DHX30 RNA-Seq in K562

General Information


RBP	DHX30
Cell_Line	K562
Method	shRNA
Exp_Name	DHX30-BGKLV24-K562
ENCODE_series_ID	ENCSR209YSW
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR345VVZ
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	DHX30_BGKLV24_15_17606
Rep2	DHX30_BGKLV24_16_17607
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	34.6
Rep2_qPCR	42.0
Rep1_WB	58.2
Rep2_WB	61.4
Antibody Cat#	A302-218A
Antibody Lot#	A302-218A
Antibody DCC ID	ENCAB596PUY
Status	Released
Project	ENCODE3
ID	560

Experiment Information (Status: Released)

	BGKLV24-15	BGKLV24-16
idx	352	353
TRCN#_or_BGC#	TRCN0000052032	TRCN0000052032
shRNA_or_gRNA_sequence	GAGTTGTTTGACGCAGCCAAA	GAGTTGTTTGACGCAGCCAAA
PAM
Name	DHX30_32	DHX30_32
Sample_ID	BGKLV24-15	BGKLV24-16
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	DHX30	DHX30
qPCR_result	34.6	42.0
Ave_qPCR	38.3
RT-qPCR_primer-F	aggctatggcagcaagaaga
RT-qPCR_primer-R	tgcgtcaaacaactcattcc
protein_conc	3532	3516
WB_result	58.2	61.4
Ave_WB	59.8
WB_DONE_date	4/6/2015
MW
IP	1	1
antibody_Cat#	A302-218A	A302-218A
Antibody DCC ID	ENCAB596PUY	ENCAB596PUY
submitted_to_DCC_date	5/4/2015
Rep1_TPM	29.6470923	0
Rep2_TPM	21.198731	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	401	402

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

	BGKLV24-15	BGKLV24-16
Sample_ID	BGKLV24-15	BGKLV24-16
Sample Name	DHX30_BGKLV24_15_17606	DHX30_BGKLV24_16_17607
Sample Name	DHX30_BGKLV24_15_17606	DHX30_BGKLV24_16_17607
RBP	DHX30	DHX30
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	858	859

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-15	BGKLV24-16
Sample #
Sample Name	DHX30-BGKLV24-15	DHX30-BGKLV24-16
Sample_Name_Alias	DHX30_BGKLV24_15_17606	DHX30_BGKLV24_16_17607
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/F2.png	DNA_Library_LV21-24/set1/G2.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C2.png	RNA_Library_LV20-22-24/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-15	BGKLV24-16
RBP	DHX30	DHX30
Batch_ID	BGKLV24	BGKLV24
WB_result	58.200	61.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2546	2547

Sequencing Information

	BGKLV24-15	BGKLV24-16
Sample_ID	BGKLV24-15	BGKLV24-16
Sample Name	DHX30_BGKLV24_15_17606	DHX30_BGKLV24_16_17607
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	41,720,000	45,780,000
total_aligned_reads	38,966,696	43,129,750
unique_aligned_reads	35,623,528	39,350,012
percent_uniqueAligned	0.85387	0.85955
correlation_replicates	0.992182	0.992182
spikein_reads	161,506	174,740
percent_spikeins	0.00387	0.00382
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1080	1081

Data Submission Information

	BGKLV24-15	BGKLV24-15
ENCODE_alias	brenton-graveley:DHX30_BGKLV24	brenton-graveley:DHX30-BGKLV24-K562
ENCODE_accession	ENCSR345VVZ	ENCSR209YSW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-15	BGKLV24-15
Sample Name	DHX30_BGKLV24_15_17606	DHX30_BGKLV24_15_17606
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2980	6665

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_BGKLV24_15_17606_ACAGTG_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1080	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17192
DHX30_BGKLV24_15_17606_ACAGTG_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1080	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17228
DHX30_BGKLV24_15_17606_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606_ACAGTG_L006_R1_001.fastq.gz,DHX30_BGKLV24_15_17606_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	17264
DHX30_BGKLV24_15_17606_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606/Aligned.sortedByCoord.out.bam		ENCORE2	17300
DHX30_BGKLV24_15_17606_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606/Aligned.sortedByCoord.out.bam		ENCORE2	17336
DHX30_BGKLV24_15_17606_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606/Aligned.sortedByCoord.out.bam		ENCORE2	17372
DHX30_BGKLV24_15_17606_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606/Aligned.sortedByCoord.out.bam		ENCORE2	17408
DHX30_BGKLV24_15_17606_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1080					GRCh38	V40	DHX30_BGKLV24_15_17606_ACAGTG_L006_R1_001.fastq.gz,DHX30_BGKLV24_15_17606_ACAGTG_L006_R2_001.fastq.gz		ENCORE2	17444
DHX30_BGKLV24_16_17607_GCCAAT_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1081	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17193
DHX30_BGKLV24_16_17607_GCCAAT_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1081	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17229
DHX30_BGKLV24_16_17607_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607_GCCAAT_L006_R1_001.fastq.gz,DHX30_BGKLV24_16_17607_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	17265
DHX30_BGKLV24_16_17607_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607/Aligned.sortedByCoord.out.bam		ENCORE2	17301
DHX30_BGKLV24_16_17607_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607/Aligned.sortedByCoord.out.bam		ENCORE2	17337
DHX30_BGKLV24_16_17607_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607/Aligned.sortedByCoord.out.bam		ENCORE2	17373
DHX30_BGKLV24_16_17607_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607/Aligned.sortedByCoord.out.bam		ENCORE2	17409
DHX30_BGKLV24_16_17607_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1081					GRCh38	V40	DHX30_BGKLV24_16_17607_GCCAAT_L006_R1_001.fastq.gz,DHX30_BGKLV24_16_17607_GCCAAT_L006_R2_001.fastq.gz		ENCORE2	17445