title: F9C5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 6


title: miRNA294_66 rep1

status: Public on Mar 08 2017

type: SRA

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

library_source: transcriptomic

data_processing:
Reads were aligned and assigned to Gencode Mouse released M4 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: GenCode Mouse released M4
Supplementary_files_format_and_content: tab-delimited text files include raw counts and  RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: ESCs were grown in DMEM, 15% FBS, LIF, and 2i (PD0325901 and CHIR99021)

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit

treatment_protocol: Cells were transfected using Dhamafect 1 transfection reagent  (Dharmacon, GE Health) following manaufacturer's instructions

tag: cell type

value: embryonic stem cells

tag: genotype

value: Dgcr8-/- plus miR-294


title: F8F1_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 F3. ATTACTCG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5

tag: strain


title: F8E6_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 F3. GAATTCGT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: F8F4_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 F3. GAGATTCC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5


title: miRNA294_55 rep1


title: F8E5_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 F3. ATTCAGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: F9D5_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. TCTCGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 6


title: F8E3_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 F3. CGCTCATT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: miRNA294_52 rep1


title: miRNA294_51 rep1


title: miRNA294_62 rep1


title: F8G2_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 F3. TCCGGAGA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 5


title: F8G3_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 F3. CGCTCATT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 5


title: miRNA294_61 rep1


title: F8F2_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 F3. TCCGGAGA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5


title: F8E1_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 F3. ATTACTCG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: miRNA294_49 rep1


title: F8D6_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 F3. GAATTCGT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: F8E4_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 F3. GAGATTCC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: F8D5_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 F3. ATTCAGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: miRNA294_5 rep1


title: F8D4_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 F3. GAGATTCC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: miRNA294_44 rep2


title: F8D3_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 F3. CGCTCATT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: miRNA294_58 rep1


title: miRNA294_57 rep1


title: miRNA294_53 rep1


title: miRNA294_44 rep1


title: F8D2_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 F3. TCCGGAGA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: F8D1_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 F3. ATTACTCG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 5


title: miRNA294_41 rep2

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: miRNA294_42 rep1


title: F8C5_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 F3. ATTCAGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: F8C6_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 F3. GAATTCGT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: miRNA294_41 rep1


title: F8C3_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 F3. CGCTCATT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: miRNA294_40 rep1


title: F8C4_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 F3. GAGATTCC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: miRNA294_39 rep1


title: F8C2_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 F3. TCCGGAGA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: F8E2_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 F3. TCCGGAGA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 5


title: F8C1_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 F3. ATTACTCG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 5


title: miRNA294_48 rep1


title: miRNA294_4 rep1


title: F8F6_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 F3. GAATTCGT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 5


title: F8B6_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 F3. GAATTCGT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: miRNA294_38 rep1


title: miRNA294_37 rep1


title: F8B4_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 F3. GAGATTCC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: miRNA294_33 rep2


title: F8B2_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 F3. TCCGGAGA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: F8B5_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 F3. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: F8B3_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 F3. CGCTCATT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: miRNA294_35 rep1


title: miRNA294_32 rep2


title: F8B1_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 F3. ATTACTCG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 5


title: F8A6_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 F3. GAATTCGT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: miRNA294_32 rep1


title: miRNA294_31 rep1


title: F8A5_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 F3. ATTCAGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: miRNA294_30 rep2

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F8A3_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 F3. CGCTCATT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: miRNA294_31 rep2


title: F8A4_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 F3. GAGATTCC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: miRNA294_30 rep1


title: miRNA294_29 rep2


title: F7G4_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 F2. TCCGCGAA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 4


title: miRNA294_33 rep1


title: F7G5_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 F2. TCTCGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 4


title: F8A1_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 F3. ATTACTCG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: F8A2_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 F3. TCCGGAGA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 5


title: miRNA294_28 rep1


title: miRNA294_25 rep2


title: miRNA294_34 rep1


title: miRNA294_25 rep1


title: F7G2_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 F2. TAATGCGC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 4


title: miRNA294_22 rep1


title: miRNA294_21 rep1


title: F7F6_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 F2. TCTCGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: F7G1_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 F2. CTGAAGCT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 4


title: miRNA294_20 rep2


title: miRNA294_20 rep1


title: F7F4_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 F2. TCCGCGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 4


title: F7F5_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 F2. TCTCGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 4


title: miRNA294_2 rep1


title: F7F1_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 F2. CTGAAGCT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 4


title: F7F3_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 F2. CGGCTATG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 4


title: miRNA294_2 rep2


title: miRNA294_14 rep1


title: miRNA294_14 rep2


title: F7G3_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 F2. CGGCTATG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 4


title: F7E6_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 F2. TCCGCGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: F7E5_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 F2. TCTCGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 4


title: F7E3_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 F2. CGGCTATG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 4


title: F9A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F5. CGGCTATG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 6


title: miRNA294_29 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F7E4_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 F2. TCCGCGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 4


title: miRNA294_12 rep1


title: miRNA294_13 rep1


title: F7E1_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 F2. CTGAAGCT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 4


title: miRNA294_12 rep2


title: miRNA294_11 rep1


title: F7E2_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 F2. TAATGCGC was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 4


title: miRNA294_10 rep2


title: miRNA294_16 rep1


title: F7D6_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 F2. CGGCTATG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: miRNA294_10 rep1


title: F7D5_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 F2. TCTCGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 4


title: MIR_294_26 rep1


title: MIR_294_19 rep1


title: MIR_294_1 rep1


title: F7D3_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 F2. CGGCTATG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 4


title: F7D2_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 F2. TAATGCGC was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 4


title: miRNA294_13 rep2


title: LET_7I_92 rep1

value: Dgcr8-/- plus let-7


title: F7C6_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 F2. TAATGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: F7C5_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 F2. TCTCGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 4


title: LET_7I_90 rep1


title: F7C4_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 F2. TCCGCGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 4


title: LET_7I_84 rep1


title: F7C3_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 F2. CGGCTATG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 4


title: LET_7I_85 rep1


title: F7C1_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 F2. CTGAAGCT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 4


title: LET_7I_82 rep1


title: LET_7I_81 rep1


title: LET_7I_80 rep1


title: F7B6_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 F2. CTGAAGCT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: F7D4_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 F2. TCCGCGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 4


title: LET_7I_8 rep1


title: F7B4_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 F2. TCCGCGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 4


title: F7B3_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 F2. CGGCTATG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 4


title: F7D1_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 F2. CTGAAGCT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 4


title: LET_7I_75 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F7B1_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 F2. CTGAAGCT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 4


title: LET_7I_78 rep2


title: F7A6_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 F2. AGCGATAG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 4


title: LET_7I_74 rep1


title: LET_7I_72 rep1


title: LET_7I_78 rep1


title: F7A5_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 F2. TCTCGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 4


title: LET_7I_83 rep1


title: LET_7I_70 rep1


title: F7C2_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 F2. TAATGCGC was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 4


title: F7A4_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 F2. TCCGCGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 4


title: F7A3_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 F2. CGGCTATG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 4


title: LET_7I_71 rep1


title: LET_7I_69 rep1


title: LET_7I_68 rep2


title: F7A2_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 F2. TAATGCGC was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 4


title: F7A1_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 F2. CTGAAGCT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 4


title: F7B5_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 F2. TCTCGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 4


title: F6G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 3


title: F6G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F2. nan was the first index barcode, nan was the second.
This sample was part of collection batch 3


title: LET_7I_68 rep1


title: F7B2_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 F2. TAATGCGC was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 4


title: LET_7I_66 rep1


title: F6G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAGATTCC was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 3


title: F6F4_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 F2. AGCGATAG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 3


title: LET_7I_61 rep1


title: F6F3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 3


title: F6F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 3


title: LET_7I_6 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F6E4_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 F2. AGCGATAG was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 3


title: LET_7I_58 rep1


title: LET_7I_53 rep1


title: LET_7I_61 rep2


title: F6E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 3


title: LET_7I_54 rep1


title: F6D4_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 F2. AGCGATAG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 3


title: LET_7I_5 rep1


title: LET_7I_49 rep1


title: F6D2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 3


title: LET_7I_44 rep1


title: LET_7I_46 rep1


title: F6C4_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 F2. AGCGATAG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 3


title: LET_7I_43 rep1


title: F6C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 3


title: LET_7I_41 rep2


title: F6B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 3


title: F6B4_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 F2. AGCGATAG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 3


title: LET_7I_41 rep1


title: miRNA294_47 rep1


title: LET_7I_55 rep1


title: LET_7I_4 rep1


title: LET_7I_38 rep1


title: F6A4_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 F2. AGCGATAG was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 3


title: F6B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 3


title: F6E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 3


title: F6A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 3


title: LET_7I_33 rep2


title: F6A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 3


title: F6D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 3


title: F5G3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 2


title: LET_7I_3 rep1


title: LET_7I_33 rep1


title: LET_7I_30 rep1


title: F7F2_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 F2. TAATGCGC was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 4


title: F5F4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: LET_7I_25 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F5G2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 2


title: LET_7I_66 rep2


title: F5F1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 2


title: F5F2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, TAATCTTA was the second.
This sample was part of collection batch 2


title: LET_7I_28 rep1


title: LET_7I_20 rep1


title: F5D4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. GAGATTCC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: F5E2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 2


title: LET_7I_2 rep1


title: LET_7I_17 rep1


title: LET_7I_15 rep1


title: F5E4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTCAGAA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: LET_7I_12 rep1


title: LET_7I_18 rep1


title: LET_7I_11 rep1


title: F5C4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: LET_7I_16 rep1


title: F5G1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 2


title: F5C3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 2


title: LET_7I_21 rep1


title: F5D1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 2


title: F5C2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 2


title: F5C1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, CCTATCCT was the second.
This sample was part of collection batch 2


title: F5B3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 2


title: F5B2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 2


title: F5B1_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, ATAGAGGC was the second.
This sample was part of collection batch 2


title: LET_7I_10 rep1


title: F5A3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 2


title: F5A2_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, TATAGCCT was the second.
This sample was part of collection batch 2


title: F5D3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, GGCTCTGA was the second.
This sample was part of collection batch 2


title: LET_7I_1 rep1

extract_protocol:
Fluidigm protocol (version PN 100-7168 G1)
Nextera XT DNA Sample Preparation kit


title: F3F1_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 F2. AGCGATAG was the first index barcode, CAGGACGT was the second.
This sample was part of collection batch 1


title: F5E3_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. CGCTCATT was the first index barcode, AGGCGAAG was the second.
This sample was part of collection batch 2


title: LET_7I_10 rep2


title: ESS3.MRE

city: SAINT LOUIS

first: Ting

last: Wang

state: MO

address: 4515 McKinley Avenue

department: Genetics

country: USA

institute: Washington University in St. Louis

data_processing:
Sequencing reads were aligned to the hg19 (GRCh37) genome build with BWA as single-end reads
The quality  report of mapped reads were gained by methylQA.
Similar to processing of MeDIP-seq data,  we perform post-alignment processing of MRE-seq data using methylQA, using the “mre” option. The methylQA package processes the MRE alignment result file (.bam) to generate alignment quality report and files formatted for various downstream needs. Resulting files include .bed file (aligned read location), .bedGraph file (MRE score), and .bigWig file (MRE score, for display on a Genome Browser). Please note the MRE data used in this protocol were generated using three enzymes, therefore all data, MRE fragment file, MRE window file, were the 3-enzyme version.
Genome_build: GRCh37
Supplementary_files_format_and_content: MRE.CpG.bigwig file lists the methylation score for each CpG sites.

organism: Homo sapiens

source_name: Endometrial stromal sarcoma

extract_protocol:
DNA extraction used a QIAamp spin column method to yield a mean of 0.68 µg DNA/specimen for LCM sample. For bulk sample, 5-10ug DNA is isolated.
For MRE, DNA was isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100-300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer's instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

treatment_protocol:
Bulk
Carcinoma and sarcoma components were separated by laser capture microdissection of frozen section slides.

tag: tissue

value: Uterus

tag: tissue type

value: Sarcoma component

tag: tumor stage

value: Low grade


title: F5A4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: ESS1.MRE


title: UCS2-Sa.MRE

treatment_protocol:
LCM
Carcinoma and sarcoma components were separated by laser capture microdissection of frozen section slides.

value: High grade


title: UCS1-Sa.MRE


title: UCS3-Sa.MRE


title: UCS3-Ca.MRE

value: Carcinoma component


title: ESS2.MRE


title: F5B4_1NP

description: library strategy: DNA-seq

extract_protocol:
Library was prepared according to Illumina's instructions accompanying the TruSeq HT kit (Part# FC-121-2003). Illumina TruSeq barcodes were used to multiplex this library as part of library pool F1. TCCGGAGA was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 2


title: ESS1.MeDIP

data_processing:
Sequencing reads were aligned to the hg19 (GRCh37) genome build with BWA as single-end reads
The quality  report of mapped reads were gained by methylQA.
Once MeDIP-seq reads are aligned and stored in a BAM file, we used methylQA for post-alignment processing. The methylQA package processes the MeDIP alignment result file (.bam) to generate alignment quality report and files formatted for various downstream needs. Resulting files include .bed file (aligned read location), bedGraph file (aligned read density), and .bigWig file (aligned read density, for display on a Genome Browser).
Genome_build: GRCh37
Supplementary_files_format_and_content: BWAseMedip.bigwig shows the methylation reads density for each coordinates.

extract_protocol:
DNA extraction used a QIAamp spin column method to yield a mean of 0.68 µg DNA/specimen for LCM sample. For bulk sample, 5-10ug DNA is isolated.
For MeDIP, DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA) was sonicated to ~100-500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2-5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml-1, Eurogentec, catalog no. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml-1, Jackson Immunoresearch, catalog no. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology, catalog no. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation, a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml-1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).Fifteen cycles of PCR were performed on 5 ul of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.


title: UCS2-Sa.MeDIP


title: UCS1-Sa.MeDIP


title: UCS2-Ca.MRE


title: UCS3-Ca.MeDIP


title: UCS3-Sa.MeDIP


title: UCS2-Ca.MeDIP


title: ESS2.MeDIP


title: UCS1-Ca.MeDIP


title: Proximal S1 intestine in zebrafish 2 weeks after SBS surgery #3

city: Los Angeles

first: Tracy

last: Grikscheit

state: California

address: 4650 Sunset Boulevard Mailstop#100

institute: Children's Hospital Los Angeles

data_processing:
Sequencing QC: FastQC
Trimming of reads for quality: Trimmomatic
Alignment: STAR
Read binning: Htseq-count
Differential Gene Expression: RUVSeq, edgeR
Genome_build: UCSC GRCz10/danRer10
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, counts, DE statistics and Annotation
Supplementary_files_format_and_content: BigWig Files for UCSC Genome Browser

organism: Danio rerio

source_name: full thickness intestine

extract_protocol:
Full thickness section of intestine was removed, and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer.
Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations

tag: status

value: SBS


title: Proximal S1 intestine in zebrafish 2 weeks after sham surgery #3

value: SHAM


title: Proximal S1 intestine in zebrafish 2 weeks after sham surgery #1


title: Proximal S1 intestine in zebrafish 2 weeks after sham surgery #2


title: Proximal S1 intestine in zebrafish 2 weeks after SBS surgery #1


title: Proximal S1 intestine in zebrafish 2 weeks after SBS surgery #2


title: JDK275-J

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: HepG2S1, Sorafenib resistant cell line derived from HepG2 (ATCC) see GSE62813 and  PMID:23111106

data_processing:
Read Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.7.1. Using FastX 0.0.14 and ShortRead 1.24.0, we filtered subsequently small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N) and low quality reads (more than 50% of the bases < Q25). With Bowtie2 v2.2.4 we identified and removed reads that mapped to the spiked-in PhiX. The number of processed reads per sample then varied between 13,831,499 and 19,366,753.
Alignment: Processed reads were aligned with STAR v2.4.1d to the reference genome of Homo sapiens (GRCh37.73), as downloaded from the Genome Reference Consortium. Default STAR parameter settings were used, except for ‘outSAMprimaryFlag=OneBestScore’, ‘twopassMode=Basic’, ‘alignIntronMin=50’, ‘alignIntronMax=500000’, ‘outSAMtype=BAM’, SortedByCoordinate. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: Transcript coordinates were extracted from the GRC reference annotation with Gffread from the Cufflinks v2.1.1 suite and merged to gene coordinates with mergeBed from the Bedtools v2.17.0 toolkit. GC content and gene length were derived from the gene coordinates. The numbers of aligned reads per gene were summarized using featureCounts 1.4.6 with parameters ‘Q=0’, ‘s=2’, ’t=exon’ and ‘g=gene_id’. We removed 45,839 genes for which all samples had less than 1 count-per-million. As such, we continued with raw counts for 17,313 genes. Raw counts were further corrected within samples for GC-content and between samples using full quantile-normalization, as implemented in the EDASeq package from Bioconductor.
Identifying differential gene expression: With the EdgeR 3.8.6 package, a negative binomial generalized linear model (GLM) was fitted against the normalized counts. We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate.
Genome_build: GRCh37
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

growth_protocol: HepG2 human hepatoblastoma cells (HB-8065) were obtained from ATCC (Rockville, MD, USA). Cells were grown in Williams Medium E (WEM, Invitrogen) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 20 mU/mL insulin, 50 nM dexamethasone, 100 U/mL penicillin, 100 μg/mL streptomycin, 2.5 μg fungizone, 50 μg/mL gentamycin and 100 μg/mL vancomycin (=WEM-C). Sorafenib (Bayer HealthCare, Leverkusen, Germany) was dissolved in 100% dimethylsulfoxid (DMSO) (Acros Organics, New Jersey, USA). The HepG2S1 cell line was developed over a period of several months by exposing the HepG2 cells to increasing doses of Sorafenib.

extract_protocol:
Rneasy kit (Qiagen)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1ug total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using the provided Second Strand Marking Master Mix. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichment PCR of 10 cycles was carried out  to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Libraries were equimolarly pooled and sequenced using high 75 cycles NextSeq v2 kits on part of an Illumina NextSeq500 flow-cell.

treatment_protocol: Cells were cultured to near confluency in TC flasks, the medium was changed and fresch medium with ACF or vehicle(DMSO) was added. After 24 hours cells were collected for transcriptome anlysis, stored in Trizol and subsequently the RNA extracted.

tag: cell line

tag: treatment

value: 5 µM ACF


title: JDK275-I


title: JDK275-G

value: 2,5 µM ACF


title: JDK275-L


title: JDK275-K


title: JDK275-F


title: JDK275-E


title: JDK275-B


title: UCS1-Ca.MRE


title: ESS3.MeDIP


title: JDK275-A


title: JDK275-D


title: PANC1_Cobalt_Acriflavin3

data_processing:
Read Preprocessing. Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and Cutadapt 1.7.1. Using FastX 0.0.13 and ShortRead 1.16.3, we filtered subsequently small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N) and low quality reads (more than 50% of the bases < Q25). With Bowtie2 v2.2.4 we identified and removed reads that mapped to the spiked-in PhiX. The number of processed reads per sample then varied between 16,160,293 and 19,694,454.
Alignment. Processed reads were aligned with Tophat v2.0.13 to the reference genome of Homo sapiens (GRCh37.73), as downloaded from the Genome Reference Consortium. Default Tophat parameter settings were used, except for ‘library-type=fr-firststrand’, 'min-intron-length=50', 'max-intron-length=500,000', 'no-coverage-search', ‘no-mixed’ and 'read-realign-edit-dist=3'. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting. Transcript coordinates were extracted from the GRC reference annotation with Gffread from the Cufflinks v2.1.1 suite and merged to gene coordinates with mergeBed from the Bedtools v2.17.0 toolkit. The numbers of aligned reads per gene were summarized using featureCounts 1.4.6 with parameters ‘Q=0’, ‘s=2’, ’t=exon’ and ‘g=gene_id’.
Genome_build: GRCh37
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

growth_protocol: Panc-1 pancreatic cancer cells were obtained from ATCC (Rockville, MD, USA) and cultured in Gibco Modified Eagles Medium (Life Technologies) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomycin.

extract_protocol:
Rneasy kit (Qiagen)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1ug total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using the provided Second Strand Marking Master Mix. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichment PCR of 10 cycles was carried out  to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Libraries were equimolarly pooled and sequenced using high 75 cycles NextSeq v2 kits on part of an Illumina NextSeq 500 flow-cell.

treatment_protocol: EMT was induced by cobalt chloride (CoCl2, Sigma Aldrich). Cells were first starved for 24 hours in 1% fetal calf serum medium to avoid interference of growth factors in the serum and then stimulated with CoCl2 (200 µM) or vehicle for 48 hours. For EMT inhibition in Panc-1 cells, acriflavine (2.5 µM, Sigma-Aldrich) was added to the cell culture together with CoCl2 (200 µM) for 48h.

value: PANC-1 pancreatic cancer cell line (ATCC, CRL-1469)

value: Cobalt + ACF


title: PANC1_Cobalt_Acriflavin2


title: PANC1_Cobalt_Acriflavin1


title: PANC1_Cobalt2

value: Cobalt


title: PANC1_Cobalt3


title: PANC1_Control1


title: PANC1_Control2


title: JDK275-H


title: Control [Sample_2a]

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
Basecalls performed using CASAVA version 1.8.1
Alignment of the reads using TopHat2 version 2.0.11
Raw count calculation using HTSeq version 0.5.3
Genome_build: danio rerio zv9
Supplementary_files_format_and_content: Raw count file generated by HTSeq

molecule: polyA RNA

source_name: Brain

extract_protocol:
The RNA extraction was made according to Qiagen protocol using RNeasy Mini Kit
The libraries were prepared according to the Illumina protocol using the TrueSeq mRNA stranded kit
Using poly-dT beads, mRNA were purified before the library preparation

value: Whole adult brain

tag: somatic transgene


title: Tumor [Sample_2e]


title: Control [Sample_2c]


title: Tumor [Sample_2f]


title: Tumor [Sample_2d]


title: Control [Sample_2b]


title: JDK275-C


title: Summer Buds

city: nanjing

first: Muhammad

middle: Khalil

last: Ur Rehman

state: Jaingsu

address: WeiGang No.1

department: Horticulture

country: China

institute: Nanjing Agricultural university

description: SD

data_processing:
HISAT 0. 1.6+ HTSEQ 0. 1.6+ DEGseq1.18.0l Softwares, DEGseq2,Pheatmap,Goseq and topGo analysis software used during analysis
We use software developed by BGI (unpublished)to deal with the data from HiSeq sequencing  adaptor sequence,  or low-quality sequence
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed. After raw reads are filtered into clean reads which will be aligned to the reference sequences with  HISAT Aligner QC of alignment is performed to determine if resequencing is needed.
We use plant targets prediction pipeline for indentify target prediction are based on those suggested by Allen et al. (microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121:207-221) - Supplemental document S1 and by Schwab et al. (Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 2005, 8: 517 - 527)
GO enrichment analysis is used on predicted target gene candidates of novel miRNAs . It will provide all GO terms significantly enriched in the predicted target gene candidates of novel miRNAs compared to the reference gene background, as well as the genes corresponding to certain biological function. The result could reveal the functions significantly related with predicted target gene candidates of novel miRNAs. This method firstly maps all target gene candidates to GO terms in the database (http://www.geneontology.org/), calculating gene numbers for each term, then using hypergeometric test to find significantly enriched GO terms in target gene candidates comparing to the reference gene background. We use the Bonferroni Correction for the p-value to obtain a corrected p-value. GO terms with corrected p-value <= 0.05 are defined as significantly enriched in target gene candidates.
KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates
Supplementary_files_format_and_content: abundance measurements

organism: Vitis vinifera

source_name: Bud

growth_protocol: The study conducted on Garapevine cultivar" Shine Muscat" grown under standard cultication condition in vineyard located in Tangshan valley Nanjing, Jiangsu provine P.R China.

extract_protocol:
The modified CTAB method
RNA libraries were prepared for sequencing using standard Illumina protocols
Ultra™ RNA Library Prep Kit for Illumina (NEB, USA)

tag: developmental stage

value: SummerBuds

tag: cultivar

value: Shine Muscat


title: Para dormancy

description: PD

value: Para Dormancy


title: 4.5h_rep3

city: La Jolla

first: Changchun

last: Xiao

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

description:
R115_100_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Basecalls performed using Illumina bcl2fastq/2.16.0.10
Reads were aligned using tophat v2.0.13 to Mouse genome, M. musculus UCSC mm10,
Generation of gene counts was performed using Partek® software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.
Genome_build: mm10
Supplementary_files_format_and_content: [.xlsx] read counts, RPKM counts

source_name: FoB cells_4.5h

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: Follicular B cells

tag: time

tag: protocol

value: spiked in ERCC Mix1 amounts:0.5uL per 3 x 10^6 cells


title: 1.5h_rep3

description:
R115_99_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

source_name: FoB cells_1.5h


title: 13.5h_rep3

description:
R115_101_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

source_name: FoB cells_13.5h

value: spiked in ERCC Mix1 amounts:1.0uL per 3 x 10^6 cells


title: 25.5h_rep3

description:
R115_102_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

source_name: FoB cells_25.5h

value: spiked in ERCC Mix1 amounts:2.0uL per 3 x 10^6 cells


title: Endodormacy stage

description: ED

value: Complete endpdormant stage


title: 25.5h_rep1

description:
R115_94_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: 25.5h_rep2

description:
R115_98_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: 13.5h_rep1

description:
R115_93_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: 1.5h_rep2

description:
R115_95_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: PANC1_Cobalt1


title: PANC1_Control3


title: 4.5h_rep1

description:
R115_92_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: 1.5h_rep1

description:
R115_91_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx


title: Naive_rep2

description:
R108_88_FoB
processed data files:
Xiao_R108_mm10_RPKM+Reads_87_88_only.xlsx
Xiao_R108_ERCC_FoB_87_88_only.xlsx

source_name: FoB cells_naive

value: naive


title: miR17_92_TG3_25.5hr

description:
Ribosome footprints
FoB25.5_TGrep3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw sequencing data were separated into individual samples using index primer sequences. Then, the miRNA linker and the first nucleotide of 5'-end are clipped and trimmed using fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads obtained from rRNAs are discarded using Bowtie v1.0.0 using 23 seed flag (Langmead et al, 2009). Illumina iGenome (mm10) were used as a reference. The non-rRNA sequencing reads were further aligned to the reference genome (mm10) using TopHat v2.0.11 with added option, "no-novel-juncs"
Only the perfect-match aligned reads were further extracted from accepted hits (accepted_hits.bam) to reduce potential noise derived from relatively short ribosome footprint length (Ingolia et al, 2012). Differential ribosome footprint levels in different genotypes were further quantified using Cuffdiff (v 2.2.1)
To accept only translated genes, we took cut-off of ribosome footprints at fragments per kilobase per million (FPKM) > 1, and only selected genes that were quantified in all three biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: [.xlsx] tab-delimited file includes FPKM values for each Sample

source_name: FoB cells_miR17_92_TG_stimulated

extract_protocol:
Purified ribosome footprints were extracted using miRNeasy Kit from Qiagen (cat. no. 217004)
RNA libraries were prepared for sequencing using ribosome profiling libary prep protocol (Ingolia et al., Nature Protocol 2012). Indexed footprint library was generated with 4 or 6 cycles of PCR using index library primers, and avoided broad, slower migrating smear bands.

tag: genotype/variation

value: TG

value: follicular B cells

value: stimulated with LPS/IL-4 for 25.5hr in B cell media


title: miR17_92_tKO3_25.5hr

description:
Ribosome footprints
FoB25.5_TKOrep3

source_name: FoB cells_miR17_92_tKO_stimulated

value: C57BL/6 x 129 mixed background

value: tKO


title: miR17_92_tKO2_25.5hr

description:
Ribosome footprints
FoB25.5_TKOrep2


title: Control_3_25.5hr

description:
Ribosome footprints
FoB25.5h_WTrep3

source_name: FoB cells_control_stimulated

value: control


title: Naive_rep1

description:
R108_87_FoB
processed data files:
Xiao_R108_mm10_RPKM+Reads_87_88_only.xlsx
Xiao_R108_ERCC_FoB_87_88_only.xlsx

value: spiked in ERCC Mix1 amounts:0.1uL per 3 x 10^6 cells


title: Control_2_25.5hr

description:
Ribosome footprints
FoB25.5h_WTrep2


title: miR17_92_TG2_25.5hr

description:
Ribosome footprints
FoB25.5_TGrep2


title: Control_1_25.5hr

description:
Ribosome footprints
FoB25.5h_WTrep1


title: breast plume_epi_II

city: Arlington

first: Ang

last: Li

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

description:
Chuong-222
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/AC were done in Partek Flow
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated in Partek Genomic Suite
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files include RPKM value for each sample

organism: Gallus gallus

source_name: breast plume

extract_protocol:
Feather epithelium and mesenchyme were separated in 2xCMF, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Version2 was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: White leghorn

tag: feather type

value: breast plume

tag: region

value: epithelium

tag: batch

value: II


title: breast plume_mes_I

description:
Chuong-223
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx

tag: tissue

value: mesenchyme

value: I


title: breast plume_mes_II

description:
Chuong-224
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx


title: 13.5h_rep2

description:
R115_97_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

tag: strain

tag: cell type

value: Follicular B cells

value: spiked in ERCC Mix1 amounts:1.0uL per 3 x 10^6 cells


title: 4.5h_rep2

description:
R115_96_FoB
processed data files:
Xiao_R115_ERCC_RPKM.xlsx
Xiao_R115_gene_count_RPKM_3.xlsx

value: spiked in ERCC Mix1 amounts:0.5uL per 3 x 10^6 cells


title: dorsal plume_mes_II

description:
Chuong-228
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx

source_name: dorsal plume

value: dorsal plume


title: primary remige_medial side_mes_II

description:
Chuong-57
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx

source_name: primary remige

value: primary remige

value: primary medial side (wide)


title: dorsal plume_epi_I

description:
Chuong-225
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx


title: dorsal plume_mes_I

description:
Chuong-227
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx


title: miR17_92_tKO1_25.5hr

description:
Ribosome footprints
FoB25.5_TKOrep1

value: follicular B cells

value: stimulated with LPS/IL-4 for 25.5hr in B cell media


title: dorsal plume_epi_II

description:
Chuong-226
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx


title: primary remige_medial side_epi_II

description:
Chuong-58
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx


title: primary remige_medial side_mes_I

description:
Chuong-36
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx


title: miR17_92_TG1_25.5hr

description:
Ribosome footprints
FoB25.5_TGrep1

value: TG


title: primary remige_lateral side_mes_II

description:
Chuong-55
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx

value: lateral side (narrow)


title: Cell_162

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

institute: University of Cambridge

description: Hypothalamic POMC-expressing neuron

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized abundance in counts per million (CPM)

source_name: Hypothalamic neuronal cell

extract_protocol:
GFP-labelled POMC neurons from microdissected Pomc-EGFP murine hypothalami were dissociated into a cell suspension using Papain.  Flurorescence-activating cell sorting (FACS) was then utilised to sort individual GFP-positive neurons into a 96 well plate with lysis buffer and RNase inhibitor.
RNA from the single cell lysate was reverse transcribed and PCR amplified into double stranded cDNA using Clontech SMART-Seq v4 Ultra Low Input RNA Kit.  Amplified cDNA was then used to generate barcoded sequencing libraries using Illumina Nextera XT library preparation kit. The pooled libraries were sequenced on an Illumina HiSeq 4000 instrument at single-end 50bp (SE50).

value: C57/BL6 Tg(Pomc-EGFP)1Low

value: Pomc-EGFP expressing neuron


title: Cell_161

description: Hypothalamic POMC-expressing neuron


title: Cell_159

description: Hypothalamic POMC-expressing neuron


title: primary remige_medial side_epi_I

description:
Chuong-54
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx

value: White leghorn


title: Cell_160

description: Hypothalamic POMC-expressing neuron


title: Cell_158

description: Hypothalamic POMC-expressing neuron


title: primary remige_lateral side_epi_I

description:
Chuong-53
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx

value: epithelium


title: Cell_155

description: Hypothalamic POMC-expressing neuron


title: Cell_157

description: Hypothalamic POMC-expressing neuron


title: primary remige_lateral side_mes_I

description:
Chuong-35
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx


title: primary remige_lateral side_epi_II

description:
Chuong-56
processed data file: LS vs MS RPKM.xlsx
processed data file: LS_vs_MS_TPM.xlsx

value: II


title: breast plume_epi_I

description:
Chuong-221
processed data file: DP vs BP RPKM.xlsx
processed data file: DP_vs_BP_TPM.xlsx

value: breast plume


title: Cell_153

description: Hypothalamic POMC-expressing neuron


title: Cell_152

description: Hypothalamic POMC-expressing neuron


title: Cell_163

description: Hypothalamic POMC-expressing neuron


title: Cell_151

description: Hypothalamic POMC-expressing neuron


title: Cell_149

description: Hypothalamic POMC-expressing neuron


title: Cell_150

description: Hypothalamic POMC-expressing neuron


title: Cell_154

description: Hypothalamic POMC-expressing neuron


title: Infected small intestine repeat 2

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

institute: Shandong Agricultural University

data_processing:
The raw reads were obtained using the Solexa deep-sequencing analyzer, then removing the low-quality reads and eliminating reads with5’ primer contaminants, without 3’ primer and insert tag, reads with poly(A) and  length (<15 bp or > 32 bp), the clean data reads were obtained and were used for further analysis.
The clean data reads were blasted to reference genome using the software bowtie which ensure the first 15bp of the read was exactly match and other site two mismatch was admitted.
After a series of filtering, the remaining sequences were blasted to precursor miRNA and mature miRNA in the miRBase 20.0
Rfam(10.0) was used to annotation the small RNA sequence to filter the rRNA,scRNA,snoRNA,snRNA and tRNA. The non-miRNA sequence was filtered from clean data and the left data was used to identify and analyze new miRNA.
Genome_build: galGal4
Supplementary_files_format_and_content: Sequence and Count

source_name: small intestine

growth_protocol: The 20-week old S. enteritidis negative white leghorn layers were randomly divided into two groups, one is control group, the other was used for treated group.The two groups were kept in seperate isolator with the same filtered-air, positive-pressure condtion, and provided with water and commercial feed ad libitum.

extract_protocol:
Small intestine was removed, flash frozen by dry ice, and RNA was isolated using Trizol reagent
The total RNA was ligated  5′ and 3′ RNA adapters  by T4 RNA ligase, followed by reverse transcription and PCR product purification.The 145-160bp fraction was obtained through PAGE electrophoresis to quantified on the Qubit (Invitrogen), then were diluted to 10 nM to finish cluster generation

treatment_protocol: The chickens in treated group were daily fed with 30 g feed containing 5.8×108 cfu SE

value: small intestine

tag: infection

value: infected


title: Infected small intestine repeat 3


title: Infected small intestine repeat 1


title: Non-infected small intestine repeat 1

value: non-infected


title: Non-infected small intestine repeat 2


title: Non-infected small intestine repeat 3


title: Cell_147

description: Hypothalamic POMC-expressing neuron


title: Cell_148

description: Hypothalamic POMC-expressing neuron


title: Cell_144

description: Hypothalamic POMC-expressing neuron


title: Cell_146

description: Hypothalamic POMC-expressing neuron


title: Cell_143

description: Hypothalamic POMC-expressing neuron


title: Cell_145

description: Hypothalamic POMC-expressing neuron


title: Sox17-RACVEC 3

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm9 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

source_name: mouse amniotic fluid cells obtained from E11.5-E13.5 embryos and transduced with lentiviruses encoding mouse transcription factors Etv2, Erg, and Fli1 as well as mouse Sox17

extract_protocol:
RNA was harvested using Trizol treatment
Illumina TruSeq PE 51x2 (RNA-seq)

value: Endothelial cells


title: Cell_142

description: Hypothalamic POMC-expressing neuron


title: Cell_156

description: Hypothalamic POMC-expressing neuron


title: Cell_141

description: Hypothalamic POMC-expressing neuron


title: Sox17-RACVEC 2


title: Sox17-RACVEC 1


title: Cell_140

description: Hypothalamic POMC-expressing neuron


title: LSEC 2

source_name: mouse liver endothelial cells directly purified by FACS


title: Cell_139

description: Hypothalamic POMC-expressing neuron


title: Cell_137

description: Hypothalamic POMC-expressing neuron


title: LSEC 1


title: Akt-RACVEC 3

source_name: mouse amniotic fluid cells obtained from E11.5-E13.5 embryos and transduced with lentiviruses encoding mouse transcription factors Etv2, Erg, and Fli1 as well as a constitutively active myristyolated Akt molecule


title: LSEC 3


title: Cell_136

description: Hypothalamic POMC-expressing neuron


title: Akt-RACVEC 2


title: Cell_135

description: Hypothalamic POMC-expressing neuron


title: Akt-RACVEC 1


title: RACVEC 2

source_name: mouse amniotic fluid cells obtained from E11.5-E13.5 embryos and transduced with lentiviruses encoding mouse transcription factors Etv2, Erg, and Fli1


title: Akt-MAC 3

source_name: mouse amniotic fluid cells obtained from E11.5-E13.5 embryos and transduced with a lentivirus encoding a constitutively active myristyolated Akt molecule

value: Amniotic cells


title: Cell_138

description: Hypothalamic POMC-expressing neuron


title: Cell_133

description: Hypothalamic POMC-expressing neuron


title: Cell_134

description: Hypothalamic POMC-expressing neuron


title: Cell_132

description: Hypothalamic POMC-expressing neuron


title: Cell_130

description: Hypothalamic POMC-expressing neuron


title: Cell_131

description: Hypothalamic POMC-expressing neuron


title: Cell_129

description: Hypothalamic POMC-expressing neuron


title: Akt-MAC 1


title: Cell_128

description: Hypothalamic POMC-expressing neuron


title: Akt-MAC 2


title: MAC 3

source_name: mouse amniotic fluid cells obtained from E11.5-E13.5 embryos


title: Cell_126

description: Hypothalamic POMC-expressing neuron


title: MAC 1


title: Cell_127

description: Hypothalamic POMC-expressing neuron


title: Akt-LEC 3

source_name: mouse lung endothelial cells transduced with a lentivirus encoding a constitutively active myristyolated Akt molecule


title: Cell_125

description: Hypothalamic POMC-expressing neuron


title: Cell_124

description: Hypothalamic POMC-expressing neuron


title: Akt-LEC 1


title: Cell_122

description: Hypothalamic POMC-expressing neuron


title: RACVEC 1


title: Akt-liver EC 3

source_name: mouse liver endothelial cells transduced with a lentivirus encoding a constitutively active myristyolated Akt molecule


title: RACVEC 3


title: Cell_121

description: Hypothalamic POMC-expressing neuron


title: F12H3_negative_control

description: library strategy: DNA-seq

organism: other sequences

source_name: no input DNA

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 F4. CGGCTATG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 9

tag: sample type

value: control


title: F12H2_negative_control

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 F4. TAATGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 9


title: F11H6_negative_control

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 F4. GAATTCGT was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 8


title: Cell_120

description: Hypothalamic POMC-expressing neuron


title: Cell_119

description: Hypothalamic POMC-expressing neuron


title: Akt-liver EC 1


title: Cell_117

description: Hypothalamic POMC-expressing neuron


title: F11H1_negative_control

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 F4. ATTACTCG was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 8


title: Cell_118

description: Hypothalamic POMC-expressing neuron


title: F10H3_negative_control

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 F4. TCTCGCGC was the first index barcode, GTACTGAC was the second.
This sample was part of collection batch 7


title: Cell_115

description: Hypothalamic POMC-expressing neuron


title: Cell_116

description: Hypothalamic POMC-expressing neuron


title: Cell_114

description: Hypothalamic POMC-expressing neuron


title: Cell_113

description: Hypothalamic POMC-expressing neuron


title: Cell_123

description: Hypothalamic POMC-expressing neuron


title: Cell_110

description: Hypothalamic POMC-expressing neuron


title: Cell_111

description: Hypothalamic POMC-expressing neuron


title: MAC 2


title: Cell_109

description: Hypothalamic POMC-expressing neuron


title: Medial pulp_input_II

data_processing:
Adaptor sequence trimming, alignment of reads (Bowtie 2 galGal4) were done in Partek flow
Peak calling was done in Galaxy MACS
Genome_build: galGal4
Supplementary_files_format_and_content: wig files were generated by Galaxy MACS

extract_protocol:
Epithelium and mesenchyme were separated in 2xCMF. Mesenchymal cells were dissociated by 0.35% collagenase digestion. Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions in USC epigenome center

value: primary remige

tag: vane dimension

value: wide

value: medial side

value: mesenchyme (pulp)

tag: antibody


title: Akt-liver EC 2


title: Lateral pulp_input_II

value: narrow

value: lateral side


title: Cell_106

description: Hypothalamic POMC-expressing neuron

value: C57/BL6 Tg(Pomc-EGFP)1Low

value: Pomc-EGFP expressing neuron


title: Cell_105

description: Hypothalamic POMC-expressing neuron


title: Cell_107

description: Hypothalamic POMC-expressing neuron


title: Medial pulp_H3K4me3_II


title: Medial pulp_input_I

value: I


title: Cell_104

description: Hypothalamic POMC-expressing neuron


title: Cell_102

description: Hypothalamic POMC-expressing neuron


title: Medial pulp_H3K4me3_I


title: Cell_103

description: Hypothalamic POMC-expressing neuron


title: Cell_101

description: Hypothalamic POMC-expressing neuron


title: Lateral pulp_input_I


title: Cell_99

description: Hypothalamic POMC-expressing neuron


title: Cell_98

description: Hypothalamic POMC-expressing neuron


title: Cell_97

description: Hypothalamic POMC-expressing neuron


title: Cell_95

description: Hypothalamic POMC-expressing neuron


title: Cell_96

description: Hypothalamic POMC-expressing neuron


title: Cell_94

description: Hypothalamic POMC-expressing neuron


title: Cell_93

description: Hypothalamic POMC-expressing neuron


title: Cell_108

description: Hypothalamic POMC-expressing neuron


title: Cell_90

description: Hypothalamic POMC-expressing neuron


title: Cell_91

description: Hypothalamic POMC-expressing neuron


title: Cell_89

description: Hypothalamic POMC-expressing neuron


title: Cell_88

description: Hypothalamic POMC-expressing neuron


title: Cell_86

description: Hypothalamic POMC-expressing neuron


title: Lateral pulp_H3K4me3_II

value: II


title: Cell_85

description: Hypothalamic POMC-expressing neuron


title: Cell_81

description: Hypothalamic POMC-expressing neuron


title: Cell_100

description: Hypothalamic POMC-expressing neuron


title: Cell_82

description: Hypothalamic POMC-expressing neuron


title: Cell_84

description: Hypothalamic POMC-expressing neuron


title: Lateral pulp_H3K4me3_I


title: Cell_80

description: Hypothalamic POMC-expressing neuron


title: Cell_78

description: Hypothalamic POMC-expressing neuron