DDX43 RNA-Seq in K562

General Information


RBP	DDX43
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX43-BGKcLV23-K562
ENCODE_series_ID	ENCSR049SQV
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR390TOZ
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	DDX43-BGKcLV23-31
Rep2	DDX43-BGKcLV23-32
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	76.2
Rep2_WB	69.1
Antibody Cat#	A302-328A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB412ETD
Status	Released
Project	ENCODE4
ID	28

Experiment Information (Status: Released)

	BGKcLV23-31	BGKcLV23-32
idx	817	818
TRCN#_or_BGC#	BGC#0000510	BGC#0000510
shRNA_or_gRNA_sequence	CGGCAGTTCCTCGTGACCAG	CGGCAGTTCCTCGTGACCAG
PAM	CGG	CGG
Name	DDX43_90	DDX43_90
Sample_ID	BGKcLV23-31	BGKcLV23-32
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	DDX43	DDX43
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GAGAGGAAGGTTTGAAATGGC
RT-qPCR_primer-R	TTTTGACATGGCACTTGTGG
protein_conc	2600	3149
WB_result	76.2	69.1
Ave_WB	72.7
WB_DONE_date	11/19/20
MW	72.8KD
IP	Rabbit / I
antibody_Cat#	A302-328A	LOT# 1
Antibody DCC ID	ENCAB412ETD
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4937	4938

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX43	Product_ID: A302-328A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX43-human

Experiment Status

	BGKcLV23-31	BGKcLV23-32
Sample_ID	BGKcLV23-31	BGKcLV23-32
Sample Name
Sample Name	DDX43-BGKcLV23-31	DDX43-BGKcLV23-32
RBP	DDX43	DDX43
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7445	7446

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-31	BGKcLV23-32
Sample #	47	48
Sample Name	DDX43-BGKcLV23-31	DDX43-BGKcLV23-32
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	291	322
Peak_Molarity	137.00	136.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/G6.png	DNA_Library_set46/set1/H6.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set46/set2/G10.png	RNA_Library_set46/set2/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-31	BGKcLV23-32
RBP	DDX43	DDX43
Batch_ID	BGKcLV23	BGKcLV23
WB_result	76.200	69.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1422	1423

Sequencing Information

	BGKcLV23-31	BGKcLV23-32
Sample_ID	BGKcLV23-31	BGKcLV23-32
Sample Name	DDX43-BGKcLV23-31	DDX43-BGKcLV23-32
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	139,992,482	218,963,912
total_aligned_reads	130,315,738	212,678,978
unique_aligned_reads	118,816,514	192,808,402
percent_uniqueAligned	0.84873	0.88055
correlation_replicates	0.983976	0.983976
spikein_reads	61,926	90,704
percent_spikeins	0.00044	0.00041
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	528	529

Data Submission Information

	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-32	BGKcLV23-32	BGKcLV23-32	BGKcLV23-32
ENCODE_alias	brenton-graveley:DDX43-BGKcLV23	brenton-graveley:DDX43-BGKcLV23-31	brenton-graveley:L-DDX43-BGKcLV23-31	brenton-graveley:DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX43-BGKcLV23-K562	brenton-graveley:DDX43-BGKcLV23-32	brenton-graveley:L-DDX43-BGKcLV23-32	brenton-graveley:DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR390TOZ	ENCBS486XNY	ENCLB648YEQ	ENCFF634ZST	ENCFF062JOZ	ENCSR049SQV	ENCBS752TGI	ENCLB888PSU	ENCFF705ZQF	ENCFF787IYZ
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	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-31	BGKcLV23-32	BGKcLV23-32	BGKcLV23-32	BGKcLV23-32
Sample Name	DDX43-BGKcLV23-31	DDX43-BGKcLV23-31	DDX43-BGKcLV23-31	DDX43-BGKcLV23-31	DDX43-BGKcLV23-31	DDX43-BGKcLV23-31	DDX43-BGKcLV23-32	DDX43-BGKcLV23-32	DDX43-BGKcLV23-32	DDX43-BGKcLV23-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		DDX43-BGKcLV23-31.pdf	L-DDX43-BGKcLV23-31.pdf				DDX43-BGKcLV23-32.pdf	L-DDX43-BGKcLV23-32.pdf
ID	2418	2473	2537	2631	2665	7182	2474	2538	2632	2666

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
DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	528	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1392
DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	528	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1456
DDX43-BGKcLV23-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25295
DDX43-BGKcLV23-31_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX43-BGKcLV23-31_GTTCCAAT+GCAGAATT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25329
DDX43-BGKcLV23-31_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	26133
DDX43-BGKcLV23-31_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	26167
DDX43-BGKcLV23-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	26201
DDX43-BGKcLV23-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	528					GRCh38	V40	DDX43-BGKcLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	26235
DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	529	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1393
DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	529	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1457
DDX43-BGKcLV23-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25296
DDX43-BGKcLV23-32_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX43-BGKcLV23-32_ACCTTGGC+ATGAGGCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25330
DDX43-BGKcLV23-32_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	26134
DDX43-BGKcLV23-32_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	26168
DDX43-BGKcLV23-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	26202
DDX43-BGKcLV23-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	529					GRCh38	V40	DDX43-BGKcLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	26236