DHX30 RNA-Seq in HepG2

General Information


RBP	DHX30
Cell_Line	HepG2
Method	shRNA
Exp_Name	DHX30-BGHLV20-HepG2
ENCODE_series_ID	ENCSR769TJS
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR853PBF
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	DHX30-32-BGHLV20-19_17714
Rep2	DHX30-32-BGHLV20-20_17715
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	81.9
Rep2_qPCR	85.0
Rep1_WB	68.8
Rep2_WB	67.4
Antibody Cat#	A302-218A
Antibody Lot#	A302-218A
Antibody DCC ID	ENCAB596PUY
Status	Released
Project	ENCODE3
ID	492

Experiment Information (Status: Released)

	BGHLV20-19	BGHLV20-20
idx	383	384
TRCN#_or_BGC#	TRCN0000052032	TRCN0000052032
shRNA_or_gRNA_sequence	GAGTTGTTTGACGCAGCCAAA	GAGTTGTTTGACGCAGCCAAA
PAM
Name	DHX30_32	DHX30_32
Sample_ID	BGHLV20-19	BGHLV20-20
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	DHX30	DHX30
qPCR_result	81.9	85.0
Ave_qPCR	83.4
RT-qPCR_primer-F	aggctatggcagcaagaaga
RT-qPCR_primer-R	tgcgtcaaacaactcattcc
protein_conc	5839	5932
WB_result	68.8	67.4
Ave_WB	68.1
WB_DONE_date	4/6/2015
MW	134kDa
IP	1	1
antibody_Cat#	A302-218A	A302-218A
Antibody DCC ID	ENCAB596PUY	ENCAB596PUY
submitted_to_DCC_date	5/4/2015
Rep1_TPM	8	0
Rep2_TPM	9.9	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2448	2449

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DHX30	Product_ID: A302-218A Lot_ID: 1 Source: Bethyl Labs Target Name: DHX30-human

Experiment Status

	BGHLV20-19	BGHLV20-20
Sample_ID	BGHLV20-19	BGHLV20-20
Sample Name	DHX30-32-BGHLV20-19_17714	DHX30-32-BGHLV20-20_17715
Sample Name	DHX30-32-BGHLV20-19_17714	DHX30-32-BGHLV20-20_17715
RBP	DHX30	DHX30
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	714	715

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-19	BGHLV20-20
Sample #
Sample Name	DHX30-BGHLV20-19	DHX30-BGHLV20-20
Sample_Name_Alias	DHX30-32-BGHLV20-19_17714	DHX30-32-BGHLV20-20_17715
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A2.png	DNA_Library_LV20-22-23/set1/B2.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C8.png	RNA_Library_LV20-22-24/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-19	BGHLV20-20
RBP	DHX30	DHX30
Batch_ID	BGHLV20	BGHLV20
WB_result	68.800	67.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2400	2401

Sequencing Information

	BGHLV20-19	BGHLV20-20
Sample_ID	BGHLV20-19	BGHLV20-20
Sample Name	DHX30-32-BGHLV20-19_17714	DHX30-32-BGHLV20-20_17715
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	43,480,000	44,710,000
total_aligned_reads	36,987,052	38,236,854
unique_aligned_reads	35,053,814	36,183,890
percent_uniqueAligned	0.80621	0.80930
correlation_replicates	0.997395	0.997395
spikein_reads	177,598	187,346
percent_spikeins	0.00408	0.00419
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1168	1169

Data Submission Information

	BGHLV20-19	BGHLV20-19
ENCODE_alias	brenton-graveley:DHX30-32-BGHLV20	brenton-graveley:DHX30-BGHLV20-HepG2
ENCODE_accession	ENCSR853PBF	ENCSR769TJS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-19	BGHLV20-19
Sample Name	DHX30-32-BGHLV20-19_17714	DHX30-32-BGHLV20-19_17714
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2906	6664

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DHX30-32-BGHLV20-19_17714_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1168	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15592
DHX30-32-BGHLV20-19_17714_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1168	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15634
DHX30-32-BGHLV20-19_17714_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714_GATCAG_L002_R1_001.fastq.gz,DHX30-32-BGHLV20-19_17714_GATCAG_L002_R2_001.fastq.gz		ENCORE2	15676
DHX30-32-BGHLV20-19_17714_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714/Aligned.sortedByCoord.out.bam		ENCORE2	15718
DHX30-32-BGHLV20-19_17714_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714/Aligned.sortedByCoord.out.bam		ENCORE2	15760
DHX30-32-BGHLV20-19_17714_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714/Aligned.sortedByCoord.out.bam		ENCORE2	15802
DHX30-32-BGHLV20-19_17714_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714/Aligned.sortedByCoord.out.bam		ENCORE2	15844
DHX30-32-BGHLV20-19_17714_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1168					GRCh38	V40	DHX30-32-BGHLV20-19_17714_GATCAG_L002_R1_001.fastq.gz,DHX30-32-BGHLV20-19_17714_GATCAG_L002_R2_001.fastq.gz		ENCORE2	15886
DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1169	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15593
DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1169	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15635
DHX30-32-BGHLV20-20_17715_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R1_001.fastq.gz,DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	15677
DHX30-32-BGHLV20-20_17715_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715/Aligned.sortedByCoord.out.bam		ENCORE2	15719
DHX30-32-BGHLV20-20_17715_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715/Aligned.sortedByCoord.out.bam		ENCORE2	15761
DHX30-32-BGHLV20-20_17715_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715/Aligned.sortedByCoord.out.bam		ENCORE2	15803
DHX30-32-BGHLV20-20_17715_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715/Aligned.sortedByCoord.out.bam		ENCORE2	15845
DHX30-32-BGHLV20-20_17715_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1169					GRCh38	V40	DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R1_001.fastq.gz,DHX30-32-BGHLV20-20_17715_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	15887