2_G05

tag: strain


title: 131194_TDPQ2_2_G09

tag: days post whisker manipulation


title: 131194_TDPQ2_2_G04

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ2_3_B09

value: double

tag: pseudotime


title: 131194_TDPQ2_2_H03

tag: state


title: 131194_TDPQ2_2_G10

tag: retro-labeled from pom

value: R


title: 131194_TDPQ2_2_G03

tag: hemisphere


title: 131194_TDPQ2_2_G02

tag: animal id


title: 131194_TDPQ6_3_D12

tag: whiskers pulled

value: Contralateral


title: 131194_TDPQ2_2_F10

value: Mixed (including C57BL/6 and CD1)

tag: hemisphere (wrt whisker pull)


title: 131194_TDPQ2_2_F03

tag: Sex


title: 131194_TDPQ2_2_F02

tag: plate

value: VPM/POm


title: 131194_TDPQ2_2_F01

tag: well

value: single cell


title: 131194_TDPQ2_2_F05

tag: sort date


title: 131194_TDPQ2_2_E10

tag: size factor


title: 131194_TDPQ2_2_F07

tag: total mrnas


title: 131194_TDPQ2_2_E09

tag: celltype


title: 131194_TDPQ2_2_E01

tag: strain


title: 131194_TDPQ2_2_E02

tag: days post whisker manipulation


title: 131194_TDPQ2_2_D04

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ2_2_D05

tag: pseudotime


title: 131194_TDPQ2_2_E05

tag: state


title: 131194_TDPQ2_2_D01

tag: retro-labeled from pom


title: 131194_TDPQ2_2_E03

tag: hemisphere


title: 131194_TDPQ2_2_C05

tag: animal id


title: 131194_TDPQ2_2_B03

tag: whiskers pulled


title: 131194_TDPQ2_2_F04

tag: hemisphere (wrt whisker pull)


title: 131194_TDPQ2_2_C02

tag: Sex


title: 131194_TDPQ2_2_B02

tag: plate


title: 131194_TDPQ2_2_B04

tag: well


title: 131194_TDPQ2_2_A04

tag: sort date


title: 131194_TDPQ2_2_C04

tag: size factor


title: 131194_TDPQ2_2_B05

tag: total mrnas


title: 131194_TDPQ2_2_A02

tag: celltype


title: 131194_TDPQ2_2_B01

tag: strain


title: 131194_TDPQ2_2_D09

tag: days post whisker manipulation


title: 131194_TDPQ2_2_D10

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_TDPQ2_2_B10

tag: pseudotime


title: 131194_NTWN1_3_G11

tag: state


title: 131194_NTWN1_3_G12

tag: retro-labeled from pom


title: 131194_NTWN1_3_H05

tag: hemisphere


title: 131194_NTWN1_3_H04

tag: animal id


title: 131194_NTWN1_3_H08

tag: whiskers pulled


title: 131194_NTWN1_3_H10

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_3_H07

tag: Sex


title: 131194_NTWN1_3_H02

tag: plate


title: 131194_NTWN1_3_G10

tag: well


title: 131194_NTWN1_3_H01

tag: sort date


title: 131194_NTWN1_3_H11

tag: size factor


title: 131194_NTWN1_3_G08

tag: total mrnas


title: 131194_NTWN1_3_G09

tag: celltype


title: 131194_NTWN1_3_H09

tag: strain


title: 131194_NTWN1_3_H06

tag: days post whisker manipulation


title: 131194_NTWN1_3_G07

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_NTWN1_3_H12

tag: pseudotime


title: 131194_NTWN1_3_G05

tag: state


title: 131194_NTWN1_3_G03

tag: retro-labeled from pom


title: 131194_NTWN1_3_G04

tag: hemisphere


title: 131194_NTWN1_3_G01

tag: animal id


title: 131194_NTWN1_3_G06

tag: whiskers pulled


title: 131194_NTWN1_3_F12

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_3_G02

tag: Sex


title: 131194_NTWN1_3_F11

tag: plate


title: 131194_NTWN1_3_F10

tag: well


title: 131194_NTWN1_3_F06

tag: sort date


title: 131194_NTWN1_3_F08

tag: size factor


title: 131194_NTWN1_3_F09

tag: total mrnas


title: 131194_NTWN1_3_F04

tag: celltype


title: 131194_NTWN1_3_F05

tag: strain


title: 131194_NTWN1_3_F03

tag: days post whisker manipulation


title: 131194_NTWN1_3_F02

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_NTWN1_3_E09

tag: pseudotime


title: 131194_NTWN1_3_E10

tag: state


title: 131194_NTWN1_3_E12

tag: retro-labeled from pom

value: VPM/POM enriched


title: 131194_NTWN1_3_E06

value: single

tag: hemisphere


title: 131194_NTWN1_3_E03

value: FALSE

tag: animal id


title: 131194_NTWN1_3_E04

value: TRUE

tag: whiskers pulled


title: 131194_NTWN1_3_E07

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_3_E01

tag: Sex


title: 131194_NTWN1_3_E02

tag: plate


title: 131194_NTWN1_3_D08

tag: well


title: 131194_NTWN1_3_D11

tag: sort date


title: 131194_NTWN1_3_D09

tag: size factor


title: 131194_NTWN1_3_D02

tag: total mrnas


title: 131194_NTWN1_3_D05

tag: celltype


title: 131194_NTWN1_3_D06

tag: strain


title: 131194_NTWN1_3_E05

tag: days post whisker manipulation


title: 131194_NTWN1_3_D04

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_NTWN1_3_D03

tag: pseudotime


title: 131194_NTWN1_3_C12

tag: state


title: 131194_NTWN1_3_D07

tag: retro-labeled from pom


title: 131194_NTWN1_3_C11

tag: hemisphere


title: 131194_NTWN1_3_E08

tag: animal id


title: 131194_NTWN1_3_C10

tag: whiskers pulled


title: 131194_NTWN1_3_D10

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_3_C07

tag: Sex


title: 131194_NTWN1_3_C06

tag: plate


title: 131194_NTWN1_3_C05

tag: well

value: Root


title: 131194_NTWN1_3_C04

tag: sort date

value: Unk


title: 131194_NTWN1_3_C03

tag: size factor


title: 131194_NTWN1_3_C01

tag: total mrnas


title: 131194_NTWN1_3_B11

tag: celltype


title: 131194_NTWN1_3_B12

tag: strain


title: 131194_NTWN1_3_B10

tag: days post whisker manipulation


title: 131194_NTWN1_3_B07

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_NTWN1_3_B09

tag: pseudotime


title: 131194_NTWN1_3_D01

tag: state


title: 131194_NTWN1_3_B05

tag: retro-labeled from pom


title: 131194_NTWN1_3_B03

tag: hemisphere


title: 131194_NTWN1_3_B02

tag: animal id


title: 131194_NTWN1_3_B01

tag: whiskers pulled


title: 131194_NTWN1_3_A11

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_3_B04

tag: Sex


title: 131194_NTWN1_3_A10

tag: plate


title: 131194_NTWN1_3_A07

tag: well


title: 131194_NTWN1_3_A06

tag: sort date


title: 131194_NTWN1_3_C08

tag: size factor


title: 131194_NTWN1_3_A03

tag: total mrnas


title: 131194_NTWN1_3_A08

tag: celltype


title: 131194_NTWN1_3_A05

tag: strain


title: 131194_NTWN1_3_C02

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tag: label (ntsr1 or ntsr1+retrobead)


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tag: pseudotime


title: 131194_NTWN1_1_H10

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tag: state


title: 131194_NTWN1_1_H12

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title: 131194_NTWN1_3_A02

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tag: animal id

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tag: whiskers pulled


title: 131194_NTWN1_1_H06

tag: hemisphere (wrt whisker pull)


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tag: Sex

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title: 131194_NTWN1_3_A12

tag: plate

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title: 131194_NTWN1_1_H03

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title: 131194_NTWN1_1_H01

tag: sort date


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tag: size factor


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title: 131194_NTWN1_1_G08

tag: strain

value: Mixed (including C57BL/6 and CD1)


title: 131194_NTWN1_1_G09

tag: days post whisker manipulation

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title: 131194_NTWN1_3_A04

tag: label (ntsr1 or ntsr1+retrobead)

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tag: pseudotime

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tag: state


title: 131194_NTWN1_1_G11

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title: 131194_NTWN1_1_G05

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value: TRUE

tag: animal id


title: 131194_NTWN1_1_G01

tag: whiskers pulled


title: 131194_NTWN1_1_F11

tag: hemisphere (wrt whisker pull)


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title: 131194_NTWN1_1_F05

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tag: days post whisker manipulation


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title: 131194_NTWN1_1_E05

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title: 131194_NTWN1_1_E08

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title: 131194_NTWN1_1_E06

tag: whiskers pulled


title: 131194_NTWN1_1_E03

tag: hemisphere (wrt whisker pull)


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title: 131194_NTWN1_1_D09

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title: 131194_NTWN1_1_D12

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title: 131194_NTWN1_1_D05

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title: 131194_NTWN1_1_D02

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title: 131194_NTWN1_1_D04

tag: days post whisker manipulation


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tag: label (ntsr1 or ntsr1+retrobead)


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title: 131194_NTWN1_1_C10

tag: whiskers pulled


title: 131194_NTWN1_1_C08

tag: hemisphere (wrt whisker pull)


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title: 131194_NTWN1_1_C04

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title: 131194_NTWN1_1_C01

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title: 131194_NTWN1_1_B08

tag: days post whisker manipulation


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tag: label (ntsr1 or ntsr1+retrobead)


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title: 131194_NTWN1_1_B01

tag: animal id


title: 131194_NTWN1_1_B05

tag: whiskers pulled


title: 131194_NTWN1_1_B02

tag: hemisphere (wrt whisker pull)


title: 131194_NTWN1_1_B04

tag: Sex


title: 131194_NTWN1_1_B06

tag: plate


title: 131194_NTWN1_1_A11

tag: well


title: 131194_NTWN1_1_A10

tag: sort date

value: Root


title: 131194_NTWN1_1_A12

value: Unk

tag: size factor


title: 131194_NTWN1_1_A09

value: L

tag: total mrnas


title: 131194_NTWN1_1_B12

tag: celltype


title: 131194_NTWN1_1_A03

tag: strain


title: 131194_NTWN1_1_A05

tag: days post whisker manipulation


title: 131194_NTWN1_1_A08

tag: label (ntsr1 or ntsr1+retrobead)


title: 131194_NTWN1_1_A04

tag: pseudotime


title: 129305_NTVX3_4_H10

value: Ipsilateral

tag: state


title: 129305_NTVX3_4_H09

tag: retro-labeled from pom

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title: 131194_NTWN1_1_A06

tag: hemisphere


title: 131194_NTWN1_1_A02

tag: animal id

value: VPM-only


title: 129305_NTVX3_4_H08

tag: whiskers pulled

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title: 129305_NTVX3_4_H06

value: double

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_H05

tag: Sex


title: 129305_NTVX3_4_H04

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title: 131194_NTWN1_1_A01

value: R

tag: well


title: 129305_NTVX3_4_H01

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title: 129305_NTVX3_4_G08

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title: 129305_NTVX3_4_H11

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title: 129305_NTVX3_4_G04

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title: 129305_NTVX3_4_G12

tag: strain


title: 129305_NTVX3_4_H03

tag: days post whisker manipulation


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tag: label (ntsr1 or ntsr1+retrobead)


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title: 129305_NTVX3_4_G10

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title: 129305_NTVX3_4_G02

tag: retro-labeled from pom


title: 129305_NTVX3_4_G06

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title: 129305_NTVX3_4_H12

tag: animal id


title: 129305_NTVX3_4_G05

tag: whiskers pulled


title: 129305_NTVX3_4_G03

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_H07

tag: Sex


title: 129305_NTVX3_4_F11

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title: 129305_NTVX3_4_F09

tag: well


title: 129305_NTVX3_4_F12

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title: 129305_NTVX3_4_G01

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title: 129305_NTVX3_4_G09

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title: 129305_NTVX3_4_G11

tag: strain


title: 131194_NTWN1_1_E01

tag: days post whisker manipulation

value: Contralateral


title: 129305_NTVX3_4_F05

value: Mixed (including C57BL/6 and CD1)

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_4_F06

value: VPM/POm

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value: single cell


title: 129305_NTVX3_4_E10

tag: retro-labeled from pom

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title: 129305_NTVX3_4_E06

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title: 129305_NTVX3_4_F04

tag: animal id


title: 129305_NTVX3_4_F10

value: single

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value: FALSE

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_F03

value: TRUE

tag: Sex


title: 129305_NTVX3_4_E03

tag: plate

value: Root


title: 129305_NTVX3_4_F02

tag: well

value: Unk


title: 129305_NTVX3_4_E05

value: L

tag: sort date


title: 129305_NTVX3_4_D12

value: Ipsilateral

tag: size factor


title: 129305_NTVX3_4_E02

value: F

tag: total mrnas


title: 129305_NTVX3_4_E04

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title: 129305_NTVX3_4_E08

tag: strain

value: VPM-only


title: 129305_NTVX3_4_F01

tag: days post whisker manipulation


title: 129305_NTVX3_4_F08

tag: label (ntsr1 or ntsr1+retrobead)

value: VPM-only enriched


title: 129305_NTVX3_4_E01

value: double

tag: pseudotime


title: 129305_NTVX3_4_D11

tag: state


title: 129305_NTVX3_4_D09

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title: 129305_NTVX3_4_D10

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title: 129305_NTVX3_4_D08

tag: animal id


title: 129305_NTVX3_4_E12

tag: whiskers pulled


title: 129305_NTVX3_4_D03

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_C09

tag: Sex


title: 129305_NTVX3_4_E07

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title: 129305_NTVX3_4_D04

tag: well


title: 129305_NTVX3_4_D02

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title: 129305_NTVX3_4_C11

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title: 129305_NTVX3_4_D06

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title: 129305_NTVX3_4_C07

tag: strain


title: 129305_NTVX3_4_C08

tag: days post whisker manipulation


title: 129305_NTVX3_4_D01

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_4_C12

tag: pseudotime


title: 129305_NTVX3_4_C03

tag: state


title: 129305_NTVX3_4_C04

tag: retro-labeled from pom


title: 129305_NTVX3_4_C05

tag: hemisphere


title: 129305_NTVX3_4_B11

tag: animal id


title: 129305_NTVX3_4_C02

tag: whiskers pulled


title: 129305_NTVX3_4_D05

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_C01

tag: Sex


title: 129305_NTVX3_4_B09

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title: 129305_NTVX3_4_B08

tag: well


title: 129305_NTVX3_4_B07

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title: 129305_NTVX3_4_B10

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title: 129305_NTVX3_4_B12

tag: total mrnas


title: 129305_NTVX3_4_B05

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title: 129305_NTVX3_4_B06

tag: strain


title: 129305_NTVX3_4_C10

tag: days post whisker manipulation


title: 129305_NTVX3_4_B04

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_4_C06

tag: pseudotime


title: 129305_NTVX3_4_A09

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title: 129305_NTVX3_4_A10

tag: retro-labeled from pom


title: 129305_NTVX3_4_B03

tag: hemisphere


title: 129305_NTVX3_4_A08

tag: animal id


title: 129305_NTVX3_4_B02

tag: whiskers pulled


title: 129305_NTVX3_4_A11

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_4_A12

tag: Sex


title: 129305_NTVX3_4_A04

tag: plate


title: 129305_NTVX3_4_A07

tag: well


title: 129305_NTVX3_4_A03

tag: sort date


title: 129305_NTVX3_4_A06

tag: size factor


title: 129305_NTVX3_3_H12

value: R

tag: total mrnas


title: 129305_NTVX3_4_A05

tag: celltype


title: 129305_NTVX3_4_A01

tag: strain


title: 129305_NTVX3_3_H11

tag: days post whisker manipulation

value: Contralateral


title: 129305_NTVX3_3_H08

value: Mixed (including C57BL/6 and CD1)

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_3_H10

tag: pseudotime


title: 129305_NTVX3_3_H09

value: VPM/POm

tag: state


title: 129305_NTVX3_4_A02

tag: retro-labeled from pom

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title: 129305_NTVX3_3_H07

tag: hemisphere


title: 129305_NTVX3_3_H05

tag: animal id


title: 129305_NTVX3_3_H06

tag: whiskers pulled


title: 129305_NTVX3_3_H04

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_3_H03

tag: Sex

value: VPM/POM enriched


title: 129305_NTVX3_3_H02

value: single

tag: plate


title: 129305_NTVX3_3_G12

value: FALSE

tag: well


title: 129305_NTVX3_3_H01

value: TRUE

tag: sort date


title: 129305_NTVX3_4_B01

tag: size factor


title: 129305_NTVX3_3_G10

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title: 129305_NTVX3_3_G09

tag: celltype


title: 129305_NTVX3_3_G08

tag: strain


title: 129305_NTVX3_3_G03

tag: days post whisker manipulation


title: 129305_NTVX3_3_G02

tag: label (ntsr1 or ntsr1+retrobead)

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title: 129305_NTVX3_3_G07

value: Unk

tag: pseudotime


title: 129305_NTVX3_3_G06

value: L

tag: state


title: 129305_NTVX3_3_G04

tag: retro-labeled from pom

value: Ipsilateral


title: 129305_NTVX3_3_G01

tag: hemisphere

value: F


title: 129305_NTVX3_3_F12

tag: animal id

value: VPM-only


title: 129305_NTVX3_3_F11

tag: whiskers pulled


title: 129305_NTVX3_3_F07

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_3_F09

tag: Sex

value: VPM-only enriched


title: 129305_NTVX3_3_F10

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title: 129305_NTVX3_3_F01

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title: 129305_NTVX3_3_E09

tag: strain


title: 129305_NTVX3_3_E10

tag: days post whisker manipulation


title: 129305_NTVX3_3_E12

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_3_E08

tag: pseudotime


title: 129305_NTVX3_3_E07

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title: 129305_NTVX3_3_E05

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title: 129305_NTVX3_3_E06

tag: hemisphere


title: 129305_NTVX3_3_G05

tag: animal id


title: 129305_NTVX3_3_F06

tag: whiskers pulled


title: 129305_NTVX3_3_D12

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_3_E01

tag: Sex


title: 129305_NTVX3_3_E03

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title: 129305_NTVX3_3_D11

tag: well


title: 129305_NTVX3_3_E11

tag: sort date


title: 129305_NTVX3_3_E02

tag: size factor


title: 129305_NTVX3_3_D06

tag: total mrnas


title: 129305_NTVX3_3_D05

tag: celltype


title: 129305_NTVX3_3_D08

tag: strain


title: 129305_NTVX3_3_D09

tag: days post whisker manipulation


title: 129305_NTVX3_3_D07

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_3_D04

tag: pseudotime


title: 129305_NTVX3_3_D10

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title: 129305_NTVX3_3_D03

tag: retro-labeled from pom


title: 129305_NTVX3_3_F02

tag: hemisphere


title: 129305_NTVX3_3_E04

tag: animal id


title: 129305_NTVX3_3_C11

tag: whiskers pulled


title: 129305_NTVX3_3_D01

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_3_C10

tag: Sex


title: 129305_NTVX3_3_C09

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title: 129305_NTVX3_3_C07

tag: well


title: 129305_NTVX3_3_C06

tag: sort date


title: 129305_NTVX3_3_C02

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title: 129305_NTVX3_3_C08

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title: 129305_NTVX3_3_C01

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title: 129305_NTVX3_3_C03

tag: strain


title: 129305_NTVX3_3_C04

tag: days post whisker manipulation


title: 129305_NTVX3_3_C05

tag: label (ntsr1 or ntsr1+retrobead)


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tag: pseudotime


title: 129305_NTVX3_3_D02

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title: 129305_NTVX3_3_B07

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title: 129305_NTVX3_3_B05

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title: 129305_NTVX3_3_B06

tag: hemisphere (wrt whisker pull)


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title: 129305_NTVX3_3_B04

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title: 129305_NTVX3_3_A08

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title: 129305_NTVX3_3_B03

tag: strain


title: 129305_NTVX3_3_B01

tag: days post whisker manipulation


title: 129305_NTVX3_3_A07

tag: label (ntsr1 or ntsr1+retrobead)


title: 129305_NTVX3_3_A04

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title: 129305_NTVX3_3_A05

tag: state


title: 129305_NTVX3_3_A02

tag: retro-labeled from pom


title: 129305_NTVX3_3_A03

tag: hemisphere


title: 129305_NTVX3_2_H12

value: double

tag: animal id


title: 129305_NTVX3_2_H08

tag: whiskers pulled


title: 129305_NTVX3_2_H09

tag: hemisphere (wrt whisker pull)


title: 129305_NTVX3_3_A10

value: R

tag: Sex


title: 129305_NTVX3_3_A12

value: Contralateral

tag: plate


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value: Mixed (including C57BL/6 and CD1)

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title: 129305_NTVX3_3_A06

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tag: total mrnas

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tag: days post whisker manipulation


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title: 129305_NTVX3_2_G04

tag: hemisphere (wrt whisker pull)


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tag: hemisphere (wrt whisker pull)


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title: 129305_NTVX3_2_D08

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title: 129305_NTVX3_2_F01

tag: label (ntsr1 or ntsr1+retrobead)


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title: 129305_NTVX3_1_C07

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