DENR RNA-Seq in K562

General Information


RBP	DENR
Cell_Line	K562
Method	CRISPR
Exp_Name	DENR-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DENR-BGKcLV46-15
Rep2	DENR-BGKcLV46-16
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	31.8
Rep2_qPCR	20.7
Rep1_WB	50.8
Rep2_WB	51.8
Antibody Cat#	A303-010A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1637

Experiment Information (Status: Submitting)

	BGKcLV46-15	BGKcLV46-16
idx	0	0
TRCN#_or_BGC#	BGC#0001230	BGC#0001230
shRNA_or_gRNA_sequence	TGACATTTCTGAATCCAGCG	TGACATTTCTGAATCCAGCG
PAM	GGG	GGG
Name	DENR_79	DENR_79
Sample_ID	BGKcLV46-15	BGKcLV46-16
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	DENR	DENR
qPCR_result	31.8	20.7
Ave_qPCR	26.3
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5017	5152
WB_result	50.8	51.8
Ave_WB
WB_DONE_date	1/2/24,1/6/25
MW
IP
antibody_Cat#	A303-010A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6003	6004

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DENR	Product_ID: A303-010A Lot_ID: 1 Source: Bethyl Labs Target Name: DENR-human

Experiment Status

	BGKcLV46-15	BGKcLV46-16
Sample_ID	BGKcLV46-15	BGKcLV46-16
Sample Name
Sample Name	DENR-BGKcLV46-15	DENR-BGKcLV46-16
RBP	DENR	DENR
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14028	14029

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-15	BGKcLV46-16
Sample #	7	8
Sample Name	DENR-BGKcLV46-15	DENR-BGKcLV46-16
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	291	296
Peak_Molarity	51.80	64.80
libSampleQC_DNA_Well	DNA_Library_set77/set1/G7.png	DNA_Library_set77/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/G1.png	RNA_Library_set77/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-15	BGKcLV46-16
RBP	DENR	DENR
Batch_ID	BGKcLV46	BGKcLV46
WB_result	50.800	51.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4666	4667

Sequencing Information

	BGKcLV46-15	BGKcLV46-16
Sample_ID	BGKcLV46-15	BGKcLV46-16
Sample Name	DENR-BGKcLV46-15	DENR-BGKcLV46-16
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	63,850,317	43,081,985
total_aligned_reads	58,426,133	38,540,110
unique_aligned_reads	53,968,517	35,551,679
percent_uniqueAligned	0.84523	0.82521
correlation_replicates	0.996717	0.996717
spikein_reads	136,608	141,168
percent_spikeins	0.00214	0.00328
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3371	3372

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
DENR-BGKcLV46-15_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3371	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32152
DENR-BGKcLV46-15_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3371	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32202
DENR-BGKcLV46-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGKcLV46-15_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32252
DENR-BGKcLV46-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_Aligned.sortedByCoord.out.bam		ENCORE2	32302
DENR-BGKcLV46-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_Aligned.sortedByCoord.out.bam		ENCORE2	32352
DENR-BGKcLV46-15_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_Aligned.sortedByCoord.out.bam		ENCORE2	32402
DENR-BGKcLV46-15_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_Aligned.sortedByCoord.out.bam		ENCORE2	32452
DENR-BGKcLV46-15_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3371					GRCh38	V40	DENR-BGKcLV46-15_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGKcLV46-15_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32502
DENR-BGKcLV46-16_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3372	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32153
DENR-BGKcLV46-16_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3372	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32203
DENR-BGKcLV46-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGKcLV46-16_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32253
DENR-BGKcLV46-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_Aligned.sortedByCoord.out.bam		ENCORE2	32303
DENR-BGKcLV46-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_Aligned.sortedByCoord.out.bam		ENCORE2	32353
DENR-BGKcLV46-16_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_Aligned.sortedByCoord.out.bam		ENCORE2	32403
DENR-BGKcLV46-16_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_Aligned.sortedByCoord.out.bam		ENCORE2	32453
DENR-BGKcLV46-16_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3372					GRCh38	V40	DENR-BGKcLV46-16_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGKcLV46-16_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32503