EIF5B RNA-Seq in K562

General Information


RBP	EIF5B
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF5B-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF5B-BGKcLV44-25
Rep2	EIF5B-BGKcLV44-26
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	5.1
Rep2_qPCR	16.7
Rep1_WB	69.2
Rep2_WB	67.4
Antibody Cat#	A301-745A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1600

Experiment Information (Status: Submitting)

	BGKcLV44-25	BGKcLV44-25	BGKcLV44-26	BGKcLV44-26
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000985	BGC#0000985	BGC#0000985	BGC#0000985
shRNA_or_gRNA_sequence	AGCGCCATTGACAAGCAATG	AGCGCCATTGACAAGCAATG	AGCGCCATTGACAAGCAATG	AGCGCCATTGACAAGCAATG
PAM	GGG	GGG	GGG	GGG
Name	EIF5B_81	EIF5B_81	EIF5B_81	EIF5B_81
Sample_ID	BGKcLV44-25	BGKcLV44-25	BGKcLV44-26	BGKcLV44-26
transduction_Date	7/30/24	7/30/24	7/30/24	7/30/24
days	D6	D6	D6	D6
RBP_name	EIF5B	EIF5B	EIF5B	EIF5B
qPCR_result	5.1	5.1	16.7	16.7
Ave_qPCR	10.9	10.9
RT-qPCR_primer-F	agagagaagccagagccaga	agagagaagccagagccaga
RT-qPCR_primer-R	tttgatggcacttcaacacc	tttgatggcacttcaacacc
protein_conc	4496	4496	4163	4163
WB_result	69.2	67.0	67.4	53.7
Ave_WB	68.3	67.0
WB_DONE_date	8/13/24	1/7/24
MW	139kd	139kd
IP
antibody_Cat#	A301-745A	A301-744A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5902	5904	5903	5905

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF5B	Product_ID: A301-745A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF5B-human

Experiment Status

	BGKcLV44-25	BGKcLV44-26
Sample_ID	BGKcLV44-25	BGKcLV44-26
Sample Name
Sample Name	EIF5B-BGKcLV44-25	EIF5B-BGKcLV44-26
RBP	EIF5B	EIF5B
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13592	13593

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-25	BGKcLV44-26
Sample #	21	22
Sample Name	EIF5B-BGKcLV44-25	EIF5B-BGKcLV44-26
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	293	283
Peak_Molarity	94.70	72.70
libSampleQC_DNA_Well	DNA_Library_set75/set1/E8.png	DNA_Library_set75/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/E2.png	RNA_Library_set75/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-25	BGKcLV44-26
RBP	EIF5B	EIF5B
Batch_ID	BGKcLV44	BGKcLV44
WB_result	69.200	67.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4580	4581

Sequencing Information

	BGKcLV44-25	BGKcLV44-26
Sample_ID	BGKcLV44-25	BGKcLV44-26
Sample Name	EIF5B-BGKcLV44-25	EIF5B-BGKcLV44-26
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	38,375,480	38,868,281
total_aligned_reads	36,677,689	36,850,175
unique_aligned_reads	34,006,253	34,228,093
percent_uniqueAligned	0.88615	0.88062
correlation_replicates	0.992993	0.992993
spikein_reads	76,676	55,058
percent_spikeins	0.00200	0.00142
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3291	3292

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
EIF5B-BGKcLV44-25_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3291	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30944
EIF5B-BGKcLV44-25_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3291	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30986
EIF5B-BGKcLV44-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGKcLV44-25_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31028
EIF5B-BGKcLV44-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_Aligned.sortedByCoord.out.bam		ENCORE2	31070
EIF5B-BGKcLV44-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_Aligned.sortedByCoord.out.bam		ENCORE2	31112
EIF5B-BGKcLV44-25_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_Aligned.sortedByCoord.out.bam		ENCORE2	31154
EIF5B-BGKcLV44-25_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_Aligned.sortedByCoord.out.bam		ENCORE2	31196
EIF5B-BGKcLV44-25_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3291					GRCh38	V40	EIF5B-BGKcLV44-25_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGKcLV44-25_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31238
EIF5B-BGKcLV44-26_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3292	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30945
EIF5B-BGKcLV44-26_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3292	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30987
EIF5B-BGKcLV44-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGKcLV44-26_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31029
EIF5B-BGKcLV44-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_Aligned.sortedByCoord.out.bam		ENCORE2	31071
EIF5B-BGKcLV44-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_Aligned.sortedByCoord.out.bam		ENCORE2	31113
EIF5B-BGKcLV44-26_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_Aligned.sortedByCoord.out.bam		ENCORE2	31155
EIF5B-BGKcLV44-26_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_Aligned.sortedByCoord.out.bam		ENCORE2	31197
EIF5B-BGKcLV44-26_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3292					GRCh38	V40	EIF5B-BGKcLV44-26_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGKcLV44-26_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31239