DDX56 RNA-Seq in HepG2

General Information


RBP	DDX56
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX56-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DDX56-BGHcLV39-11
Rep2	DDX56-BGHcLV39-12
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	23.2
Rep2_qPCR	34.2
Rep1_WB	64.1
Rep2_WB	71.3
Antibody Cat#	A302-979A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1243

Experiment Information (Status: Submitting)

	BGHcLV39-11	BGHcLV39-12
idx	1211	1212
TRCN#_or_BGC#	BGC#0000905	BGC#0000905
shRNA_or_gRNA_sequence	CCGTCTTCCCGGAGCCCGTG	CCGTCTTCCCGGAGCCCGTG
PAM	cgg	cgg
Name	DDX56_82	DDX56_82
Sample_ID	BGHcLV39-11	BGHcLV39-12
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	DDX56	DDX56
qPCR_result	23.2	34.2
Ave_qPCR	28.7
RT-qPCR_primer-F	ccggatttaccaggcttttc
RT-qPCR_primer-R	gcagctgggactcctgtaac
protein_conc	1519	1465
WB_result	64.1	71.3
Ave_WB	67.7
WB_DONE_date	7/3/23
MW	62KD
IP
antibody_Cat#	A302-979A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7402	7403

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

	BGHcLV39-11	BGHcLV39-12
Sample_ID	BGHcLV39-11	BGHcLV39-12
Sample Name
Sample Name	DDX56-BGHcLV39-11	DDX56-BGHcLV39-12
RBP	DDX56	DDX56
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11978	11979

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-11	BGHcLV39-12
Sample #	5	6
Sample Name	DDX56-BGHcLV39-11	DDX56-BGHcLV39-12
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	282	271
Peak_Molarity	26.20	20.40
libSampleQC_DNA_Well	DNA_Library_set63/set1/E9.png	DNA_Library_set63/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/E9.png	RNA_Library_set63/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-11	BGHcLV39-12
RBP	DDX56	DDX56
Batch_ID	BGHcLV39	BGHcLV39
WB_result	64.100	71.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3748	3749

Sequencing Information

	BGHcLV39-11	BGHcLV39-12
Sample_ID	BGHcLV39-11	BGHcLV39-12
Sample Name	DDX56-BGHcLV39-11	DDX56-BGHcLV39-12
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	36,021,830	38,761,390
total_aligned_reads	28,787,985	30,710,353
unique_aligned_reads	27,126,255	28,934,156
percent_uniqueAligned	0.75305	0.74647
correlation_replicates	0.999973	0.999973
spikein_reads	30,896	33,912
percent_spikeins	0.00086	0.00087
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2647	2648

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-BGHcLV39-11_S480_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2647	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8630
DDX56-BGHcLV39-11_S480_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2647	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8656
DDX56-BGHcLV39-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11_S480_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGHcLV39-11_S480_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9927
DDX56-BGHcLV39-11_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11/Aligned.sortedByCoord.out.bam		ENCORE2	9953
DDX56-BGHcLV39-11_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11/Aligned.sortedByCoord.out.bam		ENCORE2	9979
DDX56-BGHcLV39-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11/Aligned.sortedByCoord.out.bam		ENCORE2	10005
DDX56-BGHcLV39-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11/Aligned.sortedByCoord.out.bam		ENCORE2	10031
DDX56-BGHcLV39-11_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2647					GRCh38	V40	DDX56-BGHcLV39-11_S480_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGHcLV39-11_S480_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10057
DDX56-BGHcLV39-12_S481_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2648	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8631
DDX56-BGHcLV39-12_S481_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2648	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8657
DDX56-BGHcLV39-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12_S481_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGHcLV39-12_S481_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9928
DDX56-BGHcLV39-12_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12/Aligned.sortedByCoord.out.bam		ENCORE2	9954
DDX56-BGHcLV39-12_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12/Aligned.sortedByCoord.out.bam		ENCORE2	9980
DDX56-BGHcLV39-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12/Aligned.sortedByCoord.out.bam		ENCORE2	10006
DDX56-BGHcLV39-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12/Aligned.sortedByCoord.out.bam		ENCORE2	10032
DDX56-BGHcLV39-12_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2648					GRCh38	V40	DDX56-BGHcLV39-12_S481_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX56-BGHcLV39-12_S481_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10058