EPB41L2 RNA-Seq in K562

General Information


RBP	EPB41L2
Cell_Line	K562
Method	CRISPR
Exp_Name	EPB41L2-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EPB41L2-BGKcLV40-23
Rep2	EPB41L2-BGKcLV40-24
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	0.0
Rep2_qPCR	17.0
Rep1_WB	56.6
Rep2_WB	62.6
Antibody Cat#	A301-425A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1361

Experiment Information (Status: Submitting)

	BGKcLV40-23	BGKcLV40-23	BGKcLV40-24	BGKcLV40-24
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000989	BGC#0000989	BGC#0000989	BGC#0000989
shRNA_or_gRNA_sequence	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG
PAM	TGG	TGG	TGG	TGG
Name	EPB41L2-87	EPB41L2-87	EPB41L2-87	EPB41L2-87
Sample_ID	BGKcLV40-23	BGKcLV40-23	BGKcLV40-24	BGKcLV40-24
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	EPB41L2	EPB41L2	EPB41L2	EPB41L2
qPCR_result	0.0		17.0
Ave_qPCR	8.5
RT-qPCR_primer-F	ccagtttgcccctactcaga
RT-qPCR_primer-R	actgggaatcagcttgtgct
protein_conc	3533	3533	3687	3687
WB_result	56.6	59.7	62.6	55.8467
Ave_WB	59.6	57.8
WB_DONE_date	12/6/23,12/12/23,	12/6/23,12/12/23,
MW	113kd	113kd
IP
antibody_Cat#	A301-425A	A301-424A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24	1/4/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5694	5696	5695	5697

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EPB41L2	Product_ID: A301-424A Lot_ID: 1 Source: Bethyl Labs Target Name: EPB41L2-human
EPB41L2	Product_ID: A301-425A Lot_ID: 1 Source: Bethyl Labs Target Name: EPB41L2-human

Experiment Status

	BGKcLV40-23	BGKcLV40-23	BGKcLV40-24	BGKcLV40-24
Sample_ID	BGKcLV40-23	BGKcLV40-23	BGKcLV40-24	BGKcLV40-24
Sample Name
Sample Name	EPB41L2-BGKcLV40-23		EPB41L2-BGKcLV40-24
RBP	EPB41L2	EPB41L2	EPB41L2	EPB41L2
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2024-02-16	2023-12-15	2024-02-16	2023-12-15
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12766	12812	12767	12813

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-23	BGKcLV40-24
Sample #	13	14
Sample Name	EPB41L2-BGKcLV40-23	EPB41L2-BGKcLV40-24
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	285	286
Peak_Molarity	75.60	84.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/E8.png	DNA_Library_set67/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/E2.png	RNA_Library_set67/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-23	BGKcLV40-24
RBP	EPB41L2	EPB41L2
Batch_ID	BGKcLV40	BGKcLV40
WB_result	56.600	62.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4150	4151

Sequencing Information

	BGKcLV40-23	BGKcLV40-24
Sample_ID	BGKcLV40-23	BGKcLV40-24
Sample Name	EPB41L2-BGKcLV40-23	EPB41L2-BGKcLV40-24
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	43,006,462	44,738,607
total_aligned_reads	37,185,757	39,187,023
unique_aligned_reads	34,169,536	36,008,789
percent_uniqueAligned	0.79452	0.80487
correlation_replicates	0.996646	0.996646
spikein_reads	5,490	10,988
percent_spikeins	0.00013	0.00025
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2805	2806

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
EPB41L2-BGKcLV40-23_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2805	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28151
EPB41L2-BGKcLV40-23_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2805	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28195
EPB41L2-BGKcLV40-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGKcLV40-23_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28239
EPB41L2-BGKcLV40-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23/Aligned.sortedByCoord.out.bam		ENCORE2	28283
EPB41L2-BGKcLV40-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23/Aligned.sortedByCoord.out.bam		ENCORE2	28327
EPB41L2-BGKcLV40-23_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23/Aligned.sortedByCoord.out.bam		ENCORE2	28371
EPB41L2-BGKcLV40-23_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23/Aligned.sortedByCoord.out.bam		ENCORE2	28415
EPB41L2-BGKcLV40-23_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2805					GRCh38	V40	EPB41L2-BGKcLV40-23_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGKcLV40-23_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28459
EPB41L2-BGKcLV40-24_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2806	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28152
EPB41L2-BGKcLV40-24_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2806	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28196
EPB41L2-BGKcLV40-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGKcLV40-24_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28240
EPB41L2-BGKcLV40-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24/Aligned.sortedByCoord.out.bam		ENCORE2	28284
EPB41L2-BGKcLV40-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24/Aligned.sortedByCoord.out.bam		ENCORE2	28328
EPB41L2-BGKcLV40-24_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24/Aligned.sortedByCoord.out.bam		ENCORE2	28372
EPB41L2-BGKcLV40-24_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24/Aligned.sortedByCoord.out.bam		ENCORE2	28416
EPB41L2-BGKcLV40-24_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2806					GRCh38	V40	EPB41L2-BGKcLV40-24_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGKcLV40-24_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28460