DDX23 RNA-Seq in HepG2

General Information


RBP	DDX23
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX23-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DDX23-BGHcLV34-23
Rep2	DDX23-BGHcLV34-24
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	51.7
Rep2_WB	49.6
Antibody Cat#	A300-695A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	943

Experiment Information (Status: Submitting)

	BGHcLV34-23	BGHcLV34-24
idx	1093	1094
TRCN#_or_BGC#	BGC#0000751	BGC#0000751
shRNA_or_gRNA_sequence	GGACTGGCGGATCTTCCGTG	GGACTGGCGGATCTTCCGTG
PAM	AGG	AGG
Name	DDX23_92	DDX23_92
Sample_ID	BGHcLV34-23	BGHcLV34-24
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	DDX23	DDX23
qPCR_result	24.7	43.5
Ave_qPCR
RT-qPCR_primer-F	accaggtgcagttgttaggg
RT-qPCR_primer-R	gctgcttggcttccttctta
protein_conc	2701	3555
WB_result	75.0	79.0
Ave_WB	77.0
WB_DONE_date	7/23/24
MW	96KD
IP	Rabbit / I
antibody_Cat#	A300-695A	LOT #1
Antibody DCC ID		7/23/24
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7272	7273

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX23	Product_ID: A300-695A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX23-human

Experiment Status

	BGHcLV34-23	BGHcLV34-24
Sample_ID	BGHcLV34-23	BGHcLV34-24
Sample Name
Sample Name	DDX23-BGHcLV34-23	DDX23-BGHcLV34-24
RBP	DDX23	DDX23
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10803	10804

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-23	BGHcLV34-24
Sample #	7	8
Sample Name	DDX23-BGHcLV34-23	DDX23-BGHcLV34-24
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	285	278
Peak_Molarity	27.90	13.30
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/G5.png	DNA_Library_set54-56/set3/H5.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set54-56/set2/G1.png	RNA_Library_set54-56/set2/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-23	BGHcLV34-24
RBP	DDX23	DDX23
Batch_ID	BGHcLV34	BGHcLV34
WB_result	51.700	49.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3324	3325

Sequencing Information

	BGHcLV34-23	BGHcLV34-24
Sample_ID	BGHcLV34-23	BGHcLV34-24
Sample Name	DDX23-BGHcLV34-23	DDX23-BGHcLV34-24
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	70,606,102	71,344,886
total_aligned_reads	58,501,756	51,846,516
unique_aligned_reads	55,201,294	48,723,830
percent_uniqueAligned	0.78182	0.68293
correlation_replicates	0.979566	0.979566
spikein_reads	10,050	7,612
percent_spikeins	0.00014	0.00011
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2201	2202

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
DDX23-BGHcLV34-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2201	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8496
DDX23-BGHcLV34-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2201	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8546
DDX23-BGHcLV34-23_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	17742
DDX23-BGHcLV34-23_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	17792
DDX23-BGHcLV34-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	17842
DDX23-BGHcLV34-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	17892
DDX23-BGHcLV34-23_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGHcLV34-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17942
DDX23-BGHcLV34-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2201					GRCh38	V40	DDX23-BGHcLV34-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGHcLV34-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29283
DDX23-BGHcLV34-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2202	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8497
DDX23-BGHcLV34-24_S8_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2202	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8547
DDX23-BGHcLV34-24_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	17743
DDX23-BGHcLV34-24_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	17793
DDX23-BGHcLV34-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	17843
DDX23-BGHcLV34-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	17893
DDX23-BGHcLV34-24_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGHcLV34-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17943
DDX23-BGHcLV34-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2202					GRCh38	V40	DDX23-BGHcLV34-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGHcLV34-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29284