EEF1G RNA-Seq in K562

General Information


RBP	EEF1G
Cell_Line	K562
Method	CRISPR
Exp_Name	EEF1G-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	EEF1G-BGKcLV38-33
Rep2	EEF1G-BGKcLV38-34
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	66.5
Rep2_qPCR	70.2
Rep1_WB	66.0
Rep2_WB	65.8
Antibody Cat#	A300-734A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1030

Experiment Information (Status: Submitting)

	BGKcLV38-33	BGKcLV38-34
idx	1450	1451
TRCN#_or_BGC#	BGC#0000950	BGC#0000950
shRNA_or_gRNA_sequence	AATATCCTTACCTCTTGGGC	AATATCCTTACCTCTTGGGC
PAM	agg	agg
Name	EEF1G_76	EEF1G_76
Sample_ID	BGKcLV38-33	BGKcLV38-34
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EEF1G	EEF1G
qPCR_result	66.5	70.2
Ave_qPCR	68.3
RT-qPCR_primer-F	cttcttggcctatgccattc
RT-qPCR_primer-R	aaagccagatcagccacact
protein_conc	2792	3090
WB_result	66.0	65.8
Ave_WB	65.9
WB_DONE_date	11/4/22
MW	50kd
IP
antibody_Cat#	A300-734A	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	5628	5629

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EEF1G	Product_ID: A300-734A Lot_ID: 1 Source: Bethyl Labs Target Name: EEF1G-human

Experiment Status

	BGKcLV38-33	BGKcLV38-34
Sample_ID	BGKcLV38-33	BGKcLV38-34
Sample Name
Sample Name	EEF1G-BGKcLV38-33	EEF1G-BGKcLV38-34
RBP	EEF1G	EEF1G
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11034	11035

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-33	BGKcLV38-34
Sample #	69	70
Sample Name	EEF1G-BGKcLV38-33	EEF1G-BGKcLV38-34
Sample_Name_Alias
Index Well Position	C10	D10
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	287	290
Peak_Molarity	65.80	74.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/C10.png	DNA_Library_set54-56/set2/D10.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/E9.png	RNA_Library_set54-56/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-33	BGKcLV38-34
RBP	EEF1G	EEF1G
Batch_ID	BGKcLV38	BGKcLV38
WB_result	66.000	65.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3440	3441

Sequencing Information

	BGKcLV38-33	BGKcLV38-34
Sample_ID	BGKcLV38-33	BGKcLV38-34
Sample Name	EEF1G-BGKcLV38-33	EEF1G-BGKcLV38-34
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	71,487,521	91,097,581
total_aligned_reads	66,359,065	84,394,394
unique_aligned_reads	61,631,385	78,503,505
percent_uniqueAligned	0.86213	0.86175
correlation_replicates	0.998641	0.998641
spikein_reads	18,324	17,654
percent_spikeins	0.00026	0.00019
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2311	2312

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
EEF1G-BGKcLV38-33_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2311	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	8316
EEF1G-BGKcLV38-33_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2311	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	8354
EEF1G-BGKcLV38-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2311					GRCh38	V40	EEF1G-BGKcLV38-33_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGKcLV38-33_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16968
EEF1G-BGKcLV38-33_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	2311					GRCh38	V40	EEF1G-BGKcLV38-33/Aligned.sortedByCoord.out.bam		ENCORE2	17006
EEF1G-BGKcLV38-33_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	2311					GRCh38	V40	EEF1G-BGKcLV38-33/Aligned.sortedByCoord.out.bam		ENCORE2	17044
EEF1G-BGKcLV38-33_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	2311					GRCh38	V40	EEF1G-BGKcLV38-33/Aligned.sortedByCoord.out.bam		ENCORE2	17082
EEF1G-BGKcLV38-33_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	2311					GRCh38	V40	EEF1G-BGKcLV38-33/Aligned.sortedByCoord.out.bam		ENCORE2	17120
EEF1G-BGKcLV38-33_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2311					GRCh38	V40	EEF1G-BGKcLV38-33_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGKcLV38-33_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17158
EEF1G-BGKcLV38-34_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2312	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	8317
EEF1G-BGKcLV38-34_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2312	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	8355
EEF1G-BGKcLV38-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2312					GRCh38	V40	EEF1G-BGKcLV38-34_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGKcLV38-34_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16969
EEF1G-BGKcLV38-34_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	2312					GRCh38	V40	EEF1G-BGKcLV38-34/Aligned.sortedByCoord.out.bam		ENCORE2	17007
EEF1G-BGKcLV38-34_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	2312					GRCh38	V40	EEF1G-BGKcLV38-34/Aligned.sortedByCoord.out.bam		ENCORE2	17045
EEF1G-BGKcLV38-34_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	2312					GRCh38	V40	EEF1G-BGKcLV38-34/Aligned.sortedByCoord.out.bam		ENCORE2	17083
EEF1G-BGKcLV38-34_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	2312					GRCh38	V40	EEF1G-BGKcLV38-34/Aligned.sortedByCoord.out.bam		ENCORE2	17121
EEF1G-BGKcLV38-34_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2312					GRCh38	V40	EEF1G-BGKcLV38-34_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGKcLV38-34_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17159