EIF4B RNA-Seq in K562

General Information


RBP	EIF4B
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF4B-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	EIF4B-BGKcLV46-33
Rep2	EIF4B-BGKcLV46-34
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	63.2
Rep2_qPCR	69.7
Rep1_WB	76.2
Rep2_WB	77.7
Antibody Cat#	A301-766A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1641

Experiment Information (Status: Submitting)

	BGKcLV46-33	BGKcLV46-34
idx	0	0
TRCN#_or_BGC#	BGC#0000118	BGC#0000118
shRNA_or_gRNA_sequence	GTCATCGTTACTGTGCCAAG	GTCATCGTTACTGTGCCAAG
PAM	TGG	TGG
Name	EIF4B-87F	EIF4B-87F
Sample_ID	BGKcLV46-33	BGKcLV46-34
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	EIF4B	EIF4B
qPCR_result	63.2	69.7
Ave_qPCR	66.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3967	3561
WB_result	76.2	77.7
Ave_WB
WB_DONE_date	12/31/24
MW	65 kDa
IP
antibody_Cat#	A301-766A	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	6027	6028

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4B	Product_ID: A301-766A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4B-human

Experiment Status

	BGKcLV46-33	BGKcLV46-34
Sample_ID	BGKcLV46-33	BGKcLV46-34
Sample Name
Sample Name	EIF4B-BGKcLV46-33	EIF4B-BGKcLV46-34
RBP	EIF4B	EIF4B
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14036	14037

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-33	BGKcLV46-34
Sample #	15	16
Sample Name	EIF4B-BGKcLV46-33	EIF4B-BGKcLV46-34
Sample_Name_Alias
Index Well Position	G02	H02
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	297	318
Peak_Molarity	60.70	55.70
libSampleQC_DNA_Well	DNA_Library_set77/set1/G8.png	DNA_Library_set77/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/G2.png	RNA_Library_set77/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-33	BGKcLV46-34
RBP	EIF4B	EIF4B
Batch_ID	BGKcLV46	BGKcLV46
WB_result	76.200	77.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4674	4675

Sequencing Information

	BGKcLV46-33	BGKcLV46-34
Sample_ID	BGKcLV46-33	BGKcLV46-34
Sample Name	EIF4B-BGKcLV46-33	EIF4B-BGKcLV46-34
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	74,527,466	68,236,068
total_aligned_reads	69,940,601	63,157,183
unique_aligned_reads	64,635,694	58,372,855
percent_uniqueAligned	0.86727	0.85545
correlation_replicates	0.995998	0.995998
spikein_reads	134,722	262,420
percent_spikeins	0.00181	0.00385
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3379	3380

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
EIF4B-BGKcLV46-33_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3379	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	32160
EIF4B-BGKcLV46-33_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3379	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	32210
EIF4B-BGKcLV46-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3379					GRCh38	V40	EIF4B-BGKcLV46-33_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGKcLV46-33_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32260
EIF4B-BGKcLV46-33_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	3379					GRCh38	V40	EIF4B-BGKcLV46-33_Aligned.sortedByCoord.out.bam		ENCORE2	32310
EIF4B-BGKcLV46-33_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	3379					GRCh38	V40	EIF4B-BGKcLV46-33_Aligned.sortedByCoord.out.bam		ENCORE2	32360
EIF4B-BGKcLV46-33_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	3379					GRCh38	V40	EIF4B-BGKcLV46-33_Aligned.sortedByCoord.out.bam		ENCORE2	32410
EIF4B-BGKcLV46-33_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	3379					GRCh38	V40	EIF4B-BGKcLV46-33_Aligned.sortedByCoord.out.bam		ENCORE2	32460
EIF4B-BGKcLV46-33_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3379					GRCh38	V40	EIF4B-BGKcLV46-33_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGKcLV46-33_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32510
EIF4B-BGKcLV46-34_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3380	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	32161
EIF4B-BGKcLV46-34_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3380	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	32211
EIF4B-BGKcLV46-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3380					GRCh38	V40	EIF4B-BGKcLV46-34_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGKcLV46-34_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32261
EIF4B-BGKcLV46-34_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	3380					GRCh38	V40	EIF4B-BGKcLV46-34_Aligned.sortedByCoord.out.bam		ENCORE2	32311
EIF4B-BGKcLV46-34_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	3380					GRCh38	V40	EIF4B-BGKcLV46-34_Aligned.sortedByCoord.out.bam		ENCORE2	32361
EIF4B-BGKcLV46-34_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	3380					GRCh38	V40	EIF4B-BGKcLV46-34_Aligned.sortedByCoord.out.bam		ENCORE2	32411
EIF4B-BGKcLV46-34_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	3380					GRCh38	V40	EIF4B-BGKcLV46-34_Aligned.sortedByCoord.out.bam		ENCORE2	32461
EIF4B-BGKcLV46-34_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3380					GRCh38	V40	EIF4B-BGKcLV46-34_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BGKcLV46-34_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32511