DDX23 RNA-Seq in K562

General Information


RBP	DDX23
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX23-BGKcLV28-K562
ENCODE_series_ID	ENCSR053TLP
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR507WAD
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DDX23-BGKcLV28-73
Rep2	DDX23-BGKcLV28-74
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	21.2
Rep2_qPCR	25.0
Rep1_WB	64.0
Rep2_WB	57.0
Antibody Cat#	A300-695A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB902ODT
Status	Released
Project	ENCODE4
ID	845

Experiment Information (Status: Released)

	BGKcLV28-73	BGKcLV28-73	BGKcLV28-74	BGKcLV28-74
idx	1023	1023	1024	1024
TRCN#_or_BGC#	BGC#0000750	BGC#0000750	BGC#0000750	BGC#0000750
shRNA_or_gRNA_sequence	GTGGTGTACATTGGCTCCGC	GTGGTGTACATTGGCTCCGC	GTGGTGTACATTGGCTCCGC	GTGGTGTACATTGGCTCCGC
PAM	AGG	AGG	AGG	AGG
Name	DDX23_95	DDX23_95	DDX23_95	DDX23_95
Sample_ID	BGKcLV28-73	BGKcLV28-73	BGKcLV28-74	BGKcLV28-74
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	DDX23	DDX23	DDX23	DDX23
qPCR_result	21.2	21.2	25.0	25.0
Ave_qPCR	23.1	23.1
RT-qPCR_primer-F	accaggtgcagttgttaggg	accaggtgcagttgttaggg
RT-qPCR_primer-R	gctgcttggcttccttctta	gctgcttggcttccttctta
protein_conc	2370	2370	2697	2697
WB_result	64.0	72.0	57.0	76.4
Ave_WB	60.5
WB_DONE_date	6/30/21-2	7/23/24	JESS
MW	96KD		not match
IP
antibody_Cat#	A300-695A	A300-695A	LOT #1	LOT #1
Antibody DCC ID				7/23/24
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5157	5159	5158	5160

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

	BGKcLV28-73	BGKcLV28-74
Sample_ID	BGKcLV28-73	BGKcLV28-74
Sample Name
Sample Name	DDX23-BGKcLV28-73	DDX23-BGKcLV28-74
RBP	DDX23	DDX23
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9949	9950

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-73	BGKcLV28-74
Sample #	57	58
Sample Name	DDX23-BGKcLV28-73	DDX23-BGKcLV28-74
Sample_Name_Alias
Index Well Position	A12	B12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	327	333
Peak_Molarity	107.00	106.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A8.png	DNA_Library_set48-49/set3/B8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set2/A8.png	RNA_Library_set48-49/set2/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-73	BGKcLV28-74
RBP	DDX23	DDX23
Batch_ID	BGKcLV28	BGKcLV28
WB_result	64.000	57.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2118	2119

Sequencing Information

	BGKcLV28-73	BGKcLV28-74
Sample_ID	BGKcLV28-73	BGKcLV28-74
Sample Name	DDX23-BGKcLV28-73	DDX23-BGKcLV28-74
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	106,688,078	103,595,526
total_aligned_reads	104,820,450	99,265,818
unique_aligned_reads	97,006,362	91,556,184
percent_uniqueAligned	0.90925	0.88379
correlation_replicates	0.993612	0.993612
spikein_reads	36,430	15,584
percent_spikeins	0.00034	0.00015
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1869	1870

Data Submission Information

	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-74	BGKcLV28-74	BGKcLV28-74	BGKcLV28-74
ENCODE_alias	brenton-graveley:DDX23-BGKcLV28	brenton-graveley:DDX23-BGKcLV28-73	brenton-graveley:L-DDX23-BGKcLV28-73	brenton-graveley:DDX23-BGKcLV28-73_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX23-BGKcLV28-73_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX23-BGKcLV28-K562	brenton-graveley:DDX23-BGKcLV28-74	brenton-graveley:L-DDX23-BGKcLV28-74	brenton-graveley:DDX23-BGKcLV28-74_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX23-BGKcLV28-74_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR507WAD	ENCBS188SIQ	ENCLB037SNY	ENCFF317KFN	ENCFF340YIL	ENCSR053TLP	ENCBS852NWS	ENCLB420UVY	ENCFF555UKE	ENCFF921UYP
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-73	BGKcLV28-74	BGKcLV28-74	BGKcLV28-74	BGKcLV28-74
Sample Name	DDX23-BGKcLV28-73	DDX23-BGKcLV28-73	DDX23-BGKcLV28-73	DDX23-BGKcLV28-73	DDX23-BGKcLV28-73	DDX23-BGKcLV28-73	DDX23-BGKcLV28-74	DDX23-BGKcLV28-74	DDX23-BGKcLV28-74	DDX23-BGKcLV28-74
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV49_library_protocol					LV49_library_protocol
protocol_URL			L-DDX23-BGKcLV28-73.pdf					L-DDX23-BGKcLV28-74.pdf
ID	3499	3632	3766	3900	4034	7177	3633	3767	3901	4035

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-BGKcLV28-73_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1869	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3986
DDX23-BGKcLV28-73_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1869	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4044
DDX23-BGKcLV28-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGKcLV28-73_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19268
DDX23-BGKcLV28-73_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73/Aligned.sortedByCoord.out.bam		ENCORE2	19326
DDX23-BGKcLV28-73_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73/Aligned.sortedByCoord.out.bam		ENCORE2	19384
DDX23-BGKcLV28-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73/Aligned.sortedByCoord.out.bam		ENCORE2	19442
DDX23-BGKcLV28-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73/Aligned.sortedByCoord.out.bam		ENCORE2	19500
DDX23-BGKcLV28-73_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1869					GRCh38	V40	DDX23-BGKcLV28-73_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGKcLV28-73_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19558
DDX23-BGKcLV28-74_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1870	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3987
DDX23-BGKcLV28-74_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1870	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4045
DDX23-BGKcLV28-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGKcLV28-74_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19269
DDX23-BGKcLV28-74_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74/Aligned.sortedByCoord.out.bam		ENCORE2	19327
DDX23-BGKcLV28-74_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74/Aligned.sortedByCoord.out.bam		ENCORE2	19385
DDX23-BGKcLV28-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74/Aligned.sortedByCoord.out.bam		ENCORE2	19443
DDX23-BGKcLV28-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74/Aligned.sortedByCoord.out.bam		ENCORE2	19501
DDX23-BGKcLV28-74_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1870					GRCh38	V40	DDX23-BGKcLV28-74_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz,DDX23-BGKcLV28-74_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19559