title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell151


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell144

status: Public on Mar 08 2017

type: SRA

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

library_source: transcriptomic

data_processing:
Map read-pairs to the Mouse genome (Grcm38) with TopHat2
Quantify gene expression with HTSeq v0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated values with read cunt for each gene and each cell. The first column contain the Ensembl gene identifier, the first row contains the cell identifier.

molecule: polyA RNA

organism: Mus musculus

source_name: Whole cortex

extract_protocol:
Single cell were captured and RNA extracted on a C1 system, Fluidigm on a 5-10um chip, following manufacturer protocol. Lysis, reverse transcription and PCR were then performed directly on the chip using SMARTer Ultra Low RNA Kit for the C1 System (#634833,Takara® Clontech®). about 0.8 ng / ml per cell.
Illumina Nextera XT kit

tag: age


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell155


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell148


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell142


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell146


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P5, cell149


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell143


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell141


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell140


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell147


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell138


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell139


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell137


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell134


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell135


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell133


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell132


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell131


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell129


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell128


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell127


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell130


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell126


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell125


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell123


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell124


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell121


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell120


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell122


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell119


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell116


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell117


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell118


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell115


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell112


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell113


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell114


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell111


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell108


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell105


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell106


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell110


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell109


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell100


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell101


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell107


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell136


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell104


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell96


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell97


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell94


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell93


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell92


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell95


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell89


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell86


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell88


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell87


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell84


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell85


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell83


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell90


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell80


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell82


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell81


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell103


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell102


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell99


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell98


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell77


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell78


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell75


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell76


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell73


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell69


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell71


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell72


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age P2, cell91


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell68


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell66


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell65


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell63


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell64


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell61


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell67


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell60


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell58


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell79


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell59


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell55


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell57


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell74


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell53


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell54


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell51


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell52


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell56


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell48


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell50


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell70


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell46


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell47


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell45


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell43


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell42


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell41


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell62


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell37


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell38


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell40


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell36


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell35


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell39


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell34


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell32


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell31


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell30


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell29


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell27


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell26


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell25


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell49


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell28


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell22


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell24


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell21


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell44


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell20


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell18


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell19


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell23


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell16


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell17


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell13


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell15


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell12


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell14


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell10


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell9


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell11


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell8


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell7


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell33


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell5


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell6


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell4


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell3


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell2


title: Transcriptome of a single cell FACS sorted on GFP-Htr3a at age E18, cell1


title: Ly49G+ve/Ly49I-ve NK Rep 1

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

country: USA

institute: NIH

data_processing:
A bioinformatics pipeline built on RTA version 1.13.48 and CASAVA 1.8.2 software (Illumina) was used.
Raw Fastq files were aligned to mouse genome (mm10) using STAR (v. 2.3.0) followed by Rsubread and limma-voom to find differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, limma-voom processed data

molecule: total RNA

source_name: Sorted spleen NK cells

extract_protocol:
Single cell suspensions were prepared from the spleens of 20 C57Bl/6Ncr mice.  NK cells were enriched using the MACS NK Cell purification system (Miltenyi Biotec).  The Fc receptors of the resulting populations of enriched NK cells were blocked with 2.4G2 and the cells were stained with antibodies to CD3, NK1.1 (eBioscience), Ly49G2 (4D11), and Ly49C/I (5E6).  CD3-, NK1.1+,Ly49G+, Ly49C/I- and CD3-, NK1.1+,Ly49G-, Ly49C/I+ cells were sorted on a FACS Aria (BD Biosciences).
Stranded RNA-seq libraries were constructed from 0.4 µg total RNA using the TruSeq Stranded Total RNA Sample Prep Kits (Illumina).
Equal volumes of individual libraries were pooled and run on a MiSeq benchtop DNA sequencer (Illumina).  The libraries were then repooled to equimolar concentrations based on the MiSeq demultiplexing results. The final pooled library was sequenced on a HiSeq2000 sequencer (Illumina) using TruSeq Version 3 chemistry. A minimum of 40 million 100 base read pairs were generated for each library.

tag: cell type

value: Mature Ly49-positive splenic NK cell

tag: strain

value: 6-8 weeks


title: Ly49I+ve/Ly49G-ve NK Rep 3


title: Ly49I+ve/Ly49G-ve NK Rep 2


title: Ly49I+ve/Ly49G-ve NK Rep 1


title: Ly49G+ve/Ly49I-ve NK Rep 3


title: Ly49G+ve/Ly49I-ve NK Rep 2


title: F18G4_1NP

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: library strategy: DNA-seq

library_source: genomic

data_processing:
Basecalls were made using RTA version 1.17.21.3, with default filter and quality settings. The reads were demultiplexed (allowing 0 or 1 mismatches in the index sequence) with CASAVA 1.8.2
Reads were mapped to the mm9 genome assembly using bowtie v2.0.5 with all default settings. Non-unique reads or reads with low mapping quality were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command.
Samples were checked for contamination using fastq_screen v0.4.2. Samples with <15% of reads mapped or with more than 20% of reads mapped to the Human hg19 reference were excluded from further processing (but are included in this submission).
Coverage depth of each sample in 30kb windows was calculated using bedtools v2.17 and the command “multiBamCov -bed <(bedtools makewindows -w 30000 -g mm9.chrom.sizes)”. Each 30kb window was then called as positive or negative using a custom python script.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix files (ending .txt.gz) are tab-delimited tables containing one row/column per genomic locus, where the score in each cell of the matrix indicates the strength of the interaction between the corresponding two genomic loci. Segmentation files contain one row for every genomic locus, and one column for every raw data file which passed QC parameters, with the values representing the segmentation score for each sample at that genomic location.

molecule: genomic DNA

source_name: Mouse ES Cells

growth_protocol: Cells were grown at 37°C in a 5% CO2 incubator in Glasgow Modified Eagles Medium, supplemented with 10% fetal bovine serum, 2 ng/ml LIF and 1 mM 2-mercaptoethanol, on 0.1% gelatin-coated dishes. Cells were passaged every other day. After the last passage 24h before harvesting, ES cells were re-plated in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.)

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 13


title: F18D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 13


title: F18E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 13


title: F18D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 13


title: F18F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 13


title: F18E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 13


title: E1_positive_control

description: library strategy: DNA-seq

extract_protocol: Library was prepared according to Illumina's instructions accompanying the TruSeq DNA kit (Part# 15025064). Illumina TruSeq index AD005 was used to multiplex this library. The index barcode was ACAGTG(A).


title: F18F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 13


title: F18F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 13


title: F18E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 13


title: F18F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 13


title: F18G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 13


title: F18C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 13


title: F18C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 13


title: F18C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 13


title: F18C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 13


title: F18B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 13


title: F18B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 13


title: F18B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 13


title: F18G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 13


title: F18B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 13


title: F18E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 13


title: F18A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. AGCGATAG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 13


title: F18D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 13


title: F18A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCTCGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 13


title: F18D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 13


title: F18A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGCGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 13


title: F17G6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F18A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGGCTATG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 13


title: F17G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F17F7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F17G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F17E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17E7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F17G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 12


title: F17E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17C7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 12


title: F17D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 12


title: F17E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 12


title: F17D7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: F17B7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: F17C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: F17B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F17C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: C rep1

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

data_processing:
We processed our data according to the procedures described in Li et.al by ACGT101-miR v4.2 (LC Sciences). The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3); then, the dataset was further processed with an in-house program named ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA and snoRNA) and repeats.
Supplementary_files_format_and_content: Excel file with miRNA name, sequence, normalized read counts and statistical analysis.

organism: Gallus gallus

source_name: testis

extract_protocol:
Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions.
Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: A total of 80 one-day-old Cobb500 breeder cocks were randomly assigned to two groups with five replicates per treatment and 8 birds per replicate based on a single factor experimental design, including two treatments: control and dietary APS supplements (10 g/kg). The chickens in control group (C group) were fed with corn soybean diet, and 10 g APS per kilogram fodder were added to the feed of APS group (A group). Six testes samples from three replicates were selected randomly for next generation sequencing analysis of miRNAs.

tag: breed

value: 40 week

tag: tissue

value: testis

tag: treatment

value: without dietary Astragalus Polysaccharide supplement


title: C rep3


title: T rep3

value: with dietary Astragalus Polysaccharide supplement


title: C rep2


title: T rep2


title: F17B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F17B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F17B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F17A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCTCGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17A7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 12


title: F17A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TAATGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CTGAAGCT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 12


title: F17C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGGCTATG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: F16G6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: F16G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: F17B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F17B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGCGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 12


title: F16G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: F16G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: T rep1

extract_protocol:
Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions.
Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.


title: F16F7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: F16F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: F16F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: F16G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: F16G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-wt_7

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

data_processing:
reads were mapped using Tophat 2.0.6 and Bowtie2
alignment was filterd for mapping quality (samtools view -q 255) and all reads mapping to the mitochondrial genome were removed
readcounts were retrieved using BEDtools intersectBED
differential gene expression analysis was performed using the R-package Deseq
Genome_build: mm9
Supplementary_files_format_and_content: read counts are provided as matrix for all samples in a space delimited text file

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions

value: 6 months

value: Liver

tag: genotype/variation

tag: diet

value: semisynthetic diet


title: Ldlr-Mc4r_semi_wt-wt_6


title: F16F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-wt_9


title: F16F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: F16F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-wt_4


title: F16E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: F16E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-wt_3


title: Ldlr-Mc4r_semi_wt-wt_2


title: Ldlr-Mc4r_semi_wt-wt_1


title: F16E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: F16E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: F16E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: F16E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_9


title: F16D7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: F16E7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_8


title: F16F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_7


title: Ldlr-Mc4r_semi_wt-wt_8


title: F16D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: F16D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: F17C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. AGCGATAG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 12


title: F16D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: F16D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: F16D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-wt_5

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions


title: Ldlr-Mc4r_semi_wt-ko_4


title: Ldlr-Mc4r_semi_wt-ko_3


title: Ldlr-Mc4r_semi_wt-ko_5


title: F16C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: F16C7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_1


title: Ldlr-Mc4r_semi_ko-wt_9


title: Ldlr-Mc4r_semi_wt-wt_10


title: F16C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: F16C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_10


title: Ldlr-Mc4r_semi_ko-wt_8


title: Ldlr-Mc4r_semi_ko-wt_7


title: F16C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: F16C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_wt-ko_6


title: Ldlr-Mc4r_semi_ko-wt_6


title: F16C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-wt_5


title: F16B7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-wt_4


title: Ldlr-Mc4r_semi_ko-wt_3


title: F16B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: F16B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-wt_1


title: Ldlr-Mc4r_semi_ko-wt_2


title: F16B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_9


title: F16B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-wt_10


title: F16A7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 11


title: F16B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_8


title: F16A6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAATTCGT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_7


title: F16A5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTCAGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_6

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions


title: Ldlr-Mc4r_semi_ko-ko_4


title: F16A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. CGCTCATT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: F16A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. TCCGGAGA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_5


title: Ldlr-Mc4r_semi_ko-ko_3


title: Ldlr-Mc4r_semi_ko-ko_2


title: F16A1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. ATTACTCG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: F16A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_semi_ko-ko_1


title: F15H7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_semi_ko-ko_10


title: F16B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 11


title: F15H3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_9

value: regular chow


title: F15H5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_8


title: F15H1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_7


title: Ldlr-Mc4r_chow_wt-wt_6


title: F15G8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: F15G6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_5


title: F15G7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_4


title: F15G5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_2


title: F15G4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: F15G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_3


title: Ldlr-Mc4r_chow_wt-wt_1


title: F15G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-wt_10

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions


title: F16D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F7. GAGATTCC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 11


title: Ldlr-Mc4r_chow_wt-ko_8


title: Ldlr-Mc4r_chow_wt-ko_7


title: F15F8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: F15G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 10


title: F15F7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-ko_9


title: Ldlr-Mc4r_chow_wt-ko_6


title: F15F6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-ko_5


title: F15F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: F15F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-ko_3


title: Ldlr-Mc4r_chow_wt-ko_4


title: Ldlr-Mc4r_chow_wt-ko_2


title: F15F5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: F15E7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: F15E8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_9


title: Ldlr-Mc4r_chow_wt-ko_10


title: F15E6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_8


title: F15E5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: F15E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_6


title: Ldlr-Mc4r_chow_ko-wt_3


title: F15E1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_5


title: F15F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_2


title: F15D8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_4

extract_protocol:
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions


title: F15D7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-wt_1


title: Ldlr-Mc4r_chow_ko-ko_9


title: Ldlr-Mc4r_chow_ko-wt_10


title: F15F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 10


title: F15D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_wt-ko_1


title: Ldlr-Mc4r_chow_ko-ko_8


title: F15D6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-ko_6


title: Ldlr-Mc4r_chow_ko-ko_7


title: Ldlr-Mc4r_chow_ko-wt_7


title: F15D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: F15D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: F15D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-ko_5


title: F15E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: F15C8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: F15E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-ko_4


title: F15C7_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CTGAAGCT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: F15C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: F15C6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: F15C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-ko_3


title: Ldlr-Mc4r_chow_ko-ko_2


title: Ldlr-Mc4r_chow_ko-ko_10


title: F15D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 10


title: Ldlr-Mc4r_chow_ko-ko_1


title: F15C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: MBNL3-Knockdown

city: Shanghai

first: Ji-hang

last: Yuan

address: 800 Xiangyin Road

department: Department of Medical  Genetics

institute: Naval medical university

data_processing:
The samples were paired-end sequenced with a read length of 100 bp on an Illumina HiSeq 2500 sequencer.
Sequencing reads were mapped against the human reference genome version 19 using the TopHat algorithm version 2.0.9.
After alignment to the genome, the expression level of genes was determined based on the value of FPKM which was calculated by cuffdiff (version: 2.1.1).
Genome_build: human reference genome version 19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values and counts for each Sample.

organism: Homo sapiens

extract_protocol:
Total RNA was harvested from the cells using Trizol reagent. TruSeq Stranded Total RNA Library Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SMMC-7721 cells were stably transfected with MBNL3 shRNA expression vector or control.

tag: cell line

value: HCC cells SMMC-7721


title: F15C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: F15B8_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TAATGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: F15C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTACTCG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 10


title: ChIP:LMO1_A300-314A_Jurkat_103014

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: LMO1 (Bethyl Labs, A300-314A)

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 46
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: T-ALL

growth_protocol: T-ALL cell lines were cultured in RPMI-1640 medium supplemented with 10% FBS, L-glutamine, and penicillin/streptomycin (Invitrogen).

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: Jurkat


title: 293FT 100 cells 27mer location 293FT27

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

description:
gene_counts.csv
mature_miRNA_counts.csv
MIR_differential_expression_PSCvs293.csv
protein_coding_differential_expression_PSCvs293.csv

data_processing:
The raw sequencing data were processed through FASTQ Groomer using the basic options on the Galaxy website (Blankenberg et al., 2010). Reads with more than 8 As at the 3’ ends were selected for further analyses, and the A tails were clipped away using FASTQ/A Clipper (Patel and Jain, 2012). The filtered reads were aligned to human genome assembly version GRCh38 using STAR aligner (Dobin et al., 2013) with the following parameters:  --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterMatchNminOverLread 0.95 --outFilterType BySJout --outFilterMatchNmin 18. The aligned reads were assigned to the GENCODE v22 features and counted with Bedtools (Quinlan and Hall, 2010) while the strandedness was taken into account.
The mature-miRNA reads were defined by those only alingned to mature miRNA but not to primary miRNA transcripts of hsa.gff3 in miRBase 21.
The differential expression was performed with DESeq package for genes with read sums >1 across samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts.csv read counts by gene_id
Supplementary_files_format_and_content: mature_miRNA_counts.csv read counts by accession # of miRNA
Supplementary_files_format_and_content: MIR_differential_expression_PSCvsEND.csv differential expression by DESeq2
Supplementary_files_format_and_content: MIR_differential_expression_PSCvs293.csv differential expression by DESeq2
Supplementary_files_format_and_content: protein_coding_differential_expression_PSCvs293.csv differential expression by DESeq2

source_name: 293FT cells

extract_protocol:
The cells were either diluted into phosphate buffer saline (PBS) with 0.1% polyvinyl alcohol (PVA) before lysis or sorted directly into a lysis buffer .
After incubation at 37°C for 30 minutes and inactivating proteinase K, the lysate was polyadenylated in a final 4 µl of 1X PAP mixture (37°C for 15 minutes, 45°C for 5 minutes, 55°C for 5 minutes, and 65°C for 20 minutes). After supplementing 0.5 µl of 20 µM i7T20V oligo, the reaction was heated at 75°C for 1 minute and cooled back to 42°C. 5.5 µl of RT mixture were added to final 1X, and then the mixture was incubated at 42°C for 90 minutes and 70°C for 15 minutes. If further preamplification was required, the cDNA was added to 40 µl of preamplification mixture. The thermal cycling were performed with initial denaturation at 98°C for 1 minute followed by cycles at 98°C for 10 seconds, 65°C for 15 seconds, and 72°C for 1 minute, with a final extension at 72°C for 10 minutes.   The cDNA from RT reaction/preamplification, or eluted DNA from size selection was concentrated with carboxylated beads and PEG/NaCl (Rohland and Reich, 2012). Briefly, 1 µl of magnetic beads and 3 volumes of PEG/NaCl solution were mixed with the solution containing DNA. The mixtures were left at ambient temperature for 15 minutes. After being washed two times with freshly prepared 80% ethanol, the beads were dried at ambient temperature for 15 minutes on a magnetic stand and eluted with 0.1% Triton X-100 for another 15 minutes at ambient temperature.  After preamplification and concentration with PEG/NaCl, the cDNA was run in 6% denaturing PAGE and stained in a 1X TBE buffer containing 1X SYBR GOLD for 20 minutes. After visualization and size-selection, the gel pieces were crushed by spun through a 0.5 ml microtube with a pinhole at the bottom and soaked in 300 µl of 10 mM Tris 8.0, 300 mM NaCl, and 1 mM EDTA at ambient temperature overnight. After concentration with PEG/NaCl, the eluted cDNA was appended with P5 and P7 adapters by 10 cycles of PCR with KAPAHiFi DNA polymerase (conditions identical to preamplification, except P5PCRIIA and N7xx were used as primers). After another round of PEG/NaCl to remove primers, equal amounts of the indexed libraries were mixed for sequencing with the Illumina Hiseq 2500 system.

value: human embyronic kidney cells


title: F15B6_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAATTCGT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: 293FT 100 cells low 293FTL


title: 293FT 100 cells 21mer location 293FT21


title: F15B5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: F15B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. GAGATTCC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: 293FT 100 cells middle 293FTM


title: F15B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. CGCTCATT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10


title: F15B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq Nano kit (Part# FC-121-4003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F8. TCCGGAGA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 10