DDX50 RNA-Seq in K562

General Information


RBP	DDX50
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX50-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DDX50-BGKcLV37-11
Rep2	DDX50-BGKcLV37-12
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	6.6
Rep2_qPCR	10.8
Rep1_WB	56.0
Rep2_WB	54.2
Antibody Cat#	A301-312A
Antibody Lot#	lot # 1
Antibody DCC ID	ENCAB756NJZ
Status	Submitted
Project	ENCORE2
ID	1051

Experiment Information (Status: Submitting)

	BGKcLV37-11	BGKcLV37-12
idx	1363	1364
TRCN#_or_BGC#	BGC#0000901	BGC#0000901
shRNA_or_gRNA_sequence	GCTCCATAATGTCCCCCCAG	GCTCCATAATGTCCCCCCAG
PAM	agg	agg
Name	DDX50_74	DDX50_74
Sample_ID	BGKcLV37-11	BGKcLV37-12
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	DDX50	DDX50
qPCR_result	6.6	10.8
Ave_qPCR	8.7
RT-qPCR_primer-F	acggacaggaacaggaaaga
RT-qPCR_primer-R	gtttgccagttcccttgttg
protein_conc	1764	1992
WB_result	56.0	54.2
Ave_WB	55.1
WB_DONE_date	9/28/22,9/29/22	JESS, Licor
MW	83KD
IP
antibody_Cat#	A301-312A	lot # 1
Antibody DCC ID	ENCAB756NJZ
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5513	5514

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX50	Product_ID: A301-312A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX50-human

Experiment Status

	BGKcLV37-11	BGKcLV37-12
Sample_ID	BGKcLV37-11	BGKcLV37-12
Sample Name
Sample Name	DDX50-BGKcLV37-11	DDX50-BGKcLV37-12
RBP	DDX50	DDX50
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11086	11087

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-11	BGKcLV37-12
Sample #	25	26
Sample Name	DDX50-BGKcLV37-11	DDX50-BGKcLV37-12
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	304	306
Peak_Molarity	50.10	49.00
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A4.png	DNA_Library_set54-56/set1/B4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A4.png	RNA_Library_set54-56/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-11	BGKcLV37-12
RBP	DDX50	DDX50
Batch_ID	BGKcLV37	BGKcLV37
WB_result	56.000	54.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3396	3397

Sequencing Information

	BGKcLV37-11	BGKcLV37-12
Sample_ID	BGKcLV37-11	BGKcLV37-12
Sample Name	DDX50-BGKcLV37-11	DDX50-BGKcLV37-12
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	52,152,626	49,992,796
total_aligned_reads	49,099,286	47,487,996
unique_aligned_reads	45,443,599	44,201,962
percent_uniqueAligned	0.87136	0.88417
correlation_replicates	0.995047	0.995047
spikein_reads	13,066	5,706
percent_spikeins	0.00025	0.00011
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2269	2270

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
DDX50-BGKcLV37-11_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2269	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8378
DDX50-BGKcLV37-11_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2269	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8428
DDX50-BGKcLV37-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGKcLV37-11_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25619
DDX50-BGKcLV37-11_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11/Aligned.sortedByCoord.out.bam		ENCORE2	25669
DDX50-BGKcLV37-11_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11/Aligned.sortedByCoord.out.bam		ENCORE2	25719
DDX50-BGKcLV37-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11/Aligned.sortedByCoord.out.bam		ENCORE2	25769
DDX50-BGKcLV37-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11/Aligned.sortedByCoord.out.bam		ENCORE2	25819
DDX50-BGKcLV37-11_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2269					GRCh38	V40	DDX50-BGKcLV37-11_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGKcLV37-11_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25869
DDX50-BGKcLV37-12_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2270	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8379
DDX50-BGKcLV37-12_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2270	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8429
DDX50-BGKcLV37-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGKcLV37-12_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25620
DDX50-BGKcLV37-12_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12/Aligned.sortedByCoord.out.bam		ENCORE2	25670
DDX50-BGKcLV37-12_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12/Aligned.sortedByCoord.out.bam		ENCORE2	25720
DDX50-BGKcLV37-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12/Aligned.sortedByCoord.out.bam		ENCORE2	25770
DDX50-BGKcLV37-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12/Aligned.sortedByCoord.out.bam		ENCORE2	25820
DDX50-BGKcLV37-12_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2270					GRCh38	V40	DDX50-BGKcLV37-12_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX50-BGKcLV37-12_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25870