DOI: 10.5281/zenodo.1017276
title: Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part1 - genomic alignments (hg19 + hg38)

description: This repository contains genomic alignments (BED files) of paired-end nanoCAGE sequencing data (CAGEscan data) collected from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2"). FASTQ files were processed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.). Filtered pairs of reads were aligned on the human genome assemblies hg19 and hg38. See tables below for a detailed description of the samples contained in each nanoCAGE library, including barcodes and index sequences used for the demultiplexing of sequencing reads. Corresponding raw sequencing data files (FASTQ files) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1014009.


 


"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :


ID   Sample_name   Barcode_number   Barcode_sequence   Index_sequence


1   iPSC_control_rep1   4   ACAGAT   NNNNNNNN


2   iPSC_control_rep2   24   ATCGTG   NNNNNNNN


3   iPSC_control_rep3   31   CACGAT   NNNNNNNN


4   S3P1_OK_rep1   36   CACTGA   NNNNNNNN


5   S3P1_OK_rep2   46   CTGACG   NNNNNNNN


6   S3P1_OK_rep3   63   GAGTGA   NNNNNNNN


7   S4P1_OK_rep1   79   GTATAC   NNNNNNNN


8   S4P1_OK_rep2   92   TCGAGC   NNNNNNNN


9   S4P1_OK_rep3   9   ACATGA   NNNNNNNN


10   S4P2_OK_rep1   21   ATCATA   NNNNNNNN


11   S4P2_OK_rep2   33   CACGTG   NNNNNNNN


12   S4P2_OK_rep3   45   CGATGA   NNNNNNNN


13   S1P1_rep1   57   GAGATA   NNNNNNNN


14   S1P1_rep2   69   GCTCTC   NNNNNNNN


15   S1P1_rep3   81   GTATGA   NNNNNNNN


16   S3P1_FAILED_rep1   93   TCGATA   NNNNNNNN


17   S3P1_FAILED_rep2   11   AGTAGC   NNNNNNNN


18   S3P1_FAILED_rep3   23   ATCGCA   NNNNNNNN


19   S4P1_FAILED_rep1   35   CACTCT   NNNNNNNN


20   S4P1_FAILED_rep2   47   CTGAGC   NNNNNNNN


21   S4P1_FAILED_rep3   59   GAGCGT   NNNNNNNN


22   S4P2_FAILED_rep1   71   GCTGCA   NNNNNNNN


23   S4P2_FAILED_rep2   83   TATAGC   NNNNNNNN


24   S4P2_FAILED_rep3   95   TCGCGT   NNNNNNNN


 


"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):


ID   Sample_name   Barcode_number   Barcode_sequence   Index_sequence


25   PETRI_rep1   04   ACAGAT   NNNNNNNN


26   PETRI_rep2   24   ATCGTG   NNNNNNNN


27   PETRI_rep3   31   CACGAT   NNNNNNNN


28   BIOCHIP_E_rep1   6   CACTGA   NNNNNNNN


29   BIOCHIP_M_rep1   46   CTGACG   NNNNNNNN


30   BIOCHIP_S_rep1   63   GAGTGA   NNNNNNNN


31   BIOCHIP_E_rep2   79   GTATAC   NNNNNNNN


32   BIOCHIP_M_rep2   92   TCGAGC   NNNNNNNN


33   BIOCHIP_S_rep2   09   ACATGA   NNNNNNNN


34   BIOCHIP_E_rep3   21   ATCATA   NNNNNNNN


35   BIOCHIP_M_rep3   33   CACGTG   NNNNNNNN


36   BIOCHIP_S_rep3   45   CGATGA   NNNNNNNN


37   HEPATOCYTES_rep1   57   GAGATA   NNNNNNNN


38   HEPATOCYTES_rep2   69   GCTCTC   NNNNNNNN


39   iPSC_control_rep1-2   81   GTATGA   NNNNNNNN


40   BIOCHIP_E_rep2-2   93   TCGATA   NNNNNNNN


41   BIOCHIP_M_rep1-2    11   AGTAGC   NNNNNNNN


42   BIOCHIP_S_rep2-2   23   ATCGCA   NNNNNNNN