EEF2K RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-47	BGHcLV49-48
idx	1746	1747
TRCN#_or_BGC#	BGC#0000952	BGC#0000952
shRNA_or_gRNA_sequence	CAGAGAGGGTCCTTACTTGG	CAGAGAGGGTCCTTACTTGG
PAM	ggg	ggg
Name	EEF2K_82	EEF2K_82
Sample_ID	BGHcLV49-47	BGHcLV49-48
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	EEF2K	EEF2K
qPCR_result	42.0	39.0
Ave_qPCR	40.5
RT-qPCR_primer-F	gagcaatgagggagtgcttc
RT-qPCR_primer-R	ggtctacgggctcgatgtag
protein_conc	3480	4959
WB_result	67.2	63.2
Ave_WB
WB_DONE_date	6/19/25
MW	82KD
IP
antibody_Cat#	A301-686A	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	9935	9936

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EEF2K	Product_ID: A301-686A Lot_ID: 1 Source: Bethyl Labs Target Name: EEF2K-human

Experiment Status

	BGHcLV49-47	BGHcLV49-48
Sample_ID	BGHcLV49-47	BGHcLV49-48
Sample Name
Sample Name	EEF2K-BGHcLV49-47	EEF2K-BGHcLV49-48
RBP	EEF2K	EEF2K
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14344	14345

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-47	BGHcLV49-48
Sample #	41	42
Sample Name	EEF2K-BGHcLV49-47	EEF2K-BGHcLV49-48
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	277	275
Peak_Molarity	84.40	76.80
libSampleQC_DNA_Well	DNA_Library_set81/set1/C3.png	DNA_Library_set81/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/C6.png	RNA_Library_set81/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-47	BGHcLV49-48
RBP	EEF2K	EEF2K
Batch_ID	BGHcLV49	BGHcLV49
WB_result	67.200	63.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4786	4787

Sequencing Information

	BGHcLV49-47	BGHcLV49-48
Sample_ID	BGHcLV49-47	BGHcLV49-48
Sample Name	EEF2K-BGHcLV49-47	EEF2K-BGHcLV49-48
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	26,751,557	25,866,975
total_aligned_reads	22,999,682	22,709,801
unique_aligned_reads	21,707,247	21,443,113
percent_uniqueAligned	0.81144	0.82898
correlation_replicates	0.997270	0.997270
spikein_reads	69,552	72,218
percent_spikeins	0.00260	0.00279
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3513	3514

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
EEF2K-BGHcLV49-47_S126_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3513	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33182
EEF2K-BGHcLV49-47_S126_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3513	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33228
EEF2K-BGHcLV49-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_S126_L008_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGHcLV49-47_S126_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33274
EEF2K-BGHcLV49-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_Aligned.sortedByCoord.out.bam		ENCORE2	33320
EEF2K-BGHcLV49-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_Aligned.sortedByCoord.out.bam		ENCORE2	33366
EEF2K-BGHcLV49-47_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_Aligned.sortedByCoord.out.bam		ENCORE2	33412
EEF2K-BGHcLV49-47_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_Aligned.sortedByCoord.out.bam		ENCORE2	33458
EEF2K-BGHcLV49-47_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3513					GRCh38	V40	EEF2K-BGHcLV49-47_S126_L008_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGHcLV49-47_S126_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33504
EEF2K-BGHcLV49-48_S135_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3514	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33183
EEF2K-BGHcLV49-48_S135_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3514	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33229
EEF2K-BGHcLV49-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_S135_L008_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGHcLV49-48_S135_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33275
EEF2K-BGHcLV49-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_Aligned.sortedByCoord.out.bam		ENCORE2	33321
EEF2K-BGHcLV49-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_Aligned.sortedByCoord.out.bam		ENCORE2	33367
EEF2K-BGHcLV49-48_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_Aligned.sortedByCoord.out.bam		ENCORE2	33413
EEF2K-BGHcLV49-48_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_Aligned.sortedByCoord.out.bam		ENCORE2	33459
EEF2K-BGHcLV49-48_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3514					GRCh38	V40	EEF2K-BGHcLV49-48_S135_L008_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGHcLV49-48_S135_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33505