EIF3K RNA-Seq in K562

General Information


RBP	EIF3K
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3K-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	EIF3K-BGKcLV46-31
Rep2	EIF3K-BGKcLV46-32
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	83.5
Rep2_qPCR	81.5
Rep1_WB	69.5
Rep2_WB	87.1
Antibody Cat#	A301-763A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1640

Experiment Information (Status: Submitting)

	BGKcLV46-31	BGKcLV46-32
idx	0	0
TRCN#_or_BGC#	BGC#0000972	BGC#0000972
shRNA_or_gRNA_sequence	GTGCAAGTGCATGATCGACC	GTGCAAGTGCATGATCGACC
PAM	AGG	AGG
Name	EIF3K_96	EIF3K_96
Sample_ID	BGKcLV46-31	BGKcLV46-32
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	EIF3K	EIF3K
qPCR_result	83.5	81.5
Ave_qPCR	82.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3898	3674
WB_result	69.5	87.1
Ave_WB
WB_DONE_date	12/31/24
MW	25kd
IP
antibody_Cat#	A301-763A	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	6025	6026

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3K	Product_ID: A301-763A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3K-human

Experiment Status

	BGKcLV46-31	BGKcLV46-32
Sample_ID	BGKcLV46-31	BGKcLV46-32
Sample Name
Sample Name	EIF3K-BGKcLV46-31	EIF3K-BGKcLV46-32
RBP	EIF3K	EIF3K
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14034	14035

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-31	BGKcLV46-32
Sample #	13	14
Sample Name	EIF3K-BGKcLV46-31	EIF3K-BGKcLV46-32
Sample_Name_Alias
Index Well Position	E02	F02
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	303	333
Peak_Molarity	92.10	46.40
libSampleQC_DNA_Well	DNA_Library_set77/set1/E8.png	DNA_Library_set77/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/E2.png	RNA_Library_set77/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-31	BGKcLV46-32
RBP	EIF3K	EIF3K
Batch_ID	BGKcLV46	BGKcLV46
WB_result	69.500	87.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4672	4673

Sequencing Information

	BGKcLV46-31	BGKcLV46-32
Sample_ID	BGKcLV46-31	BGKcLV46-32
Sample Name	EIF3K-BGKcLV46-31	EIF3K-BGKcLV46-32
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	56,515,403	67,347,202
total_aligned_reads	52,356,111	63,405,581
unique_aligned_reads	48,248,796	58,539,135
percent_uniqueAligned	0.85373	0.86921
correlation_replicates	0.997863	0.997863
spikein_reads	85,710	144,196
percent_spikeins	0.00152	0.00214
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3377	3378

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
EIF3K-BGKcLV46-31_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3377	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	32158
EIF3K-BGKcLV46-31_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3377	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	32208
EIF3K-BGKcLV46-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3377					GRCh38	V40	EIF3K-BGKcLV46-31_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF3K-BGKcLV46-31_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32258
EIF3K-BGKcLV46-31_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	3377					GRCh38	V40	EIF3K-BGKcLV46-31_Aligned.sortedByCoord.out.bam		ENCORE2	32308
EIF3K-BGKcLV46-31_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	3377					GRCh38	V40	EIF3K-BGKcLV46-31_Aligned.sortedByCoord.out.bam		ENCORE2	32358
EIF3K-BGKcLV46-31_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	3377					GRCh38	V40	EIF3K-BGKcLV46-31_Aligned.sortedByCoord.out.bam		ENCORE2	32408
EIF3K-BGKcLV46-31_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	3377					GRCh38	V40	EIF3K-BGKcLV46-31_Aligned.sortedByCoord.out.bam		ENCORE2	32458
EIF3K-BGKcLV46-31_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3377					GRCh38	V40	EIF3K-BGKcLV46-31_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF3K-BGKcLV46-31_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32508
EIF3K-BGKcLV46-32_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3378	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	32159
EIF3K-BGKcLV46-32_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3378	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	32209
EIF3K-BGKcLV46-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3378					GRCh38	V40	EIF3K-BGKcLV46-32_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF3K-BGKcLV46-32_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32259
EIF3K-BGKcLV46-32_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	3378					GRCh38	V40	EIF3K-BGKcLV46-32_Aligned.sortedByCoord.out.bam		ENCORE2	32309
EIF3K-BGKcLV46-32_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	3378					GRCh38	V40	EIF3K-BGKcLV46-32_Aligned.sortedByCoord.out.bam		ENCORE2	32359
EIF3K-BGKcLV46-32_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	3378					GRCh38	V40	EIF3K-BGKcLV46-32_Aligned.sortedByCoord.out.bam		ENCORE2	32409
EIF3K-BGKcLV46-32_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	3378					GRCh38	V40	EIF3K-BGKcLV46-32_Aligned.sortedByCoord.out.bam		ENCORE2	32459
EIF3K-BGKcLV46-32_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3378					GRCh38	V40	EIF3K-BGKcLV46-32_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF3K-BGKcLV46-32_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32509