DDX54 RNA-Seq in K562

General Information


RBP	DDX54
Cell_Line	K562
Method	CRISPR
Exp_Name	DDX54-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	DDX54-BGKcLV37-13
Rep2	DDX54-BGKcLV37-14
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	36.3
Rep2_qPCR	22.2
Rep1_WB	87.8
Rep2_WB	72.9
Antibody Cat#	A301-314A
Antibody Lot#	lot # 2
Antibody DCC ID	ENCAB899BVE
Status	Submitted
Project	ENCORE2
ID	1052

Experiment Information (Status: Submitting)

	BGKcLV37-13	BGKcLV37-14
idx	1365	1366
TRCN#_or_BGC#	BGC#0000904	BGC#0000904
shRNA_or_gRNA_sequence	GCCATGGCAGCTCGCGACCG	GCCATGGCAGCTCGCGACCG
PAM	agg	agg
Name	DDX54_96	DDX54_96
Sample_ID	BGKcLV37-13	BGKcLV37-14
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	DDX54	DDX54
qPCR_result	36.3	22.2
Ave_qPCR	29.3
RT-qPCR_primer-F	GATGAAGCCCAGAACCTGAC
RT-qPCR_primer-R	TGTCCTGACTGTCCCACAAA
protein_conc	1996	1756
WB_result	87.8	72.9
Ave_WB	80.3
WB_DONE_date	9/28/22,9/29/22	JESS, Licor
MW	99KD
IP
antibody_Cat#	A301-314A	lot # 2
Antibody DCC ID	ENCAB899BVE
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	5515	5516

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX54	Product_ID: A301-314A Lot_ID: 2 Source: Bethyl Labs Target Name: DDX54-human

Experiment Status

	BGKcLV37-13	BGKcLV37-14
Sample_ID	BGKcLV37-13	BGKcLV37-14
Sample Name
Sample Name	DDX54-BGKcLV37-13	DDX54-BGKcLV37-14
RBP	DDX54	DDX54
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11088	11089

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-13	BGKcLV37-14
Sample #	27	28
Sample Name	DDX54-BGKcLV37-13	DDX54-BGKcLV37-14
Sample_Name_Alias
Index Well Position	C04	D04
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	315	300
Peak_Molarity	57.00	61.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/C4.png	DNA_Library_set54-56/set1/D4.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/C4.png	RNA_Library_set54-56/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-13	BGKcLV37-14
RBP	DDX54	DDX54
Batch_ID	BGKcLV37	BGKcLV37
WB_result	87.800	72.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3398	3399

Sequencing Information

	BGKcLV37-13	BGKcLV37-14
Sample_ID	BGKcLV37-13	BGKcLV37-14
Sample Name	DDX54-BGKcLV37-13	DDX54-BGKcLV37-14
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	67,859,567	46,772,727
total_aligned_reads	64,102,047	42,569,957
unique_aligned_reads	59,719,397	39,573,604
percent_uniqueAligned	0.88004	0.84608
correlation_replicates	0.996038	0.996038
spikein_reads	3,402	3,120
percent_spikeins	0.00005	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2271	2272

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
DDX54-BGKcLV37-13_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2271	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	8380
DDX54-BGKcLV37-13_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2271	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	8430
DDX54-BGKcLV37-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2271					GRCh38	V40	DDX54-BGKcLV37-13_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX54-BGKcLV37-13_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25621
DDX54-BGKcLV37-13_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	2271					GRCh38	V40	DDX54-BGKcLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	25671
DDX54-BGKcLV37-13_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	2271					GRCh38	V40	DDX54-BGKcLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	25721
DDX54-BGKcLV37-13_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	2271					GRCh38	V40	DDX54-BGKcLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	25771
DDX54-BGKcLV37-13_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	2271					GRCh38	V40	DDX54-BGKcLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	25821
DDX54-BGKcLV37-13_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2271					GRCh38	V40	DDX54-BGKcLV37-13_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX54-BGKcLV37-13_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25871
DDX54-BGKcLV37-14_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2272	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	8381
DDX54-BGKcLV37-14_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2272	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	8431
DDX54-BGKcLV37-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2272					GRCh38	V40	DDX54-BGKcLV37-14_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX54-BGKcLV37-14_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25622
DDX54-BGKcLV37-14_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	2272					GRCh38	V40	DDX54-BGKcLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	25672
DDX54-BGKcLV37-14_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	2272					GRCh38	V40	DDX54-BGKcLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	25722
DDX54-BGKcLV37-14_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	2272					GRCh38	V40	DDX54-BGKcLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	25772
DDX54-BGKcLV37-14_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	2272					GRCh38	V40	DDX54-BGKcLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	25822
DDX54-BGKcLV37-14_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2272					GRCh38	V40	DDX54-BGKcLV37-14_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX54-BGKcLV37-14_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25872