DDX5 RNA-Seq in HepG2

General Information


RBP	DDX5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX5-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	DDX5-BGHcLV39-5
Rep2	DDX5-BGHcLV39-6
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	58.7
Rep2_qPCR	57.3
Rep1_WB	86.6
Rep2_WB	95.7
Antibody Cat#	A300-522A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1242

Experiment Information (Status: Submitting)

	BGHcLV39-5	BGHcLV39-5	BGHcLV39-5	BGHcLV39-6	BGHcLV39-6	BGHcLV39-6
idx	1205	1205	1205	1206	1206	1206
TRCN#_or_BGC#	BGC#0000899	BGC#0000899	BGC#0000899	BGC#0000899	BGC#0000899	BGC#0000899
shRNA_or_gRNA_sequence	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG	TTTGGTGCACCTCGATTTGG
PAM	agg	agg	agg	agg	agg	agg
Name	DDX5_86	DDX5_86	DDX5_86	DDX5_86	DDX5_86	DDX5_86
Sample_ID	BGHcLV39-5	BGHcLV39-5	BGHcLV39-5	BGHcLV39-6	BGHcLV39-6	BGHcLV39-6
transduction_Date	6/10/23	6/10/23	6/10/23	6/10/23	6/10/23	6/10/23
days	D6	D6	D6	D6	D6	D6
RBP_name	DDX5	DDX5	DDX5	DDX5	DDX5	DDX5
qPCR_result			58.7			57.3
Ave_qPCR			58.0
RT-qPCR_primer-F			cccaagttgcttcagttggt
RT-qPCR_primer-R			gtatctgtcccgacggtcat
protein_conc	1722	1722	1722	2181	2181	2181
WB_result	NO CLEAR BAND ON THE POSITION	73.4	86.6		70.1	95.7
Ave_WB		71.8	91.2
WB_DONE_date	6/28/23	7/5/23	6/29/23
MW	69kd	69kd	69kd
IP
antibody_Cat#	9877S	A300-523A	A300-522A	lot # 2	lot # 3	lot # 1
Antibody DCC ID
submitted_to_DCC_date		9/6/23	9/6/23
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action			Ready			Ready
Library_start_date
repeat_library
Note
ID	7392	7394	7396	7393	7395	7397

Western Blot

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

Experiment Status

	BGHcLV39-5	BGHcLV39-5	BGHcLV39-5	BGHcLV39-6	BGHcLV39-6	BGHcLV39-6
Sample_ID	BGHcLV39-5	BGHcLV39-5	BGHcLV39-5	BGHcLV39-6	BGHcLV39-6	BGHcLV39-6
Sample Name
Sample Name	DDX5-BGHcLV39-5			DDX5-BGHcLV39-6
RBP	DDX5	DDX5	DDX5	DDX5	DDX5	DDX5
Cell_Line	HepG2	HepG2	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	NotSatisfied	Submitting	NotSatisfied	NotSatisfied
Status_date	2023-12-30	2023-08-28	2023-08-28	2023-12-30	2023-08-28	2023-08-28
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	11976	12002	12004	11977	12003	12005

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-5	BGHcLV39-6
Sample #	3	4
Sample Name	DDX5-BGHcLV39-5	DDX5-BGHcLV39-6
Sample_Name_Alias
Index Well Position	C01	D01
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	286	277
Peak_Molarity	36.60	48.30
libSampleQC_DNA_Well	DNA_Library_set63/set1/C9.png	DNA_Library_set63/set1/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/C9.png	RNA_Library_set63/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-5	BGHcLV39-6
RBP	DDX5	DDX5
Batch_ID	BGHcLV39	BGHcLV39
WB_result	86.600	95.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3746	3747

Sequencing Information

	BGHcLV39-5	BGHcLV39-6
Sample_ID	BGHcLV39-5	BGHcLV39-6
Sample Name	DDX5-BGHcLV39-5	DDX5-BGHcLV39-6
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	16,607,197	15,392,248
total_aligned_reads	13,636,388	12,576,991
unique_aligned_reads	12,821,842	11,852,721
percent_uniqueAligned	0.77207	0.77004
correlation_replicates	0.998284	0.998284
spikein_reads	42,210	15,638
percent_spikeins	0.00254	0.00102
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2645	2646

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-BGHcLV39-5_S478_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2645	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	8632
DDX5-BGHcLV39-5_S478_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2645	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	8658
DDX5-BGHcLV39-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2645					GRCh38	V40	DDX5-BGHcLV39-5_S478_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGHcLV39-5_S478_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9929
DDX5-BGHcLV39-5_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	2645					GRCh38	V40	DDX5-BGHcLV39-5/Aligned.sortedByCoord.out.bam		ENCORE2	9955
DDX5-BGHcLV39-5_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	2645					GRCh38	V40	DDX5-BGHcLV39-5/Aligned.sortedByCoord.out.bam		ENCORE2	9981
DDX5-BGHcLV39-5_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	2645					GRCh38	V40	DDX5-BGHcLV39-5/Aligned.sortedByCoord.out.bam		ENCORE2	10007
DDX5-BGHcLV39-5_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	2645					GRCh38	V40	DDX5-BGHcLV39-5/Aligned.sortedByCoord.out.bam		ENCORE2	10033
DDX5-BGHcLV39-5_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2645					GRCh38	V40	DDX5-BGHcLV39-5_S478_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGHcLV39-5_S478_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10059
DDX5-BGHcLV39-6_S479_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2646	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	8633
DDX5-BGHcLV39-6_S479_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2646	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	8659
DDX5-BGHcLV39-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2646					GRCh38	V40	DDX5-BGHcLV39-6_S479_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGHcLV39-6_S479_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9930
DDX5-BGHcLV39-6_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	2646					GRCh38	V40	DDX5-BGHcLV39-6/Aligned.sortedByCoord.out.bam		ENCORE2	9956
DDX5-BGHcLV39-6_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	2646					GRCh38	V40	DDX5-BGHcLV39-6/Aligned.sortedByCoord.out.bam		ENCORE2	9982
DDX5-BGHcLV39-6_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	2646					GRCh38	V40	DDX5-BGHcLV39-6/Aligned.sortedByCoord.out.bam		ENCORE2	10008
DDX5-BGHcLV39-6_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	2646					GRCh38	V40	DDX5-BGHcLV39-6/Aligned.sortedByCoord.out.bam		ENCORE2	10034
DDX5-BGHcLV39-6_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2646					GRCh38	V40	DDX5-BGHcLV39-6_S479_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX5-BGHcLV39-6_S479_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10060