https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=3&WebEnv=MCID_64a22f9db107af540cd194c6&o=acc_s%3Aa&s=SRR1039508,SRR1039509,SRR1039510,SRR1039511,SRR1039512,SRR1039513,SRR1039514,SRR1039515,SRR1039516,SRR1039517,SRR1039518,SRR1039519,SRR1039520,SRR1039521,SRR1039522,SRR1039523

Airway smooth muscle cells

Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. “RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.” PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

From the abstract, a brief description of the RNA-Seq experiment on airway smooth muscle (ASM) cell lines: “Using RNA-Seq, a high-throughput sequencing method, we characterized transcriptomic changes in four primary human ASM cell lines that were treated with dexamethasone - a potent synthetic glucocorticoid (1 micromolar for 18 hours).

Sample	Run	BioSample	AvgSpotLen	Bases	Bytes	Cell_line	ercc_mix	Experiment	GEO_Accession	create_date	Sample Name	Treatment
1	SRR1039508	SAMN02422669	126	2.89 G	1.55 Gb	N61311	-	SRX384345	GSM1275862	2013-11-2616:39:00Z	GSM1275862	Untreated
2	SRR1039509	SAMN02422675	126	2.67 G	1.45 Gb	N61311	-	SRX384346	GSM1275863	2013-11-2616:38:00Z	GSM1275863	Dexamethasone
3	SRR1039510	SAMN02422668	126	2.88 G	1.56 Gb	N61311	-	SRX384347	GSM1275864	2013-11-2616:41:00Z	GSM1275864	Albuterol
4	SRR1039511	SAMN02422667	126	2.76 G	1.48 Gb	N61311	-	SRX384348	GSM1275865	2013-11-2616:42:00Z	GSM1275865	Albuterol_Dexamethasone
5	SRR1039512	SAMN02422678	126	3.55 G	2.01 Gb	N052611	-	SRX384349	GSM1275866	2013-11-2616:47:00Z	GSM1275866	Untreated
6	SRR1039513	SAMN02422670	87	3.79 G	2.22 Gb	N052611	1	SRX384350	GSM1275867	2013-11-2617:02:00Z	GSM1275867	Dexamethasone
7	SRR1039514	SAMN02422681	126	5.04 G	3.03 Gb	N052611	1	SRX384351	GSM1275868	2013-11-2616:49:00Z	GSM1275868	Albuterol
8	SRR1039515	SAMN02422671	114	3.38 G	1.86 Gb	N052611	1	SRX384352	GSM1275869	2013-11-2617:03:00Z	GSM1275869	Albuterol_Dexamethasone
9	SRR1039516	SAMN02422682	120	3.61 G	2.10 Gb	N080611	-	SRX384353	GSM1275870	2013-11-2617:03:00Z	GSM1275870	Untreated
10	SRR1039517	SAMN02422673	126	4.32 G	2.59 Gb	N080611	-	SRX384354	GSM1275871	2013-11-2616:49:00Z	GSM1275871	Dexamethasone
11	SRR1039518	SAMN02422679	126	3.84 G	2.30 Gb	N080611	-	SRX384355	GSM1275872	2013-11-2616:49:00Z	GSM1275872	Albuterol
12	SRR1039519	SAMN02422672	107	3.38 G	1.96 Gb	N080611	-	SRX384356	GSM1275873	2013-11-2617:02:00Z	GSM1275873	Albuterol_Dexamethasone
13	SRR1039520	SAMN02422683	101	3.52 G	2.06 Gb	N061011	1	SRX384357	GSM1275874	2013-11-2617:04:00Z	GSM1275874	Untreated
14	SRR1039521	SAMN02422677	98	4.07 G	2.39 Gb	N061011	1	SRX384358	GSM1275875	2013-11-2617:08:00Z	GSM1275875	Dexamethasone
15	SRR1039522	SAMN02422680	125	3.56 G	1.96 Gb	N061011	1	SRX384359	GSM1275876	2013-11-2617:04:00Z	GSM1275876	Albuterol
16	SRR1039523	SAMN02422674	126	3.92 G	2.22 Gb	N061011	1	SRX384360	GSM1275877	2013-11-2616:52:00Z	GSM1275877	Albuterol_Dexamethasone

Fetching FASTQ files from SRA

Install the sra-tool kit if not yet installed. For example:

Code Block
#Create a conda environment conda create -n sra -c bioconda sra-tools conda activate sra

Save a list of SRA accession numbers to download in a file called SraAccList.txt

Code Block

language	bash

SRR1039508
SRR1039509
SRR1039510
SRR1039511
SRR1039512
SRR1039513
SRR1039514
SRR1039515
SRR1039516
SRR1039517
SRR1039518
SRR1039519
SRR1039520
SRR1039521
SRR1039522
SRR1039523

Use the following PBS Pro submission script to fetch the FASTQ files for all listed samples. Note, data will be downloaded to the folder where the job is submitted. Example script (fetch_SraAccList.pbs).

Option 1:

Code Block

language	bash

#!/bin/bash
#usage: ./fetch_SraAccList.sh SraAccList.txt

for r1 in `cat $1`;
do

  qsub <<EOF
#!/bin/bash -l

#PBS -N $(basename $r1)
#PBS -l walltime=10:00:00
#PBS -l mem=8G
#PBS -l ncpus=4

cd $PBS_O_WORKDIR

#activate conda environment
conda activate sra

#fetch FASTQ files
prefetch $r1
fastq-dump --split-files $r1  

EOF
done

Option 2:

Code Block

language	bash

#!/bin/bash
#PBS -N SRA
#PBS -l walltime=12:00:00
#PBS -l mem=8G
#PBS -l ncpus=4

cd $PBS_O_WORKDIR

#activate conda environment
conda activate sra

LIST='SraAccList.txt'

#fetch FASTQ files
for i in `cat $LIST`;
do
  echo $i
  prefetch $i
  fastq-dump --split-files $i
done

Submit the job to the HPC cluster:

Code Block

language	powershell

./fetch_SraAccList.sh SraAccList.txt

Monitor jobs:

Code Block
qjobs

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