EEF2K RNA-Seq in K562

General Information


RBP	EEF2K
Cell_Line	K562
Method	CRISPR
Exp_Name	EEF2K-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EEF2K-BGKcLV38-35
Rep2	EEF2K-BGKcLV38-36
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	53.4
Rep2_qPCR	52.4
Rep1_WB	63.1
Rep2_WB	54.6
Antibody Cat#	A301-686A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1031

Experiment Information (Status: Submitting)

	BGKcLV38-35	BGKcLV38-36
idx	1452	1453
TRCN#_or_BGC#	BGC#0000952	BGC#0000952
shRNA_or_gRNA_sequence	CAGAGAGGGTCCTTACTTGG	CAGAGAGGGTCCTTACTTGG
PAM	ggg	ggg
Name	EEF2K_82	EEF2K_82
Sample_ID	BGKcLV38-35	BGKcLV38-36
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EEF2K	EEF2K
qPCR_result	53.4	52.4
Ave_qPCR	52.9
RT-qPCR_primer-F	gagcaatgagggagtgcttc
RT-qPCR_primer-R	ggtctacgggctcgatgtag
protein_conc	3444	3656
WB_result	63.1	54.6
Ave_WB	58.8
WB_DONE_date	10/28/22
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	5630	5631

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

	BGKcLV38-35	BGKcLV38-36
Sample_ID	BGKcLV38-35	BGKcLV38-36
Sample Name
Sample Name	EEF2K-BGKcLV38-35	EEF2K-BGKcLV38-36
RBP	EEF2K	EEF2K
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11036	11037

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-35	BGKcLV38-36
Sample #	71	72
Sample Name	EEF2K-BGKcLV38-35	EEF2K-BGKcLV38-36
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	283	280
Peak_Molarity	78.90	74.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/E10.png	DNA_Library_set54-56/set2/F10.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/G9.png	RNA_Library_set54-56/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-35	BGKcLV38-36
RBP	EEF2K	EEF2K
Batch_ID	BGKcLV38	BGKcLV38
WB_result	63.100	54.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3442	3443

Sequencing Information

	BGKcLV38-35	BGKcLV38-36
Sample_ID	BGKcLV38-35	BGKcLV38-36
Sample Name	EEF2K-BGKcLV38-35	EEF2K-BGKcLV38-36
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	68,511,211	74,699,232
total_aligned_reads	63,580,254	68,106,731
unique_aligned_reads	59,056,767	63,241,258
percent_uniqueAligned	0.86200	0.84661
correlation_replicates	0.995121	0.995121
spikein_reads	8,052	12,698
percent_spikeins	0.00012	0.00017
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2313	2314

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-BGKcLV38-35_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2313	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8318
EEF2K-BGKcLV38-35_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2313	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8356
EEF2K-BGKcLV38-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGKcLV38-35_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16970
EEF2K-BGKcLV38-35_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35/Aligned.sortedByCoord.out.bam		ENCORE2	17008
EEF2K-BGKcLV38-35_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35/Aligned.sortedByCoord.out.bam		ENCORE2	17046
EEF2K-BGKcLV38-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35/Aligned.sortedByCoord.out.bam		ENCORE2	17084
EEF2K-BGKcLV38-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35/Aligned.sortedByCoord.out.bam		ENCORE2	17122
EEF2K-BGKcLV38-35_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2313					GRCh38	V40	EEF2K-BGKcLV38-35_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGKcLV38-35_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17160
EEF2K-BGKcLV38-36_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2314	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8319
EEF2K-BGKcLV38-36_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2314	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8357
EEF2K-BGKcLV38-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGKcLV38-36_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16971
EEF2K-BGKcLV38-36_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36/Aligned.sortedByCoord.out.bam		ENCORE2	17009
EEF2K-BGKcLV38-36_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36/Aligned.sortedByCoord.out.bam		ENCORE2	17047
EEF2K-BGKcLV38-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36/Aligned.sortedByCoord.out.bam		ENCORE2	17085
EEF2K-BGKcLV38-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36/Aligned.sortedByCoord.out.bam		ENCORE2	17123
EEF2K-BGKcLV38-36_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2314					GRCh38	V40	EEF2K-BGKcLV38-36_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF2K-BGKcLV38-36_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17161