Open Access Highly Accessed Research article

Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood

Candida Vaz1, Hafiz M Ahmad2, Pratibha Sharma3, Rashi Gupta1, Lalit Kumar3, Ritu Kulshreshtha2 and Alok Bhattacharya12*

Author Affiliations

1 School of Information Technology, Jawaharlal Nehru University, New Delhi, India

2 School of Life Sciences, Jawaharlal Nehru University, New Delhi, India

3 Department of Medical Oncology, Institute Rotary Cancer Hospital, All India Institute of Medical Science, New Delhi, India

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BMC Genomics 2010, 11:288  doi:10.1186/1471-2164-11-288

Published: 7 May 2010

Additional files

Additional file 1:

The known miRNAs expression pattern for all the 4 samples. The known miRNAs found in the 4 samples with their corresponding frequency and TPM values.

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Additional file 2:

miRNA cluster analysis. Cluster analysis of the known miRNAs in Normal1, Normal2, K562 and HL60.

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Additional file 3:

Comparison of the sensitivity of the three miRNA detection methods (Deep sequencing reads, RNase Protection assay and quantitative RT-PCR). Fold change differences in normal PBMC versus K562 is presented for miR-27a and miR-22 using the three transcript detection methods.

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Additional file 4:

List of predicted targets of differentially regulated miRNAs showing inverse correlation in microarray data in K562.

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Additional file 5:

List of predicted targets of differentially regulated miRNAs showing inverse correlation in microarray data in HL60.

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Additional file 6:

List of the predicted 370 novel miRNAs. The precursor and mature sequences of the total novel miRNAs are given as text file. When the relative abundances clearly indicate which the predominantly expressed miRNA is, the mature sequences are assigned names of the form, jnuhsa-233 (the predominant product) and jnuhsa-233* (from the opposite arm of the precursor). When the data are not sufficient to determine which sequence is the predominant one, names like jnuhsa-118-5p (from the 5' arm) and jnuhsa-118-3p (from the 3' arm) have been used.

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Additional file 7:

Details of the intronic novel miRNAs of the 4 samples. List of the novel miRNAs predicted sample wise, with the information on their frequency, isomiRs, chromosomal location and prediction scores from CID-miRNA, CSHMM, miRDeep, MiPred.

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Additional file 8:

Details of the intergenic novel miRNAs of the 4 samples. List of the novel miRNAs predicted sample wise, with the information on their frequency, isomiRs, chromosomal location and prediction scores from CID-miRNA, CSHMM, miRDeep, MiPred.

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Additional file 9:

A list of primers used for amplification of precursors of novel miRNAs.

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Additional file 10:

The normalized expression data along with a list of differentially regulated genes (> 1.5 fold) obtained using Ocimum microarray platform for K562 and HL60.

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