title: 129305_NTVX3_1_A01

tag: retro-labeled from pom


title: 129305_NTVX3_1_A09

status: Public on Dec 31 2017

type: SRA

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

country: USA

institute: Johns Hopkins University

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

library_source: transcriptomic

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.

molecule: polyA RNA

organism: Mus musculus

source_name: Single 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.

tag: strain

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: single

value: FALSE

value: TRUE

tag: hemisphere

value: R

tag: animal id

tag: whiskers pulled

value: L

tag: hemisphere (wrt whisker pull)

value: Contralateral

tag: Sex

value: F

tag: plate

tag: well

tag: sort date

value: Unk

tag: size factor

tag: total mrnas

tag: celltype

value: VPM/POm

tag: pseudotime

tag: state

value: VPM/POM enriched

value: single cell


title: 123520_NTSP4_4_H11

value: double

tag: retro-labeled from pom

value: Root


title: 123520_NTSP4_4_H09

tag: strain


title: 123520_NTSP4_4_H08

tag: days post whisker manipulation


title: 123520_NTSP4_4_H06

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_4_H02

tag: hemisphere

value: VPM-only


title: 123520_NTSP4_4_H03

tag: animal id


title: 123520_NTSP4_4_H01

tag: whiskers pulled


title: 123520_NTSP4_4_G12

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_4_H07

tag: Sex


title: 123520_NTSP4_4_G09

tag: plate


title: 123520_NTSP4_4_G11

tag: well


title: 123520_NTSP4_4_H05

tag: sort date


title: 123520_NTSP4_4_G06

tag: size factor


title: 129305_NTVX3_1_A07

tag: total mrnas


title: 123520_NTSP4_4_G10

tag: celltype


title: 123520_NTSP4_4_H04

tag: pseudotime


title: 123520_NTSP4_4_G05

tag: state


title: 123520_NTSP4_4_G04

tag: retro-labeled from pom


title: 129305_NTVX3_1_A06

tag: strain


title: 123520_NTSP4_4_G02

tag: days post whisker manipulation


title: 123520_NTSP4_4_F12

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_4_F11

tag: hemisphere


title: 123520_NTSP4_4_F10

tag: animal id


title: 123520_NTSP4_4_H10

tag: whiskers pulled


title: 129305_NTVX3_2_D10

tag: hemisphere (wrt whisker pull)

value: Ipsilateral


title: 123520_NTSP4_4_F06

tag: Sex


title: 123520_NTSP4_4_F05

tag: plate


title: 123520_NTSP4_4_F07

tag: well


title: 123520_NTSP4_4_F08

tag: sort date


title: 123520_NTSP4_4_G08

tag: size factor


title: 123520_NTSP4_4_F02

tag: total mrnas


title: 123520_NTSP4_4_F03

tag: celltype


title: 123520_NTSP4_4_F01

tag: pseudotime


title: 123520_NTSP4_4_E12

tag: state


title: 123520_NTSP4_4_G03

tag: retro-labeled from pom


title: 123520_NTSP4_4_E02

tag: strain


title: 123520_NTSP4_4_E03

tag: days post whisker manipulation


title: 123520_NTSP4_4_E11

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_4_E09

tag: hemisphere


title: 123520_NTSP4_4_E08

tag: animal id


title: 123520_NTSP4_4_E10

tag: whiskers pulled


title: 123520_NTSP4_4_D08

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_4_E06

tag: Sex


title: 123520_NTSP4_4_D12

tag: plate


title: 123520_NTSP4_4_E04

tag: well


title: 123520_NTSP4_4_E01

tag: sort date


title: 123520_NTSP4_4_E05

tag: size factor


title: 123520_NTSP4_4_F09

tag: total mrnas


title: 123520_NTSP4_4_D10

tag: celltype


title: Col_leaf

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

description: Small RNA

data_processing:
After de-multiplexing, 36-nt reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation (or GFP transgene) with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.

extract_protocol:
Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10%) for 3 min, followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Purification of pollen expressing the GFP-miR845b sensor in dcl1-5/+ and dcl1/+,dcl2/dcl4 mutants was performed by vortexing open flowers in 1 mL of PEB and filtering through a 30um mesh before FACS. Pollen population was identified in SSC/FSC scatter plots, and GFP fluorescence was analyzed by excitation with a 488nm laser and detected with a 530/30 bandpass filter. Pollen total RNA was extracted using Trizol LS reagent (Life Technologies) by vortexing with glass beads for 5 minutes, and concentrated with Direct-zol columns (Zymo Research).
Small RNAs were purified by running total RNA on acrylamide gels (15% polyacrylamide, 7M urea) and performing size selection of approximately 18 to 30-nt region using a small RNA ladder (Zymo Research). The small RNA fraction was isolated from acrylamide gel plugs by grinding with a plastic pestle in Trizol LS (Life Technologies), and concentrated using Direct-zol columns (Zymo Research). Libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina) following manufacturer instructions.

tag: ecotype

tag: tissue

value: Leaf


title: 123520_NTSP4_4_D06

value: Mixed (including C57BL/6 and CD1)

tag: retro-labeled from pom

tag: pseudotime

tag: state


title: Mix-stage embryo in 25 °C

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
The original raw data from Illumina HiSeq are transformed to Sequenced Reads by base calling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic, then mapped to to C. elegans genome (WS257) using Tophat2, with min intron size equal 10, max intron size equals 5000 and max read mismatch equals 2.
Only genes with at least one intron are used the further analysis. The initial exon and intron annotations are fetched from WormBase annotation GFF file. For one gene, the exons from all possible mRNA isoforms are merged as “exon” regions, while the “intron” regions are defined as the regions in this gene without overlapping of any exons. After mapping with tophat2, htseq-count is employed to count the reads mapped to the “intron” and “exon” region, respectively. The ratio of intron reads and exon reads are calculated to measure the degree of intron retention.
Genome_build: WS257
Supplementary_files_format_and_content: csv file containing the raw read count within exon or intron region for each gene.

organism: Caenorhabditis elegans

source_name: mix-stage embryo in 25 °C (Exp)

extract_protocol:
Mix-stage embryo samples were collected from strain BW1943 (gad-1(ct226) dpy-11(e224) V) at 16 °C and 25 °C by bleaching. Total RNAs were extracted using TRIzol (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual

tag: strain

tag: developmental stage

value: embryo

tag: temperature

value: 25 °C


title: 123520_NTSP4_4_F04

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: TRUE

value: FALSE

tag: hemisphere

tag: animal id

tag: whiskers pulled


title: 123520_NTSP4_4_D02

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

tag: well

tag: sort date


title: nrpd1a_pollen

description: Small RNA

source_name: Pollen

tag: ecotype

tag: tissue

value: Pollen


title: 123520_NTSP4_4_D04

tag: retro-labeled from pom

tag: size factor

tag: total mrnas

tag: celltype

tag: pseudotime


title: 123520_NTSP4_4_D03

tag: strain

tag: days post whisker manipulation

tag: state


title: 123520_NTSP4_4_C12

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: animal id


title: 123520_NTSP4_4_C10

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex


title: 123520_NTSP4_4_C11

tag: plate

tag: well

tag: sort date


title: 123520_NTSP4_4_C08

tag: retro-labeled from pom


title: 123520_NTSP4_4_C09

tag: size factor


title: 123520_NTSP4_4_C03

tag: total mrnas


title: 123520_NTSP4_4_C07

tag: celltype


title: 123520_NTSP4_4_B11

tag: pseudotime


title: 123520_NTSP4_4_C06

tag: strain


title: 123520_NTSP4_4_C05

tag: days post whisker manipulation


title: 123520_NTSP4_4_B10

tag: state


title: 123520_NTSP4_4_B12

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_4_C02

tag: hemisphere


title: 123520_NTSP4_4_B08

tag: animal id


title: 123520_NTSP4_4_B07

tag: whiskers pulled


title: 123520_NTSP4_4_B09

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_4_C01

tag: Sex


title: 129305_NTVX3_1_F05

value: R

value: L

value: Contralateral

tag: plate


title: dcl1_FACS_pollen

description: Small RNA

tag: ecotype

tag: tissue


title: 123520_NTSP4_4_B06

tag: retro-labeled from pom

value: Unk

value: F

tag: well

tag: sort date


title: 123520_NTSP4_4_D01

tag: size factor

tag: total mrnas

tag: celltype

value: VPM/POm

value: single cell


title: PINCH1_mut_3

city: Porto

middle: (Porto

last: Portugal)

address: Rua Alfredo Allen, 208

country: Portugal

institute: Instituto de Biologia Molecular e Celular (IBMC)/I3S

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument as 75 bp paired end runs
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters (Cutadapt v1.9.1) to remove the standard Illumina adapter sequence. Reads were then mapped to the mouse GRCm38 genome assembly using HISAT2 v2.0.5 guided by the gene models from the Ensembl v70 release. BAM files were imported to Seqmonk v36.0 .(http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: SeqMonk count table; The quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) gene name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl); (8-16) raw read count

source_name: PINCH1 mutant_mouse sciatic nerve

extract_protocol:
Total RNA was prepared from pools of nerves collected from males and females (each biological replicate consisted in a pool of four SN from 1 male and 1 female to avoid gender-related differences) using Trizol followed by PureLink RNA kit (Thermo Fisher) according to the manufacturer’s instructions.
Illumina’s TruSeq (an outsourced service at the Oxford Genomics Centre)

treatment_protocol: Sciatic nerves from P14 days animals from PINCH1 and PINCH2 mutants and control littermates were dissected, stripped of the epineurium and immediately frozen in liquid nitrogen. All mice were housed, bred and treated in strict accordance to the guidelines approved by the Swiss Cantonal Veterinary Office, the Portuguese Veterinary Office (DGAV) and EU directives.

tag: strain background

tag: genotype/variation

value: PINCH1 mutant

tag: developmental stage

value: Postnatal day 15

value: Sciatic nerve


title: PINCH2_mut_1

source_name: PINCH2 mutant_mouse sciatic nerve

value: PINCH2 mutant


title: 123520_NTSP4_4_B05

tag: strain

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: double

tag: hemisphere

tag: pseudotime

tag: state

value: Root


title: 123520_NTSP4_4_D05

value: TRUE

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate


title: 123520_NTSP4_4_B04

tag: retro-labeled from pom

value: FALSE

tag: well

tag: sort date

tag: size factor


title: Mix-stage embryo in 16 °C

source_name: mix-stage embryo in 16 °C (Con)

value: embryo

tag: temperature

value: 16 °C


title: 123520_NTSP4_4_B03

tag: total mrnas

tag: celltype


title: PINCH1_mut_2

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: PINCH1_mut_1


title: PINCH2_mut_3


title: 123520_NTSP4_4_A11

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: pseudotime

tag: state


title: CTR_3

source_name: control_mouse sciatic nerve

value: control


title: Creobese-3

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
laser-captured hypothalamic region
SLX-12913.D711_D502

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using htseq-count
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts per Million (CPM) matrix in tab-delimited text

source_name: Mediobasal hypothalamus

extract_protocol:
Hypothalamic regions were laser-capture microdissected from cryosections using a P.A.L.M Microlaser system, and RNA extracting using the miRNeasy micro RNA extraction kit (Qiagen).
Amplification and cDNA library prepartion was performed using the Pico Input Mammalian SMARTer Stranded RNA-Seq kit (Takara Bio).

treatment_protocol: Male mice with a floxed Snord116 deletion (B6(Cg)-Snord116tm1Uta/J - JAX stock no 008118) were stereotaxically injected with AAV-Cre or AAV-GFP in the mediobasal hypothalamus and brains were fresh frozen at 10 weeks post injection.

tag: genotype

tag: Sex

value: Male

tag: treatment

value: AAV-Cre

tag: weight phenotype

value: Non-obese


title: 123520_NTSP4_4_A12

tag: retro-labeled from pom

value: Unk

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

value: F

tag: plate

tag: well

tag: sort date

tag: size factor

value: VPM/POm


title: 123520_NTSP4_4_A08

tag: strain

tag: days post whisker manipulation

tag: total mrnas

tag: celltype

value: single cell


title: CTR_2

tag: strain background

tag: genotype/variation

tag: developmental stage

value: Postnatal day 15

tag: tissue

value: Sciatic nerve


title: Gfp-3

description:
laser-captured hypothalamic region
SLX-12913.D706_D503

tag: genotype

tag: Sex

tag: treatment

value: AAV-GFP

tag: weight phenotype

value: Control


title: CTR_1


title: Creobese-1

description:
laser-captured hypothalamic region
SLX-12913.D707_D502


title: PINCH2_mut_2

value: PINCH2 mutant


title: Cre-3

description:
laser-captured hypothalamic region
SLX-12913.D705_D502

value: Obese


title: Gfp-2

description:
laser-captured hypothalamic region
SLX-12913.D703_D503


title: Cre-2

description:
laser-captured hypothalamic region
SLX-12913.D703_D502


title: Gfp-1

description:
laser-captured hypothalamic region
SLX-12913.D701_D503


title: 123520_NTSP4_4_A09

value: Mixed (including C57BL/6 and CD1)

tag: label (ntsr1 or ntsr1+retrobead)

value: double

tag: retro-labeled from pom

value: TRUE

value: FALSE

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: pseudotime

tag: state

value: Root


title: Cre-1

description:
laser-captured hypothalamic region
SLX-12913.D701_D502

tag: strain

value: Male

value: AAV-Cre


title: 123520_NTSP4_4_A10

tag: days post whisker manipulation

value: Unk

tag: plate

tag: well

tag: sort date

tag: size factor

tag: total mrnas

tag: celltype


title: 123520_NTSP4_4_A05

tag: Sex

value: F

value: VPM-only


title: 123520_NTSP4_4_A07

tag: label (ntsr1 or ntsr1+retrobead)

value: VPM/POm

value: single cell


title: 123520_NTSP4_4_A03

tag: retro-labeled from pom


title: Creobese-2

description:
laser-captured hypothalamic region
SLX-12913.D709_D502

tag: genotype

tag: treatment

tag: weight phenotype

value: Non-obese


title: 123520_NTSP4_4_A04

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_3_H10

tag: strain

tag: days post whisker manipulation

value: single

tag: pseudotime

tag: state


title: 123520_NTSP4_3_H09

tag: plate

tag: well

tag: sort date

tag: size factor


title: 123520_NTSP4_4_A02

tag: label (ntsr1 or ntsr1+retrobead)

tag: Sex

tag: total mrnas

tag: celltype


title: 123520_NTSP4_4_A01

tag: retro-labeled from pom


title: 123520_NTSP4_3_H12

tag: hemisphere


title: Himchana 1_S6 - Rep3

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: processed data: HS6_FPKM.txt

data_processing:
Illumina 1.5/1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Kabuli chickpea genome (http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip); Genome visualization at: http://cicar.comparative-legumes.org/gb2/gbrowse/Ca1.0/
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

organism: Cicer arietinum

source_name: Mature plants

growth_protocol: Plants were grown in the field.

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma of modified protocol proposed by Wang et al (2011, Phytochemical Analysis).
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

treatment_protocol: Leaves were collected from the field-grown chickpea plants during mid maturation stage of seed development. Seven different stages of seeds (whole seed) representing the major events occurring within the seed, were collected from the field-grown plants. The tissues were collected in at least three biological replicates.

tag: cultivar

value: Himchana 1

tag: tissue

value: Seed

tag: developmental stage

value: seed stage 6


title: Himchana 1_S7 - Rep1

description: processed data: HS7_FPKM.txt

value: seed stage 7


title: Himchana 1_S7 - Rep3

description: processed data: HS7_FPKM.txt


title: 123520_NTSP4_3_H08

tag: strain

value: Mixed (including C57BL/6 and CD1)

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: Himchana 1_S7 - Rep2

description: processed data: HS7_FPKM.txt


title: Himchana 1_S5 - Rep3

description: processed data: HS5_FPKM.txt

value: seed stage 5


title: Himchana 1_S6 - Rep2

description: processed data: HS6_FPKM.txt


title: Himchana 1_S6 - Rep1

description: processed data: HS6_FPKM.txt


title: Himchana 1_S5 - Rep2

description: processed data: HS5_FPKM.txt


title: 123520_NTSP4_3_H05

tag: days post whisker manipulation

value: FALSE

tag: plate

tag: pseudotime

tag: state


title: 123520_NTSP4_3_H06

tag: label (ntsr1 or ntsr1+retrobead)

tag: well

tag: sort date

tag: size factor

value: Root


title: 123520_NTSP4_3_H04

tag: retro-labeled from pom

tag: Sex

tag: total mrnas

tag: celltype


title: 123520_NTSP4_3_H03

tag: hemisphere


title: 123520_NTSP4_3_H11

tag: strain


title: 123520_NTSP4_4_B01

value: double

value: TRUE

tag: animal id

value: VPM-only enriched


title: Himchana 1_S4 - Rep2

description: processed data: HS4_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage

value: seed stage 4


title: Himchana 1_S4 - Rep3

description: processed data: HS4_FPKM.txt


title: Himchana 1_S5 - Rep1

description: processed data: HS5_FPKM.txt


title: 123520_NTSP4_3_H07

tag: days post whisker manipulation

value: Unk

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

value: F

tag: plate

value: VPM-only


title: Himchana 1_S4 - Rep1

description: processed data: HS4_FPKM.txt


title: 123520_NTSP4_3_H02

tag: label (ntsr1 or ntsr1+retrobead)

tag: well

value: VPM/POm

tag: pseudotime

tag: state

value: single cell


title: Himchana 1_S3 - Rep2

description: processed data: HS3_FPKM.txt

value: Himchana 1

value: seed stage 3


title: Himchana 1_S3 - Rep3

description: processed data: HS3_FPKM.txt

value: Seed


title: 123520_NTSP4_3_G05

value: single

tag: retro-labeled from pom

tag: Sex

tag: sort date

tag: size factor


title: 123520_NTSP4_3_G10

tag: strain

value: Mixed (including C57BL/6 and CD1)

tag: hemisphere

tag: total mrnas

tag: celltype


title: Himchana 1_S3 - Rep1

description: processed data: HS3_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage


title: Himchana 1_S2 - Rep1

description: processed data: HS2_FPKM.txt

value: seed stage 2


title: 123520_NTSP4_3_G06

tag: days post whisker manipulation

value: FALSE

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_3_G11

tag: label (ntsr1 or ntsr1+retrobead)

tag: plate

tag: well

tag: pseudotime

value: Root


title: Himchana 1_S2 - Rep2

description: processed data: HS2_FPKM.txt


title: 123520_NTSP4_3_H01

tag: retro-labeled from pom

tag: Sex

tag: sort date

tag: state


title: 123520_NTSP4_3_G08

tag: strain

tag: hemisphere

tag: size factor

tag: total mrnas


title: 123520_NTSP4_3_G07

tag: celltype


title: 123520_NTSP4_3_G12

tag: days post whisker manipulation


title: Himchana 1_S1 - Rep3

description: processed data: HS1_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage

value: seed stage 1


title: Himchana 1_S1 - Rep1

description: processed data: HS1_FPKM.txt


title: Himchana 1_S1 - Rep2

description: processed data: HS1_FPKM.txt


title: Himchana 1_Leaf - Rep3

description: processed data: HL_FPKM.txt

value: Leaf

value: Mature plants


title: 123520_NTSP4_3_G02

tag: label (ntsr1 or ntsr1+retrobead)

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: Himchana 1_Leaf - Rep2

description: processed data: HL_FPKM.txt


title: 123520_NTSP4_3_F12

tag: retro-labeled from pom

tag: plate

tag: well

tag: pseudotime


title: Himchana 1_Leaf - Rep1

description: processed data: HL_FPKM.txt


title: 123520_NTSP4_3_F11

tag: strain

tag: Sex

tag: sort date

tag: state


title: JGK3_S7 - Rep3

description: processed data file: JS7_FPKM.txt

value: seed stage 7


title: 123520_NTSP4_3_G01

tag: hemisphere

value: Unk

tag: size factor

tag: total mrnas

tag: celltype


title: 123520_NTSP4_3_G09

tag: days post whisker manipulation

value: F


title: 123520_NTSP4_3_F10

tag: label (ntsr1 or ntsr1+retrobead)


title: Himchana 1_S2 - Rep3

description: processed data: HS2_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage


title: 123520_NTSP4_3_F09

tag: retro-labeled from pom

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: JGK3_S7 - Rep2

description: processed data file: JS7_FPKM.txt


title: JGK3_S7 - Rep1

description: processed data file: JS7_FPKM.txt


title: JGK3_S6 - Rep3

description: processed data file: JS6_FPKM.txt

value: seed stage 6


title: 123520_NTSP4_3_F08

tag: strain

tag: plate

tag: well

value: VPM-only

tag: pseudotime


title: 123520_NTSP4_3_E09

tag: hemisphere

tag: Sex

tag: sort date

value: VPM/POm

tag: state

value: single cell


title: 123520_NTSP4_3_F04

tag: days post whisker manipulation

tag: size factor

tag: total mrnas

tag: celltype


title: 123520_NTSP4_3_F06

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_3_F07

tag: retro-labeled from pom


title: 123520_NTSP4_3_F01

tag: animal id


title: 123520_NTSP4_3_E12

tag: whiskers pulled


title: 123520_NTSP4_3_E08

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_3_E04

tag: strain


title: 123520_NTSP4_3_F03

tag: plate


title: 123520_NTSP4_3_E06

tag: well


title: 123520_NTSP4_3_E07

tag: pseudotime


title: 123520_NTSP4_3_E05

tag: hemisphere


title: JGK3_S1 - Rep2

description: processed data file: JS1_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage


title: JGK3_S2 - Rep1

description: processed data file: JS2_FPKM.txt


title: JGK3_S1 - Rep3

description: processed data file: JS1_FPKM.txt


title: JGK3_S2 - Rep2

description: processed data file: JS2_FPKM.txt


title: JGK3_S1 - Rep1

description: processed data file: JS1_FPKM.txt


title: JGK3_S4 - Rep1

description: processed data file: JS4_FPKM.txt

value: seed stage 4


title: JGK3_S3 - Rep1

description: processed data file: JS3_FPKM.txt

value: Seed

value: seed stage 3


title: JGK3_S4 - Rep2

description: processed data file: JS4_FPKM.txt


title: JGK3_S4 - Rep3

description: processed data file: JS4_FPKM.txt


title: JGK3_S6 - Rep2

description: processed data file: JS6_FPKM.txt


title: JGK3_S2 - Rep3

description: processed data file: JS2_FPKM.txt


title: JGK3_S5 - Rep2

description: processed data file: JS5_FPKM.txt

value: seed stage 5


title: JGK3_S3 - Rep3

description: processed data file: JS3_FPKM.txt


title: 123520_NTSP4_3_D12

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

value: single

tag: Sex

tag: sort date

tag: state


title: JGK3_S5 - Rep3

description: processed data file: JS5_FPKM.txt


title: 123520_NTSP4_3_D09

tag: label (ntsr1 or ntsr1+retrobead)

value: FALSE

tag: size factor

tag: total mrnas

tag: celltype

value: Root


title: JGK3_S3 - Rep2

description: processed data file: JS3_FPKM.txt


title: 123520_NTSP4_3_D10

tag: retro-labeled from pom

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_3_D11

tag: strain

tag: plate

tag: well

tag: pseudotime


title: JGK3_S5 - Rep1

description: processed data file: JS5_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage


title: 123520_NTSP4_3_E03

tag: days post whisker manipulation

tag: hemisphere

tag: Sex

tag: sort date


title: 123520_NTSP4_3_E01

tag: label (ntsr1 or ntsr1+retrobead)

tag: size factor

tag: total mrnas

tag: state


title: JGK3_Leaf - Rep1

description: processed data file: JL_FPKM.txt

value: Leaf


title: JGK3_Leaf - Rep2

description: processed data file: JL_FPKM.txt

value: Mature plants


title: 123520_NTSP4_3_D06

tag: retro-labeled from pom

tag: animal id

tag: whiskers pulled

tag: celltype


title: JGK3_Leaf - Rep3

description: processed data file: JL_FPKM.txt


title: 123520_NTSP4_3_D08

tag: strain

tag: hemisphere (wrt whisker pull)

tag: plate

tag: well


title: 123520_NTSP4_3_D05

tag: pseudotime


title: 123520_NTSP4_3_D04

tag: days post whisker manipulation


title: 123520_NTSP4_3_D03

tag: hemisphere


title: JGK3_S6 - Rep1

description: processed data file: JS6_FPKM.txt

tag: cultivar

tag: tissue

tag: developmental stage


title: 123520_NTSP4_3_D02

tag: label (ntsr1 or ntsr1+retrobead)

tag: Sex

tag: sort date

tag: size factor


title: 123520_NTSP4_3_C12

tag: retro-labeled from pom

tag: animal id

tag: total mrnas

tag: state


title: 123520_NTSP4_3_D01

tag: strain

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: celltype


title: 123520_NTSP4_3_C10

tag: days post whisker manipulation

tag: plate

tag: well

tag: pseudotime


title: 123520_NTSP4_3_D07

tag: hemisphere


title: 123520_NTSP4_3_C03

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_3_C05

tag: Sex


title: 123520_NTSP4_3_C02

tag: sort date


title: 123520_NTSP4_3_C01

tag: size factor


title: 123520_NTSP4_3_C07

tag: retro-labeled from pom


title: 123520_NTSP4_3_C09

tag: animal id


title: 123520_NTSP4_3_C08

tag: total mrnas


title: 123520_NTSP4_3_C06

tag: state


title: 123520_NTSP4_3_B08

tag: strain


title: 123520_NTSP4_3_B09

tag: whiskers pulled


title: 123520_NTSP4_3_B11

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP4_3_B12

tag: celltype


title: 123520_NTSP4_3_B05

tag: days post whisker manipulation


title: 123520_NTSP4_3_B06

tag: plate


title: 123520_NTSP4_3_B03

tag: well


title: 123520_NTSP4_3_B02

tag: pseudotime


title: 123520_NTSP4_3_B10

tag: hemisphere


title: 123520_NTSP4_3_B07

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP4_3_B04

tag: Sex


title: 123520_NTSP4_3_C04

tag: sort date


title: 123520_NTSP4_3_A10

tag: size factor


title: 123520_NTSP4_3_A12

tag: retro-labeled from pom


title: 123520_NTSP4_4_A06

value: double

value: TRUE

tag: animal id


title: 123520_NTSP4_3_A11

value: Unk

value: F

tag: total mrnas


title: 123520_NTSP4_3_A09

value: VPM-only

tag: state


title: 123520_NTSP4_3_A07

tag: strain


title: 123520_NTSP4_3_A06

tag: whiskers pulled

value: VPM/POm


title: 123520_NTSP4_3_A05

tag: hemisphere (wrt whisker pull)

value: single cell


title: 123520_NTSP4_3_A04

tag: celltype


title: 123520_NTSP4_3_A03

tag: days post whisker manipulation


title: 123520_NTSP4_3_A08

tag: plate


title: 123520_NTSP3_2_H09

value: M

tag: well


title: 123520_NTSP4_3_A02

tag: pseudotime


title: 123520_NTSP3_2_H01

tag: hemisphere


title: 123520_NTSP3_2_G11

tag: label (ntsr1 or ntsr1+retrobead)

value: VPM-only enriched


title: 123520_NTSP3_2_H05

tag: Sex


title: 123520_NTSP3_2_H11

tag: sort date


title: 123520_NTSP3_2_H10

tag: size factor


title: 123520_NTSP3_2_G09

tag: retro-labeled from pom


title: 123520_NTSP3_2_H07

tag: animal id


title: 123520_NTSP4_3_A01

tag: total mrnas


title: 123520_NTSP3_2_F12

tag: state


title: 123520_NTSP3_2_H06

tag: strain


title: 123520_NTSP3_2_G01

tag: whiskers pulled


title: 123520_NTSP3_2_G05

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP3_2_H02

tag: celltype


title: 123520_NTSP3_2_H04

tag: days post whisker manipulation


title: 123520_NTSP3_2_F11

tag: plate


title: 123520_NTSP3_2_F09

tag: well


title: 123520_NTSP3_2_F08

tag: pseudotime


title: 123520_NTSP3_2_G08

tag: hemisphere


title: 123520_NTSP3_2_G06

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP3_2_G07

tag: Sex


title: 123520_NTSP3_2_G04

tag: sort date


title: 123520_NTSP3_2_G03

tag: size factor


title: 123520_NTSP3_2_F07

tag: retro-labeled from pom


title: 123520_NTSP3_2_H03

tag: animal id


title: 123520_NTSP4_3_B01

tag: total mrnas


title: 123520_NTSP3_2_F04

tag: state


title: 123520_NTSP3_2_E10

tag: strain


title: 123520_NTSP3_2_E09

tag: whiskers pulled


title: 123520_NTSP3_2_E02

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP3_2_F06

tag: celltype


title: 123520_NTSP3_2_E11

tag: days post whisker manipulation


title: 123520_NTSP3_2_F02

tag: plate


title: 123520_NTSP3_2_F05

tag: well


title: 123520_NTSP3_2_E05

tag: pseudotime


title: 123520_NTSP3_2_E08

tag: hemisphere


title: 123520_NTSP3_2_E03

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP3_2_E04

tag: Sex


title: 123520_NTSP3_2_D09

tag: sort date


title: 123520_NTSP3_2_D10

tag: size factor


title: 123520_NTSP3_2_D06

tag: retro-labeled from pom


title: 123520_NTSP3_2_D05

tag: animal id


title: 123520_NTSP3_2_D04

tag: total mrnas


title: 123520_NTSP3_2_G02

tag: state


title: 123520_NTSP3_2_D02

tag: strain


title: 123520_NTSP3_2_D03

tag: whiskers pulled


title: 123520_NTSP3_2_D08

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP3_2_C11

tag: celltype


title: 123520_NTSP3_2_C09

tag: days post whisker manipulation


title: 123520_NTSP3_2_C10

tag: plate


title: 123520_NTSP3_2_F03

tag: well


title: 123520_NTSP3_2_C07

tag: pseudotime


title: 123520_NTSP3_2_D11

tag: hemisphere


title: 123520_NTSP3_2_C06

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP3_2_C05

tag: Sex


title: 123520_NTSP3_2_B05

tag: sort date


title: 123520_NTSP3_2_C04

tag: size factor


title: 123520_NTSP3_2_B08

tag: retro-labeled from pom


title: 123520_NTSP3_2_B10

tag: animal id


title: 123520_NTSP3_2_B09

tag: total mrnas


title: 123520_NTSP3_2_B12

tag: state


title: 123520_NTSP3_2_B06

tag: strain


title: 123520_NTSP3_2_B11

tag: whiskers pulled


title: 123520_NTSP3_2_B07

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP3_2_B04

tag: celltype


title: 123520_NTSP3_2_C03

tag: days post whisker manipulation


title: 123520_NTSP3_2_C02

tag: plate


title: 123520_NTSP3_2_A10

tag: well


title: 123520_NTSP3_2_B03

tag: pseudotime


title: 123520_NTSP3_2_A08

tag: hemisphere


title: 123520_NTSP3_2_A06

tag: label (ntsr1 or ntsr1+retrobead)


title: 123520_NTSP3_2_C08

tag: Sex


title: 123520_NTSP3_2_A04

tag: sort date


title: 123520_NTSP3_1_H11

tag: size factor


title: 123520_NTSP3_1_H12

tag: retro-labeled from pom


title: 123520_NTSP3_2_A03

tag: animal id


title: 123520_NTSP3_2_A02

tag: total mrnas


title: 123520_NTSP3_2_A05

tag: state


title: 123520_NTSP3_2_A11

tag: strain


title: 123520_NTSP3_1_H10

tag: whiskers pulled


title: 123520_NTSP3_2_A09

tag: hemisphere (wrt whisker pull)


title: 123520_NTSP3_1_H09

tag: celltype


title: 123520_NTSP3_1_H08

tag: days post whisker manipulation


title: MCF7-shPRMT5 Rep3

city: Birmingham

first: Kelly

last: Chiang

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

description: P5; Prmt5KD_4_AGCGATA-GTACTGA

data_processing:
Sequenced reads were mapped to build hg19 of the human genome from the University of California Santa Cruz (UCSC) genome database using TopHat version 2.0.12
FPKMs were calculated by Cufflink (2.2.1) and differential expressed genes were identified by cuffdiff with a thresholdof FDR < 0.05 and fold change > 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff analysis results of gene level expressions

organism: Homo sapiens

source_name: MCF7 shPRMT5 ESA+CD24lowCD44+ cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% foetal bovine serum, 5mM Glutamine and pen/strep

extract_protocol:
RNA was extracted using the GenElute Total Mammalian RNA Isolation Kit and rRNA depleted using the Low Input Ribominus kit (v2) according to manufacturer's instructions.
Library prep was performed using the TruSeq® Stranded mRNA kit (RS-122-2101) according to manufacturer's instructions

tag: cell line background

tag: genotype/variation

tag: cell type

value: ESA+CD24lowCD44+ cells


title: MCF7-shPRMT5 Rep1

description: P5; Prmt5KD_2_TCCGCGA-GTACTGA


title: 123520_NTSP3_1_H06

tag: hemisphere

tag: plate

tag: well

tag: pseudotime


title: MCF7-shCTRL Rep2

description: UT_CTRL; ctrl3_S73

source_name: MCF7 shCTRL ESA+CD24lowCD44+ cells

value: shCTRL


title: 123520_NTSP3_1_H07

value: Mixed (including C57BL/6 and CD1)

tag: label (ntsr1 or ntsr1+retrobead)

tag: Sex

tag: sort date

tag: size factor


title: 123520_NTSP3_1_H05

value: single

tag: retro-labeled from pom

tag: animal id

tag: total mrnas

tag: state


title: MCF7-shCTRL Rep1

description: UT_CTRL; ctrl2_CTGAAGC-CAGGACG


title: 123520_NTSP3_1_H03

tag: strain

value: FALSE

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: celltype


title: 123520_NTSP3_1_H04

tag: days post whisker manipulation

value: Root


title: 8_S8_R1_001

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 1 Gilbert St

institute: Yale

data_processing:
CLC Genomics Workbench 9.0 (Qiagen) was used to process data, normalize, and map to reference human genome.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file showing log RPKM reads

source_name: Chorionic villus explant

growth_protocol: Chorionic villus explants were maintained in DMEM F/12 with 10% FBS after dissection.

extract_protocol:
RNA was isloated using GenElute Total RNA Miniprep Kit (Sigma).
cDNA libraries were prepared from RNA using NEB Ultra ibrary kit.

treatment_protocol: Explants were treated with 1000 U recombinant IFNB or 1000U IFNL (R&D systems) for 24 hours.

tag: treatment

value: IFNB

tag: tissue

value: Placenta

tag: tissue compartment

value: Chorionic villus

tag: gestational age

tag: tissue code

value: Female


title: 7_S7_R1_001

value: Mock

tag: Sex


title: 123520_NTSP3_1_G09

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

value: Unk

tag: plate

tag: well

tag: sort date

tag: pseudotime


title: 6_S6_R1_001

value: IFNL


title: 5_S5_R1_001


title: 4_S4_R1_001


title: 3_S3_R1_001

value: Male


title: 123520_NTSP3_1_G10

tag: strain

tag: retro-labeled from pom

tag: animal id

tag: size factor

tag: total mrnas

value: VPM/POm

tag: state

value: single cell


title: 123520_NTSP3_1_G08

tag: days post whisker manipulation

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

value: M

tag: celltype

value: VPM-only


title: 123520_NTSP3_1_G07

tag: Sex


title: MCF7-shPRMT5 Rep2

description: P5; Prmt5KD_3_TCTCGCG-GTACTGA

tag: cell line background

tag: genotype/variation

tag: cell type

value: ESA+CD24lowCD44+ cells


title: 123520_NTSP3_1_G06

value: Mixed (including C57BL/6 and CD1)

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: plate

tag: well


title: 9_S9_R1_001

tag: treatment

tag: tissue

tag: tissue compartment

tag: gestational age

tag: tissue code


title: SCC21_40

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG

data_processing:
HiSeq 2500 standard base-calling
RNAworld in-house allingment and annotation pipeline (see PMID: 22836126)
Genome_build: hg19
Supplementary_files_format_and_content: Tables in xlsx format; 4 sheets: mature/star miRNA counts, precursor cluster counts, sequence family counts, miRNA group definitions

source_name: normal human primary keratinocytes

extract_protocol:
TRIzol-based (see PMID: 24489795)
ligation/gel-based small RNA cDNA library (see PMID: 24489795)

value: skin

tag: grade

value: normal

tag: barcode


title: 1_S1_R1_001


title: 123520_NTSP3_1_H01

tag: strain

tag: days post whisker manipulation

value: single

tag: retro-labeled from pom

value: FALSE

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: sort date

tag: size factor

tag: total mrnas

tag: pseudotime

tag: state

value: Root


title: 123520_NTSP3_1_G11

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: Sex

tag: plate

tag: well

tag: celltype


title: SCC21_39

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: grade

tag: barcode


title: SCC21_38

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG


title: SCC21_37

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG

source_name: immortal non cancer human keratinocytes

tag: cell line

value: HaCaT

value: other


title: SCC21_36

description:
(Cancer Res 1983; 43: 5995-6011)
3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG

source_name: cell line

value: SCLII

value: SCC


title: 123520_NTSP3_1_G04

tag: strain

tag: days post whisker manipulation

tag: retro-labeled from pom

value: Unk

tag: animal id

tag: whiskers pulled


title: 123520_NTSP3_1_G03

tag: hemisphere (wrt whisker pull)

tag: sort date

tag: size factor

tag: total mrnas

tag: pseudotime


title: 123520_NTSP3_1_G02

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: Sex

tag: plate

tag: state


title: 123520_NTSP3_1_F10

tag: well

tag: celltype

value: VPM-only enriched


title: 123520_NTSP3_1_G05

tag: strain

value: VPM/POm


title: SCC21_35

description:
(Cancer Res 1983; 43: 5995-6011)
3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: cell line

value: SCLI

tag: grade

tag: barcode


title: 123520_NTSP3_1_H02

tag: days post whisker manipulation

tag: retro-labeled from pom

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

value: M

value: single cell


title: 123520_NTSP3_1_F08

tag: label (ntsr1 or ntsr1+retrobead)

tag: sort date

tag: size factor

tag: total mrnas

value: VPM-only

tag: pseudotime


title: SCC21_33

description:
(Br J Cancer 2006; 94: 1446-1451)
3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: 123520_NTSP3_1_F07

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

value: Mixed (including C57BL/6 and CD1)

tag: hemisphere

tag: Sex

tag: plate

tag: well

tag: state


title: 2_S2_R1_001

tag: treatment

value: IFNB

tag: tissue

value: Placenta

tag: tissue compartment

value: Chorionic villus

tag: gestational age

tag: tissue code

value: Male


title: 123520_NTSP3_1_F09

tag: strain

tag: days post whisker manipulation

value: single

tag: retro-labeled from pom

value: FALSE

tag: animal id

tag: whiskers pulled

tag: celltype

value: Root


title: SCC21_34

description:
(Br J Cancer 2006; 94: 1446-1451)
3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG

value: skin

tag: cell line

tag: grade

tag: barcode


title: SCC21_32

description:
(Cancer Res 1981; 41: 1657-1663)
3' adapter sequence: TAACGTCGTATGCCGTCTTCTGCTTG

value: SCC


title: SCC21_31

description:
(Cancer Res 1981; 41: 1657-1663)
3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG


title: 123520_NTSP3_1_F06

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

value: Unk

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

tag: sort date

tag: size factor

tag: total mrnas

tag: pseudotime


title: SCC21_30

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: tissue preparation


title: 123520_NTSP3_1_F04

tag: strain

tag: days post whisker manipulation

tag: retro-labeled from pom

tag: animal id

tag: well

tag: state


title: 123520_NTSP3_1_F05

tag: label (ntsr1 or ntsr1+retrobead)

tag: whiskers pulled

tag: celltype


title: 123520_NTSP3_1_G01

tag: hemisphere

tag: hemisphere (wrt whisker pull)

tag: Sex


title: SCC21_29

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG

tag: grade

tag: barcode


title: 123520_NTSP3_1_F03

tag: plate

tag: sort date

tag: size factor

tag: total mrnas

tag: pseudotime


title: 123520_NTSP3_1_F02

tag: strain

tag: days post whisker manipulation

tag: retro-labeled from pom


title: Protein deficiency and infected dam (G4_R4)

city: Sainte Anne de Bellevue

first: Manjurul

last: Haque

state: Quebec

address: Institute of Parasitology, Mac campus

department: Institute of Parasitology

country: Canada

institute: McGill University

data_processing:
BAM files obtained from Genome Quebec, McGill University, Canada
Htseq used for count of expressed gene
Genome_build: mm9
Supplementary_files_format_and_content: gene counts

source_name: 18 day old fetal brain

growth_protocol: Pregnant mice were purchased on gestation day 4 and kept in indivudual cages in 10 h dark and 14h light cycles

extract_protocol:
Commercial kit was used to extract the total RNA
By Genome Quebec, McGill University, Canada

treatment_protocol: On gestation day 5 mice were randoml assigned to two diet groups (protein suffieient and deficient) and two infection groups (sham and infected). Food was given ad libitum and infections were given on gestation day 5, 10 and 15

value: CD1 outbred

tag: maternal diet

value: Protein deficiency

tag: maternal infection

value: infected dam

tag: tissue

value: whole fetal brain


title: Protein deficiency and infected dam (G4_R3)


title: SCC21_28

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG

tag: tissue preparation


title: Protein deficiency and infected dam (G4_R1)


title: SCC21_26

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: SCC21_27

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: 123520_NTSP3_1_E12

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

tag: label (ntsr1 or ntsr1+retrobead)

tag: hemisphere

tag: animal id

tag: whiskers pulled

value: M

tag: well

tag: celltype

tag: state

value: VPM-only enriched

value: single cell


title: Protein deficiency and uninfected dam (G3_R3)

value: uninfected dam


title: Protein sufficient and infected dam (G2_R3)

value: Protein sufficient


title: SCC21_25

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG

tag: grade

tag: barcode


title: 123520_NTSP3_1_F01

value: Mixed (including C57BL/6 and CD1)

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

tag: sort date

tag: size factor

tag: total mrnas

value: VPM/POm

tag: pseudotime


title: Protein deficiency and uninfected dam (G3_R1)

tag: strain

tag: maternal diet

tag: maternal infection

tag: tissue


title: Protein sufficient and infected dam (G2_R1)


title: SCC21_23

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG

tag: tissue preparation


title: 123520_NTSP3_1_E09

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: single

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: well

value: VPM-only


title: 123520_NTSP3_2_F10

value: double

value: TRUE

value: FALSE

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

tag: celltype

tag: state

value: Root


title: Protein sufficient and infected dam (G2_R4)

tag: strain

value: CD1 outbred


title: Protein deficiency and infected dam (G4_R2)

tag: maternal diet

value: Protein deficiency


title: 123520_NTSP3_1_E08

value: Unk

tag: sort date

tag: size factor

tag: total mrnas

tag: pseudotime


title: 123520_NTSP3_1_E10

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)


title: Protein deficiency and uninfected dam (G3_R4)

tag: maternal infection

tag: tissue

value: whole fetal brain


title: SCC21_22

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG

value: skin

tag: tissue preparation

tag: grade

tag: barcode


title: SCC21_24

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: Protein sufficient and uninfected dam (G1_R4)


title: Protein sufficient and uninfected dam (G1_R2)


title: Protein sufficient and uninfected dam (G1_R3)


title: SCC21_21

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG


title: Protein deficiency and uninfected dam (G3_R2)


title: Protein sufficient and uninfected dam (G1_R1)


title: mouse upf1 depletion replicate 3

city: Santa Cruz

first: Manuel

last: Ares

state: CA

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.

tag: cell type


title: SCC1_9

value: SE


title: Bulk wt WGBS

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

address: 675 West 10th Avenue

department: Michael Smith Genome Sciences Centre

institute: BC Cancer Agency

description: Barcode: TTAGGC

library_source: genomic

data_processing:
The first 6 bases of read1 and read2 were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.143 using the parameters --clip_R1 6 --clip_R2 6 -paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), -a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ² 20), and -u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17.
Duplicates were marked using Picard (1.31) and removed. CpG methylation status was called using Samtools (0.1.13) mpileup and Novomethyl (1.01), according to the protocol specified by Novocraft (http://www.novocraft.com/documentation/novoalign-2/novoalign-user-guide/bisulphite-treated-reads/novomethyl-analyzing-methylation-status/). CHG and CHH calls were removed, as well as all CpG calls with <5 reads. The remaining CpG calls were converted into separate bigWIG files, containing per-CpG methylation and coverage, respectively.
Instructions for use of fastq files in readme.txt.
Genome_build: mm10
Supplementary_files_format_and_content: bw: coverage, number of methylated reads, percent methylation
Supplementary_files_format_and_content: tar.gz: compressed sets of adjacency data, by library and region type, in Rdata format (see supplementary materials of manuscript for code to use these to reproduce the figures)

molecule: genomic DNA

source_name: Bone marrow (femur, pelvis, tibia)

extract_protocol:
Bone marrow was harvested from the femur, tibia and pelvic bones of 8–10 week old, mixed sex C57BL/6 mice, pooled, and subjected to ammonium chloride mediated red blood cell lysis. The sample was stained with a Lineage/Sca1/Kit staining cocktail, and 10,000 Lin-Sca1+Kit- cells were FACS sorted into an Eppendorf tube, and DNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, 80204) according to manufacturer’s instructions.
4 uL of purified DNA (25 ng/uL) was mixed with 1 uL of T7 Phage Lambda DNA spikeins (1 ng/uL), and the mixture was used directly as input to bisulfite conversion and desulphonation as described for single-cells, except neither DNase nor UV decontamination was performed on the reagents, and 5 uL of beads was used instead of 1.8 uL. After bisulfite conversion and desulphonation, the DNA was eluted in 40 uL of EB buffer before used as input for one round of double-stranding with 2.5 uL of 10 mM dNTPs, 2 uL of 500 uM random hexamers, 1 uL of 50 U/uL Klenow exo- (NEB, M0212M) and 5 uL of 10X NEB Buffer 2. Library construction was the same for single-cells except only 4 rounds of PCR was used. Libraries were ran on agilent and sequenced directly without qPCR quality control.

value: Lin-Sca1+Kit- cells

tag: age

value: 8-10 week old


title: 123520_NTSP3_1_E05

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

value: M

tag: plate

tag: well

tag: celltype

value: single cell


title: Protein sufficient and infected dam (G2_R2)

tag: strain

tag: maternal diet

value: Protein sufficient

value: infected dam


title: SCC1_8

tag: tissue


title: 123520_NTSP3_1_E04

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: single

tag: sort date

tag: size factor

tag: total mrnas

value: VPM-only

tag: pseudotime

tag: state


title: mouse upf1 depletion replicate 1

tag: cell type


title: SCC1_7

tag: tissue preparation

tag: grade

tag: barcode


title: 123520_NTSP3_1_E03

tag: retro-labeled from pom

value: FALSE

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate


title: SCC1_6

tag: tissue

value: normal


title: mouse stau depletion replicate 1


title: mouse control replicate 3


title: 123520_NTSP3_1_E07

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: well

tag: sort date

tag: celltype

value: Root


title: SCC1_5

tag: tissue preparation


title: mouse control replicate 1

tag: cell type


title: 123520_NTSP3_1_E02

tag: size factor

tag: total mrnas

tag: pseudotime

tag: state


title: mouse control replicate 2


title: mouse upf1 depletion replicate 2


title: 123520_NTSP3_1_E06

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

tag: whiskers pulled


title: 123520_NTSP3_1_E01

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate


title: SCC1_4

description:
not included in analyses
3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: grade

tag: barcode


title: mouse stau depletion replicate 2


title: mouse stau depletion replicate 3


title: Jak1 wt_Sample 6

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Alignment was performed using the STAR aligner (version 2.3.0e) and mouse genome mm10 as reference.
Aligned results were annotated using the Refseq gene model and featureCounts program from the Subread package for gene level read count.
Genome_build: mm10
Supplementary_files_format_and_content: text file for gene read count

source_name: LT-HSC

extract_protocol:
Trizol
Standard poly-A v2 TruSeq RNA protocol

treatment_protocol: poly(I:C) injections; to induce gene deletion, 4 doses, 4-6 wks prior to BM harvest

tag: cre status

value: neg

tag: strain

value: Bone marrow


title: 123520_NTSP3_1_D11

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: Unk

tag: well

tag: sort date

tag: celltype


title: SCC1_3

value: skin

tag: tissue preparation


title: Jak1 wt_Sample 5


title: Jak1 KO_Sample 4

value: pos


title: Jak1 KO_Sample 5


title: SCC1_20

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG


title: Jak1 KO_Sample 2


title: Jak1 KO_Sample 3


title: Jak1 wt_Sample 4


title: 123520_NTSP3_1_D09

tag: retro-labeled from pom

tag: hemisphere

tag: size factor

tag: total mrnas

tag: pseudotime

tag: state

value: VPM-only enriched


title: 123520_NTSP3_1_D08

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate


title: Jak1 KO_Sample 1

tag: cre status

tag: strain

tag: tissue


title: SCC1_19

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG

tag: grade

tag: barcode


title: Jak1 wt_Sample 3


title: Jak1 KO_Sample 6


title: SCC1_18

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG

tag: tissue preparation


title: 123520_NTSP3_1_D06

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

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: well

tag: sort date

tag: celltype

value: VPM/POm


title: SCC1_17

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: Jak1 wt_Sample 2


title: SCC1_16

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: 123520_NTSP3_1_D07

tag: hemisphere

tag: animal id

value: M

tag: size factor

tag: total mrnas

tag: pseudotime

tag: state


title: 123520_NTSP3_1_D05

tag: strain

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

value: single cell


title: Jak1 wt_Sample 1

tag: cre status

tag: tissue


title: SCC1_15

description: 3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG

tag: tissue preparation

tag: grade

tag: barcode


title: 123520_NTSP3_1_D04

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: well

tag: sort date

tag: celltype


title: SCC1_14

description: 3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG


title: 123520_NTSP3_1_D03

tag: hemisphere

tag: animal id

tag: size factor

tag: total mrnas

tag: pseudotime

tag: state


title: 123520_NTSP3_1_D02

tag: strain

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate


title: SCC1_13

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: tissue preparation

tag: grade

tag: barcode


title: 123520_NTSP3_1_D01

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: well

tag: sort date


title: MCF7-shCTRL Rep3

description: UT_CTRL; ctrl4_CGGCTAT-CAGGACG

tag: cell line background

tag: genotype/variation

value: shCTRL

tag: cell type

value: ESA+CD24lowCD44+ cells


title: SCC1_11

description: 3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG

value: SE


title: 123520_NTSP3_1_C12

tag: strain

value: Mixed (including C57BL/6 and CD1)

value: single

tag: hemisphere

tag: animal id

tag: size factor

tag: total mrnas

tag: celltype

tag: pseudotime

tag: state


title: 123520_NTSP3_1_C10

value: FALSE

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

value: VPM-only


title: 123520_NTSP3_1_C11

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: well


title: SCC1_10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG

tag: tissue

tag: tissue preparation

tag: grade

tag: barcode


title: 123520_NTSP3_1_C08

tag: strain

tag: hemisphere

tag: animal id

tag: sort date

tag: size factor

value: Root


title: SCC1_1

value: normal


title: Old_3

first: Ryan

last: Molony

address: 300 Cedar Street

institute: Yale University

description: Sample 11

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim.
The trimmed reads were mapped to human genome (GRCh37) by tophat2.
The counts of reads for each gene were based on Ensembl annotation (release 70).
After the counts are collected, the differential expression analysis was done by DEseq2, which calculated the adjusted p-values.
Genome_build: GRCh37
Supplementary_files_format_and_content: normalized counts

source_name: Peripheral blood

extract_protocol:
Stimulated cells were washed once with PBS and were then lysed in RLT buffer (Qiagen) and this extract was stored at -80C. RNA was isolated from the lysate using the RNeasy Kit (Qiagen) according to standard manufacturer's protocols.
Library construction was completed by Hudson Alpha using a protocol for low input RNA-seq. Details from their website: "The GSL uses the Ovation RNA-Seq System V2 kit (Nugen) for initial RNA amplification which provides a fast and simple method for preparing amplified cDNA from total RNA for RNA-Seq applications. Our low input RNA-seq service requires 1ng-10ng of total RNA with a RIN score of 7.0 or higher. It allows amplification of both mRNA and non-polyadenylated transcripts. After purification, the cDNA is fragmented to the appropriate size and further library prep steps are followed to prepare sequencing library. There is no directional module available for this RNA-seq service."

treatment_protocol: Cells were transfected with our RIG-I specific ligand complexed with Lipfectamine 2000 for 6 hours prior to RNA collection.

tag: cell type

value: Peripheral Blood Monocytes

tag: donor age

value: Old (65-years)


title: 123520_NTSP3_1_C07

value: Unk

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: total mrnas

tag: celltype

tag: pseudotime

tag: state


title: 21656

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
We used Tophat2 to align RNA-seq reads to the human genome, using annotations of GENCODE as gene model.  HTSeq was used to quantify gene expression levels
Genome_build: hg19
Supplementary_files_format_and_content: raw count data matrix

source_name: buttock_skin biopsy_psoriasis

extract_protocol:
After local anaesthesia, five 6mm punch biopsies were obtained from each subject
Tissue was snap frozen in liquid nitrogen and stored at -80C until processing.  At processing samples were pulverized and RNA isolated using RNeasy kit (Qiagen).

tag: subject status

value: psoriasis patient

tag: patient id

tag: body part

value: buttock

tag: tissue

value: skin biopsy

tag: tissue type

value: psoriasis


title: 21658

source_name: thigh_skin biopsy_uninvolved

value: thigh

value: uninvolved


title: 21657

source_name: thigh_skin biopsy_psoriasis


title: SCC1_12

description: 3' adapter sequence: TAACGTCGTATGCCGTCTTCTGCTTG

value: skin

tag: tissue preparation

tag: grade

tag: barcode


title: 21655

source_name: back_skin biopsy_psoriasis

value: back


title: Old_2

description: Sample 4

tag: cell type


title: 21654

source_name: abdomen_skin biopsy_psoriasis

value: abdomen


title: 21653


title: 123520_NTSP3_1_C06

tag: strain

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

value: single

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

value: M

tag: plate

tag: well

tag: sort date

tag: size factor

value: VPM/POm

value: single cell


title: Old_1

description: Sample 3

value: Peripheral Blood Monocytes

tag: donor age


title: 21652

source_name: leg_skin biopsy_psoriasis

tag: subject status

tag: patient id

tag: body part

value: leg

tag: tissue


title: Young_2

description: Sample 2

value: Young (21-30 years)


title: 123520_NTSP3_1_C04

value: FALSE

value: Unk

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: total mrnas

tag: celltype

value: VPM-only

tag: pseudotime

tag: state

value: Root


title: 21650

value: psoriasis patient

value: skin biopsy

tag: tissue type

value: psoriasis


title: 123520_NTSP3_1_C05

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

tag: plate


title: 21649

source_name: arm_skin biopsy_psoriasis

tag: subject status

tag: patient id

tag: body part

value: arm


title: 123520_NTSP3_1_C03

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: well

tag: sort date

tag: size factor

value: VPM-only enriched


title: 21651

value: thigh

tag: tissue


title: 123520_NTSP3_1_D10

value: Mixed (including C57BL/6 and CD1)

value: single

tag: Sex

tag: total mrnas

tag: celltype

tag: pseudotime

tag: state


title: 21648

tag: tissue type

value: uninvolved


title: 123520_NTSP3_1_C02

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: hemisphere

tag: animal id

value: M

value: single cell


title: 12_RSS27a_CeLi02_12_1143_SE_IFNg_N702_S504

city: La Jolla

first: Cecilia

middle: Lindestam

last: Arlehamn

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy & Immunology (LJI)

data_processing:
Bulk RNA-seq data was mapped against the human hg19 reference using TopHat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: CD4+ memory T cells

extract_protocol:
Epitope-specific T cells were sorted based on IFNg production or expression of CD25 and OX40. RNA was purified using miRNAeasy micro kit from Qiagen.
Nextera XT DNA sample preparation kit and index kit from Illumina

tag: assay

value: IFNg capture

tag: epitope set

value: Type 2 (SE)


title: 21646

tag: subject status

tag: patient id

tag: body part


title: 11_RSS27a_CeLi02_11_1143_ML_IFNg_N702_S503

value: Type 1 (ML)


title: 123520_NTSP3_1_C01

value: FALSE

value: Unk

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

tag: plate

tag: well

tag: sort date

tag: size factor

value: VPM/POm


title: 21645

value: psoriasis patient

tag: tissue

tag: tissue type


title: 21643

source_name: buttock_skin biopsy_uninvolved

value: buttock

value: skin biopsy


title: 09_RSS27a_CeLi02_9_1145_ML_IFNg_N702_S517


title: 21644

value: arm

value: psoriasis


title: 123520_NTSP3_1_B12

tag: strain

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: total mrnas

tag: celltype

tag: pseudotime

tag: state

value: VPM-only enriched


title: 21642

tag: subject status

tag: patient id

tag: body part


title: 21641


title: 21638

value: thigh


title: 08_RSS27a_CeLi02_8_1155_ML_IFNg_N701_S508

tag: assay

tag: epitope set


title: Young_1

description: Sample 1

tag: cell type

value: Peripheral Blood Monocytes

tag: donor age

value: Young (21-30 years)


title: 21639

value: back

tag: tissue


title: 10_RSS27a_CeLi02_10_1145_SE_IFNg_N702_S502


title: 07_RSS27a_CeLi02_7_1143_SE_AIM_pos_N701_S507

value: Activation induced marker (AIM)


title: 21640

tag: tissue type


title: 123520_NTSP3_1_B10

tag: strain

value: Mixed (including C57BL/6 and CD1)

value: single

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

value: M

tag: plate

tag: well

tag: sort date

tag: size factor

value: VPM-only

value: Root

value: single cell


title: 21637

tag: subject status

value: psoriasis patient

tag: patient id

tag: body part


title: 21647

value: leg


title: 123520_NTSP3_1_B09

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

value: FALSE

value: Unk

tag: total mrnas

tag: celltype

tag: pseudotime

tag: state


title: 21635

value: abdomen

tag: tissue

value: skin biopsy

tag: tissue type

value: psoriasis


title: 123520_NTSP3_1_B11

tag: strain

tag: hemisphere

tag: animal id

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

value: VPM/POm


title: 06_RSS27a_CeLi02_6_1143_ML_AIM_pos_N701_S506

tag: assay

tag: epitope set

value: Type 1 (ML)


title: 21634

tag: subject status

tag: patient id

tag: body part

value: arm


title: 21636

value: back


title: 123520_NTSP3_1_B08

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: retro-labeled from pom

tag: plate

tag: well

tag: sort date

tag: size factor

tag: total mrnas


title: 123520_NTSP3_1_B07

tag: strain

value: single

tag: hemisphere

tag: animal id

tag: celltype

tag: pseudotime

tag: state


title: SCC1_2

tag: tissue

value: skin

tag: tissue preparation

tag: grade

value: normal

tag: barcode


title: 123520_NTSP3_1_B05

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex

value: M

value: VPM-only

value: Root


title: 03_RSS27a_CeLi02_3_1145_ML_AIM_pos_N701_S503

tag: assay

value: Activation induced marker (AIM)

tag: epitope set


title: 05_RSS27a_CeLi02_5_1155_SE_IFNg_N701_S505

value: IFNg capture

value: Type 2 (SE)


title: 04_RSS27a_CeLi02_4_1145_SE_AIM_pos_N701_S504


title: 02_RSS27a_CeLi02_2_1155_SE_AIM_pos_N701_S502


title: 123520_NTSP3_1_B04

tag: strain

tag: retro-labeled from pom

value: FALSE

value: Unk

tag: plate

tag: well

tag: sort date

tag: size factor

tag: total mrnas

value: single cell


title: 01_RSS27a_CeLi02_1_1155_ML_AIM_pos_N701_S517


title: siREST_N1 RNA-seq

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

data_processing:
Data generated with an Illumina HiSeq 2500 platform
Sequenced reads were trimmed for adaptor sequence with cutadapt and low quality bases (Q<20)  with prinseq
Mapping and count with Tophat
Count analysis with DESeq (Bioconductor)
Splicing  analysis with FARLINE pipeline (publication in progress)
genome build: hg19
processed data files format and content: excel file containing DESeq results
processed data files format and content: excel files containing splicing events differentially observed (events : acceptor, donor, mutually exclusive, multi exon skipping)

source_name: neuroblastoma cells

growth_protocol: Human SH-SY5Y neuroblastoma cell line (European Collection of Cell Cultures, ECACC) was cultured as recommended by the supplier.

extract_protocol: Total RNA were extracted 48h after transfection. cDNA synthesis was made from polyA-containing transcripts using Illumina's Stranded mRNA Sample Prep kit. High throughput sequencing of 100 bp paired-end reads was carried out on an Illumina HiSeq 2500 platform (Aros Applied Biotechnology, Aarhus, Denmark), generating an average number of 60 millions of mating pairs of reads.

treatment_protocol: Cells were transfected with Lipofectamine RNAiMax (Thermo Fisher Scientific) in standard conditions, with a total of 40 nM siRNA, as follows: 40 nM control siRNA, 20 nM siRNA-DDX5/DDX17 + 20 nM of control siRNA, 20 nM siRNA-REST + 20 nM of control siRNA, 20 nM siRNA-DDX5/DDX17 + 20 nM siRNA-REST.

tag: cell line

tag: cell type

value: neuroblastoma


title: 123520_NTSP3_1_B03

last: Goff

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

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.

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.

tag: hemisphere

tag: animal id

tag: celltype

tag: pseudotime

tag: state


title: 123520_NTSP3_1_B01

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex


title: 123520_NTSP3_1_B02

tag: strain

tag: retro-labeled from pom

tag: plate

value: VPM/POm


title: siPP_siREST_N1 RNA-seq


title: siREST_N2 RNA-seq


title: siPP_siREST_N2 RNA-seq


title: 123520_NTSP3_1_A12

tag: well

tag: sort date

tag: size factor


title: 123520_NTSP3_1_A07

tag: total mrnas


title: 123520_NTSP3_1_A11

tag: hemisphere


title: siPP_N1 RNA-seq

tag: cell line

tag: cell type


title: 123520_NTSP3_1_A09

tag: animal id

tag: celltype

tag: pseudotime


title: siCTL_N2 RNA-seq


title: siPP_N2 RNA-seq


title: 123520_NTSP3_1_A04

tag: days post whisker manipulation

tag: label (ntsr1 or ntsr1+retrobead)

tag: state


title: 123520_NTSP3_1_A05

tag: whiskers pulled

tag: hemisphere (wrt whisker pull)

tag: Sex


title: siCTL_N1 RNA-seq


title: 123520_NTSP3_1_A03

tag: strain

tag: retro-labeled from pom

tag: plate


title: 123520_NTSP3_1_A02

tag: well

tag: sort date

tag: size factor


title: 123520_NTSP3_1_A06

tag: hemisphere

tag: total mrnas


title: Combined A+B rep2

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

country: China

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
sequencing reads were processed to remove adaptors, and cleaned by Q30 value. Reads with >20% bases <Q30, and N base >10% were filtered. The remaining reads were further filtered if read length was >46 bp or <17 bp. The derived reads were mapped to miRBase v.21, Rfam 11.0, UCSC and pirnabank databases to annotate the composition of the small RNA population.
by mapping sequences from all the samples against all known miRNAs in miRBase v.21 and removing those with read number less than 10, in total 26,359,376 reads were retrieved. After further retaining reads found in both replicates for each treatment, 378 miRNAs belonging to 249 conserved miRNA families were obtained. We also implemented Mireap core algorithms (https://sourceforge.net/projects/mireap/) for the discovery of the new miRNAs.
using TargetScan, miRDB and miRanda algorithms, we predicted the target genes of all the identified miRNAs in our study, and retained 28 miRNAs with targets independently predicted via at least two algorithms.
all the identified targets were annotated by BlastX to NR, followed by GO term analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: spreadsheets include sequencing statistic, miRNA list, predicted miRNA target list, etc:
Supplementary_files_format_and_content: Suppl.Table 1.xlsx: statistics of sRNA sequences from human embryonic kidney 293 cells upon mycotoxin treatment
Supplementary_files_format_and_content: Suppl.Table 2.xlsx: conserved miRNAs identified from human embryonic kidney 293 cells upon mycotoxin treatment
Supplementary_files_format_and_content: Suppl.Table 3.xlsx: predicted novel miRNAs from human embryonic kidney 293 cells upon mycotoxin treatment
Supplementary_files_format_and_content: Suppl.Table 4.xlsx: differentially expressed miRNAs identified from human embryonic kidney 293 cells upon mycotoxin treatment
Supplementary_files_format_and_content: Suppl.Table 5.xlsx: predicted targets for all differentially expressed miRNAs upon mycotoxin treatment
Supplementary_files_format_and_content: Suppl.Table 6.xlsx: GO enrichment analysis for targets of differentially expressed miRNAs upon mycotoxin treatment

source_name: embryonic kidney cells

growth_protocol: HEK 293 cells (purchased from ATCC) were grown in DMEM medium containing glutamine and supplemented with 10% fetal bovine serum.

extract_protocol:
HEK293 cells were washed by PBS, then centrifuged at 800 rpm for 5 min.
15 μg of total RNA for each sample was used for the construction of libraries using a Small RNA Library Preparation kit (Illumina Inc., San Diego, CA, USA) according to the manufacturer’s protocol. Each library was barcoded with different indices and stored in a −80 °C freezer before sequencing. Sequencing was performed in a v3 flowcell on an Illumina HiSeq 2500 sequencer, generating SE:1×50bp reads.

treatment_protocol: HEK293 cells were seeded in 96-well plates at concentration of 8*103 cells/well, and incubated for 24 h at 37 °C and 5 % CO2, then treated by the mycotoxins with doses series till 48h.

tag: cell line

value: HEK 293

tag: cell type

value: embryonic kidney cells

tag: treatment

value: cells treated by Citrinin and Ochratoxin A after 48h


title: 123520_NTSP3_1_A01

city: Baltimore

first: Loyal

value: Mixed (including C57BL/6 and CD1)

tag: days post whisker manipulation

value: single

tag: animal id

tag: celltype

tag: pseudotime


title: Mycotoxin B rep2

description: small RNA

value: cells treated by Ochratoxin A after 48h


title: 2i ES XX rep1

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

data_processing:
RNA-seq reads were aligned to the UCSC mouse genes (mm9) using Tophat (version 2.0.13). Only the uniquely mapped reads were retained for analysis in this study.
We used Cuffdiff (version 2.2.1) to calculate the expression abundance of each gene as fragments per kilobase per million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tab-delimited file showing gene expresssion levels with FPKM.

source_name: 2i cultured embryonic stem cells (XX)

growth_protocol: ESC XX derived from Oct-GFP (C57) background and maintained in ES medium contains DMEM (Merck Millipore) supplemented with 15% (v/v) fetal bovine serum (HyClone), 1 mM L-glutamine (Merck Millipore), 0.1 mMmercaptoethanol (Merck Millipore), 1% nonessential amino acid stock (Merck Millipore), penicillin/streptomycin (100×, Merck Millipore), nucleosides (100×, Merck Millipore), and 1000 U/ml LIF (Merck Millipore),and 2i.

extract_protocol:
The cells used for RNA-seq were collection after feeder-free treatment and washed by DPBS.RNA were exstracted by QIAGEN Allprep DNA/RNA mini Kit.
RNA libraray were constructed used KAPA stranded mRNA-seq kit illumina platform and sequenced at the Berry genomic corporation.

tag: tissue

value: 2i cultured embryonic stem cells (XX)


title: Mycotoxin A rep1

description: small RNA

value: cells treated by Citrinin after 48h


title: CK rep1

description: small RNA

value: normal cells


title: VMH-D-Fed-127

description:
laser-captured hypothalamic nucleus (region)
cpm_del.txt

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts per Million (CPM) matrix in tab-delimited text

source_name: ventromedial nucleus

extract_protocol:
Hypothalamic nuclei were laser-capture microdissection from cryosections using a P.A.L.M Microlaser system, and RNA extracting using the miRNeasy micro RNA extraction kit (Qiagen).
Total RNA was amplified using an Ovation RNA-Seq System V2 (NuGEN), after which cDNA libraries were prepared using the Encore Rapid DR Multiplex System (NuGEN).

treatment_protocol: Male mice with a paternal Snord116 deletion (B6(Cg)-Snord116tm1.1Uta/J - JAX stock no 008149) were either ad-libitum fed or fasted for 24-hours prior to brain dissection.

tag: nutritional state

value: Fed

tag: batch


title: RNA-Seq GD16 Index23

city: Neuherberg

first: Steffen

last: Sass

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

description:
long-coding and non-coding RNA
expression_mrna.tsv

data_processing:
Adapter trimming using trim_galore / cutadapt v 0.4.0 using standard settings for illumina reads
Read mapping using STAR aligner v 2.4.1d against hg38 genome using standard settings
Overlap of aligned reads with RefSeq gene annotations (Feb 2016) obtained from UCSC. MiRNA annotations were obtained from miRbase Release 21
log2-counts per million (logCPM) were generated from resulting raw read counts using voom (R package limma version 3.24.15)
Genome_build: hg38
Supplementary_files_format_and_content: expression_mrna.tsv and expression_mirna.tsv: tab-separated text files

source_name: whole blood cells

extract_protocol:
Whole blood was collected in PAXgene Blood RNA Tubes (PreanalytiX) after overnight fasting. Next, total RNA was isolated using the Paxgene Blood miRNA kit (PreanalytiX) according to the manufacturer’s specifications.
NEBNext small RNA library Prep Set for Illumina and NuGen Ovation RNA-Seq system v2 were used according to the manufacturer’s recommendations to generate small and long RNA-Seq libraries.

tag: health status

value: GDM

tag: individual id


title: VMH-D-Fed-308

first: Brian

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

institute: University of Cambridge

tag: strain


title: RNA-Seq GD15 Index22

value: NGT


title: Combined A+B rep1

description: small RNA


title: VMH-D-Fed-313


title: VMH-D-Fast-85

value: Fast


title: CK rep2

description: small RNA


title: VMH-D-Fed-125


title: VMH-D-Fed-111


title: VMH-D-Fast-311


title: RNA-Seq GD13 Index20


title: RNA-Seq GD11 Index11


title: Mycotoxin A rep2

description: small RNA


title: RNA-Seq GD10 Index10


title: 2i ES XX rep2


title: VMH-D-Fast-100


title: RNA-Seq GD9 Index9


title: PVN-D-Fed-92

source_name: paraventricular nucleus


title: Mycotoxin B rep1

description: small RNA


title: VMH-D-Fast-305


title: RNA-Seq GD7 Index7


title: RNA-Seq GD8 Index8


title: RNA-Seq GD14 Index21


title: VMH-D-Fast-86


title: PVN-D-Fed-308


title: RNA-Seq GD4 Index4


title: RNA-Seq GD5 Index5


title: RNA-Seq GD12 Index12


title: PVN-D-Fed-127


title: RNA-Seq GD3 Index3


title: RNA-Seq GD2 Index2


title: PVN-D-Fast-86


title: VMH-D-Fast-101


title: PVN-D-Fed-125


title: PVN-D-Fast-85


title: RNA-Seq GD1 Index1


title: sncRNA-Seq GD16 Index16

description:
sncRNA
expression_mirna.tsv


title: PVN-D-Fed-111


title: PVN-D-Fast-101


title: PVN-D-Fast-305


title: sncRNA-Seq GD15 Index15

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD14 Index14

description:
sncRNA
expression_mirna.tsv


title: DMH-D-Fed-92

source_name: dorsomedial nucleus


title: sncRNA-Seq GD13 Index13

description:
sncRNA
expression_mirna.tsv


title: RNA-Seq GD6 Index6


title: sncRNA-Seq GD11 Index11

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD12 Index12

description:
sncRNA
expression_mirna.tsv


title: PVN-D-Fed-313


title: sncRNA-Seq GD10 Index10

description:
sncRNA
expression_mirna.tsv


title: PVN-D-Fast-311


title: DMH-D-Fed-313


title: DMH-D-Fed-308


title: sncRNA-Seq GD8 Index8

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD7 Index7

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD9 Index9

description:
sncRNA
expression_mirna.tsv


title: DMH-D-Fed-111


title: sncRNA-Seq GD6 Index6

description:
sncRNA
expression_mirna.tsv


title: DMH-D-Fed-127


title: DMH-D-Fast-311


title: DMH-D-Fast-86


title: PVN-D-Fast-100


title: DMH-D-Fast-305


title: sncRNA-Seq GD5 Index5

description:
sncRNA
expression_mirna.tsv


title: DMH-D-Fast-100


title: DMH-D-Fast-101


title: sncRNA-Seq GD4 Index4

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD2 Index2

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD1 Index1

description:
sncRNA
expression_mirna.tsv


title: sncRNA-Seq GD3 Index3

description:
sncRNA
expression_mirna.tsv


title: ARC-D-Fed-308

source_name: arcuate nucleus


title: ARC-D-Fed-125


title: ARC-D-Fed-127


title: PBMCs sample_PCH007RP

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

data_processing:
The raw RNA-Seq reads for each sample were aligned to the reference human genome (hg19) using Bowtie as the short read aligner, and splice junctions were identified using TopHat
Estimation of Transcript abundance was estimated at the level of the whole gene as counts per million (cpm) values using the tool htseq-count of the open source python package HTSeq (Andres et al. 2015).
The final dataset consists of 55 RNAseq single end 100bp samples with a total of 13,282 genes that had a cpm of 1 or more in at least 3 of the samples.
cpm values were normalized using the Trimmed of the M-values (TMM) procedure with the edgeR package from Bioconductor and transformed to logarithm base 2.
Genome_build: hg19
Supplementary_files_format_and_content: excel file include normalize expression values matrix for all samples

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
Whole blood mRNA was extracted using TempusTM Blood RNA Tube isolation kits provided by the manufacturer Applied Biosystems, and the quality was determined based on the Agilent Bioanalyzer 2100 RNA Integrity score (RIN).
Illumina RNA seq kit was used for sequence library preparation using the Illumina TruSeq RNA Sample Prep Guide: Low Throughput (LT) Protocol.

value: blood

value: PBMC

tag: gender

value: F

tag: age

tag: time

value: PreChallenge

tag: group

value: RASP

tag: protected/suceptibible/duffy

value: Protected


title: PBMCs sample_PCH025RP

tag: cell type


title: PBMCs sample_PCH001RP


title: ARC-D-Fast-86

city: Cambridge


title: PBMCs sample_PCH012RP


title: DMH-D-Fed-125


title: ARC-D-Fed-111


title: PBMCs sample_PCH026RNS

value: RASNP


title: PBMCs sample_PCH017RNP

value: M

value: Suceptible


title: PBMCs sample_PCH021RNP


title: ARC-D-Fast-100