DOI: 10.20350/digitalcsic/18113
title: "RNA-Seq raw data of two maize near isogenic lines (NILs), NIL16 and NIL95, under infestation with Sesamia nonagrioides and control conditions"

description: The original raw data from Illumina platform were transformed to Sequenced Reads, known as Raw Data or RAW Reads, by base calling. Raw data are recorded in a FASTQ file, which contains sequencing reads and corresponding sequencing quality. Every read in FASTQ format is stored in four lines, as indicated below: @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT NAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT + #55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHH Line 1 begins with a '@' character and is followed by the Illumina Sequence Identifiers and an optional description. The details of Illumina sequence identifier are listed in the table below. Identifier Meaning HWI-ST1276 Instrument – unique identifier of the sequencer 71 Run number – Run number on instrument C1162ACXX Flow Cell ID – ID of flow cell 1 Lane Number – positive integer 1101 Tile Number – positive integer 1208 X – x coordinate of the spot. Integer which can be negative 2458 Y – y coordinate of the spot. Integer which can be negative 1 Read number. 1 can be single read or Read 2 of paired-end. N Y if the read is filtered (did not pass), N otherwise. 0 Control number - 0 when none of the control bits are on, otherwise it is an even number CGATGT Illumina index sequences Line 2 is the raw sequence of the read. Line 3 begins with a '+' character and is optionally followed by the same sequence identifiers and descriptions as in Line 1. Line 4 encodes the quality values for the bases in Line 2 and contains the same number of characters as the bases in the read.
description: The objective of this study was to disentangle the genes behind co-localized QTLs for increased yield and stem susceptibility to the maize stem borer, Sesamia nonagrioides Lef. (Mediterranean stem borer, MSB) in the long arm of chromosome 8 of maize. Fine-mapping of QTLs for both traits was performed in a mapping population derived from two near isogenic lines (NILs), NIL16 and NIL95, and RNA-seq has been used to facilitate the identification of QTL candidate genes. RNA-seq analysis was done with RNA extracted from the stem pith of NIL16 and NIL95 collected 30 days after infestation in infested and control plants using four biological replicates for each NIL-treatment combination. Samples were barcoded and prepared for sequencing at Novogene Co., Ltd, where 150 bp paired-end (PE) reads were obtained on an Illumina 1.9.
description: Sequences of 150 bp cDNA paired-end recorded in FASTQ format and contained in files fq.gz. Files (=reads) for each sample are saved in the same folder: Folder S_16_1: Infestation with Sesamia nonagrioides, NIL16, biological replicate 1: S_16_1_MKRN240010851-1A_22C2L2LT4_L4_1.fq.gz S_16_1_MKRN240010851-1A_22C2L2LT4_L4_2.fq.gz S_16_1_MKRN240010851-1A_22CHMWLT4_L8_1.fq.gz S_16_1_MKRN240010851-1A_22CHMWLT4_L8_2.fq.gz Folder S_16_2: Infestation with Sesamia nonagrioides, NIL16, biological replicate 2: S_16_2_MKRN240010852-1A_22F27GLT4_L8_1.fq.gz S_16_2_MKRN240010852-1A_22F27GLT4_L8_2.fq.gz Folder S_16_3: Infestation with Sesamia nonagrioides, NIL16, biological replicate 3: S_16_3_MKRN240010853-1A_22C2L2LT4_L4_1.fq.gz S_16_3_MKRN240010853-1A_22C2L2LT4_L4_2.fq.gz S_16_3_MKRN240010853-1A_22CHMWLT4_L8_1.fq.gz S_16_3_MKRN240010853-1A_22CHMWLT4_L8_2.fq.gz Folder S_16_4: Infestation with Sesamia nonagrioides, NIL16, biological replicate 4: S_16_4_MKRN240010854-1A_22F27GLT4_L8_1.fq.gz S_16_4_MKRN240010854-1A_22F27GLT4_L8_2.fq.gz Folder S_95_1: Infestation with Sesamia nonagrioides, NIL95, biological replicate 1: S_95_1_MKRN240010855-1A_22F27GLT4_L8_1.fq.gz S_95_1_MKRN240010855-1A_22F27GLT4_L8_2.fq.gz Folder S_95_2: Infestation with Sesamia nonagrioides, NIL95, biological replicate 2: S_95_2_MKRN240010856-1A_22F27GLT4_L8_1.fq.gz S_95_2_MKRN240010856-1A_22F27GLT4_L8_2.fq.gz Folder S_95_3: Infestation with Sesamia nonagrioides, NIL95, biological replicate 3: S_95_3_MKRN240010857-1A_22F27GLT4_L8_1.fq.gz S_95_3_MKRN240010857-1A_22F27GLT4_L8_2.fq.gz Folder S_95_5: Infestation with Sesamia nonagrioides, NIL95, biological replicate 4: S_95_5_MKRN240010858-1A_22F27GLT4_L8_1.fq.gz S_95_5_MKRN240010858-1A_22F27GLT4_L8_2.fq.gz Folder C_16_1: Control, NIL16, biological replicate 1: C_16_1_MKRN240010839-1A_22C2L2LT4_L4_1.fq.gz C_16_1_MKRN240010839-1A_22C2L2LT4_L4_2.fq.gz Folder C_16_2: Control, NIL16, biological replicate 2: C_16_2_MKRN240010840-1A_22C2LCLT4_L8_1.fq.gz C_16_2_MKRN240010840-1A_22C2LCLT4_L8_2.fq.gz Folder C_16_3: Control, NIL16, biological replicate 3: C_16_3_MKRN240010841-1A_22C2LCLT4_L8_1.fq.gz C_16_3_MKRN240010841-1A_22C2LCLT4_L8_2.fq.gz Folder C_16_4: Control, NIL16, biological replicate 4: C_16_4_MKRN240010842-1A_22C2LCLT4_L8_1.fq.gz C_16_4_MKRN240010842-1A_22C2LCLT4_L8_2.fq.gz Folder C_95_1: Control, NIL95, biological replicate 1: C_95_1_MKRN240010843-1A_22C2LCLT4_L8_1.fq.gz C_95_1_MKRN240010843-1A_22C2LCLT4_L8_2.fq.gz Folder C_95_2: Control, NIL95, biological replicate 2: C_95_2_MKRN240010844-1A_22F27GLT4_L7_1.fq.gz C_95_2_MKRN240010844-1A_22F27GLT4_L7_2.fq.gz Folder C_95_3: Control, NIL95, biological replicate 3: C_95_3_MKRN240010845-1A_22F27GLT4_L8_1.fq.gz C_95_3_MKRN240010845-1A_22F27GLT4_L8_2.fq.gz Folder C_95_4: Control, NIL95, biological replicate 4: C_95_4_MKRN240010846-1A_22F27GLT4_L8_1.fq.gz C_95_4_MKRN240010846-1A_22F27GLT4_L8_2.fq.gz