DDX5 RNA-Seq in K562

General Information


RBP	DDX5
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX5-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DDX5-BGKcLV37-9
Rep2	DDX5-BGKcLV37-10
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	44.7
Rep2_qPCR	52.1
Rep1_WB	59.6
Rep2_WB	64.8
Antibody Cat#	A300-523A
Antibody Lot#	lot # 3
Antibody DCC ID	ENCAB374ZWM
Status	Submitted
Project	ENCORE2
ID	1050

Experiment Information (Status: Submitting)

	BGKcLV37-9	BGKcLV37-9	BGKcLV37-10	BGKcLV37-10
idx	1361	0	1362	0
TRCN#_or_BGC#	BGC#0000899	BGC#0000899	BGC#0000899	BGC#0000899
shRNA_or_gRNA_sequence	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG
PAM	agg	agg	agg	agg
Name	DDX5_86	DDX5_86	DDX5_86	DDX5_86
Sample_ID	BGKcLV37-9	BGKcLV37-9	BGKcLV37-10	BGKcLV37-10
transduction_Date	9/20/22	9/20/22	9/20/22	9/20/22
days	D6	D6	D6	D6
RBP_name	DDX5	DDX5	DDX5	DDX5
qPCR_result	44.7	44.7	52.1	52.1
Ave_qPCR	48.4	48.4
RT-qPCR_primer-F	cccaagttgcttcagttggt	cccaagttgcttcagttggt
RT-qPCR_primer-R	gtatctgtcccgacggtcat	gtatctgtcccgacggtcat
protein_conc	1716	1716	1629	1629
WB_result	59.6	55.1	64.8	59.4
Ave_WB	62.2	57.2
WB_DONE_date	10/12/22	10/18/22	JESS, Licor
MW	69KD	69KD
IP
antibody_Cat#	A300-523A	A300-522A	lot # 3	lot # 1
Antibody DCC ID	ENCAB374ZWM	ENCAB538ILD
submitted_to_DCC_date	8/29/23	8/29/23
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5509	5511	5510	5512

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX5	Product_ID: A300-523A Lot_ID: 3 Source: Bethyl Labs Target Name: DDX5-human
DDX5	Product_ID: A300-522A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX5-human

Experiment Status

	BGKcLV37-9	BGKcLV37-10
Sample_ID	BGKcLV37-9	BGKcLV37-10
Sample Name
Sample Name	DDX5-BGKcLV37-9	DDX5-BGKcLV37-10
RBP	DDX5	DDX5
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11084	11085

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-9	BGKcLV37-10
Sample #	23	24
Sample Name	DDX5-BGKcLV37-9	DDX5-BGKcLV37-10
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	305	302
Peak_Molarity	51.40	53.60
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G3.png	DNA_Library_set54-56/set1/H3.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set54-56/set1/G3.png	RNA_Library_set54-56/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-9	BGKcLV37-10
RBP	DDX5	DDX5
Batch_ID	BGKcLV37	BGKcLV37
WB_result	59.600	64.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3394	3395

Sequencing Information

	BGKcLV37-9	BGKcLV37-10
Sample_ID	BGKcLV37-9	BGKcLV37-10
Sample Name	DDX5-BGKcLV37-9	DDX5-BGKcLV37-10
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	53,749,350	37,265,083
total_aligned_reads	50,999,153	35,061,049
unique_aligned_reads	47,304,757	32,616,696
percent_uniqueAligned	0.88010	0.87526
correlation_replicates	0.982535	0.982535
spikein_reads	5,574	5,984
percent_spikeins	0.00010	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2267	2268

Data Submission Information DCC submission information was not avaliable

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
DDX5-BGKcLV37-9_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2267	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8385
DDX5-BGKcLV37-9_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2267	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8435
DDX5-BGKcLV37-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGKcLV37-9_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25626
DDX5-BGKcLV37-9_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9/Aligned.sortedByCoord.out.bam		ENCORE2	25676
DDX5-BGKcLV37-9_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9/Aligned.sortedByCoord.out.bam		ENCORE2	25726
DDX5-BGKcLV37-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9/Aligned.sortedByCoord.out.bam		ENCORE2	25776
DDX5-BGKcLV37-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9/Aligned.sortedByCoord.out.bam		ENCORE2	25826
DDX5-BGKcLV37-9_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2267					GRCh38	V40	DDX5-BGKcLV37-9_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGKcLV37-9_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25876
DDX5-BGKcLV37-10_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2268	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8384
DDX5-BGKcLV37-10_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2268	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8434
DDX5-BGKcLV37-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGKcLV37-10_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25625
DDX5-BGKcLV37-10_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10/Aligned.sortedByCoord.out.bam		ENCORE2	25675
DDX5-BGKcLV37-10_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10/Aligned.sortedByCoord.out.bam		ENCORE2	25725
DDX5-BGKcLV37-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10/Aligned.sortedByCoord.out.bam		ENCORE2	25775
DDX5-BGKcLV37-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10/Aligned.sortedByCoord.out.bam		ENCORE2	25825
DDX5-BGKcLV37-10_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2268					GRCh38	V40	DDX5-BGKcLV37-10_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGKcLV37-10_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25875