DDX56 RNA-Seq in K562

General Information


RBP	DDX56
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX56-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	DDX56-BGKcLV37-15
Rep2	DDX56-BGKcLV37-16
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	28.1
Rep2_qPCR	23.8
Rep1_WB	64.9
Rep2_WB	79.9
Antibody Cat#	A302-979A
Antibody Lot#	lot # 1
Antibody DCC ID	ENCAB108KLZ
Status	Submitted
Project	ENCORE2
ID	1053

Experiment Information (Status: Submitting)

	BGKcLV37-15	BGKcLV37-16
idx	1367	1368
TRCN#_or_BGC#	BGC#0000905	BGC#0000905
shRNA_or_gRNA_sequence	CCGTCTTCCCGGAGCCCGTG	CCGTCTTCCCGGAGCCCGTG
PAM	cgg	cgg
Name	DDX56_82	DDX56_82
Sample_ID	BGKcLV37-15	BGKcLV37-16
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	DDX56	DDX56
qPCR_result	28.1	23.8
Ave_qPCR	25.9
RT-qPCR_primer-F	ccggatttaccaggcttttc
RT-qPCR_primer-R	gcagctgggactcctgtaac
protein_conc	1988	2212
WB_result	64.9	79.9
Ave_WB	72.4
WB_DONE_date	9/28/22	JESS
MW	62KD
IP
antibody_Cat#	A302-979A	lot # 1
Antibody DCC ID	ENCAB108KLZ
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5517	5518

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX56	Product_ID: A302-979A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX56-human

Experiment Status

	BGKcLV37-15	BGKcLV37-16
Sample_ID	BGKcLV37-15	BGKcLV37-16
Sample Name
Sample Name	DDX56-BGKcLV37-15	DDX56-BGKcLV37-16
RBP	DDX56	DDX56
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11090	11091

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-15	BGKcLV37-16
Sample #	29	30
Sample Name	DDX56-BGKcLV37-15	DDX56-BGKcLV37-16
Sample_Name_Alias
Index Well Position	E04	F04
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	308	296
Peak_Molarity	59.10	58.00
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E4.png	DNA_Library_set54-56/set1/F4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/E4.png	RNA_Library_set54-56/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-15	BGKcLV37-16
RBP	DDX56	DDX56
Batch_ID	BGKcLV37	BGKcLV37
WB_result	64.900	79.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3400	3401

Sequencing Information

	BGKcLV37-15	BGKcLV37-16
Sample_ID	BGKcLV37-15	BGKcLV37-16
Sample Name	DDX56-BGKcLV37-15	DDX56-BGKcLV37-16
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	44,428,694	57,609,934
total_aligned_reads	42,374,763	54,375,091
unique_aligned_reads	39,566,907	50,355,451
percent_uniqueAligned	0.89057	0.87408
correlation_replicates	0.990175	0.990175
spikein_reads	1,498	3,268
percent_spikeins	0.00003	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2273	2274

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
DDX56-BGKcLV37-15_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2273	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	8382
DDX56-BGKcLV37-15_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2273	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	8432
DDX56-BGKcLV37-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2273					GRCh38	V40	DDX56-BGKcLV37-15_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGKcLV37-15_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25623
DDX56-BGKcLV37-15_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	2273					GRCh38	V40	DDX56-BGKcLV37-15/Aligned.sortedByCoord.out.bam		ENCORE2	25673
DDX56-BGKcLV37-15_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	2273					GRCh38	V40	DDX56-BGKcLV37-15/Aligned.sortedByCoord.out.bam		ENCORE2	25723
DDX56-BGKcLV37-15_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	2273					GRCh38	V40	DDX56-BGKcLV37-15/Aligned.sortedByCoord.out.bam		ENCORE2	25773
DDX56-BGKcLV37-15_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	2273					GRCh38	V40	DDX56-BGKcLV37-15/Aligned.sortedByCoord.out.bam		ENCORE2	25823
DDX56-BGKcLV37-15_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2273					GRCh38	V40	DDX56-BGKcLV37-15_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGKcLV37-15_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25873
DDX56-BGKcLV37-16_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2274	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	8383
DDX56-BGKcLV37-16_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2274	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	8433
DDX56-BGKcLV37-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2274					GRCh38	V40	DDX56-BGKcLV37-16_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGKcLV37-16_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25624
DDX56-BGKcLV37-16_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	2274					GRCh38	V40	DDX56-BGKcLV37-16/Aligned.sortedByCoord.out.bam		ENCORE2	25674
DDX56-BGKcLV37-16_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	2274					GRCh38	V40	DDX56-BGKcLV37-16/Aligned.sortedByCoord.out.bam		ENCORE2	25724
DDX56-BGKcLV37-16_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	2274					GRCh38	V40	DDX56-BGKcLV37-16/Aligned.sortedByCoord.out.bam		ENCORE2	25774
DDX56-BGKcLV37-16_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	2274					GRCh38	V40	DDX56-BGKcLV37-16/Aligned.sortedByCoord.out.bam		ENCORE2	25824
DDX56-BGKcLV37-16_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2274					GRCh38	V40	DDX56-BGKcLV37-16_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGKcLV37-16_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25874