EEF1G RNA-Seq in HepG2

General Information


RBP	EEF1G
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EEF1G-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EEF1G-BGHcLV39-41
Rep2	EEF1G-BGHcLV39-42
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	64.8
Rep2_qPCR	70.1
Rep1_WB	67.5
Rep2_WB	67.1
Antibody Cat#	A300-734A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1249

Experiment Information (Status: Submitting)

	BGHcLV39-41	BGHcLV39-42
idx	1243	1244
TRCN#_or_BGC#	BGC#0000950	BGC#0000950
shRNA_or_gRNA_sequence	AATATCCTTACCTCTTGGGC	AATATCCTTACCTCTTGGGC
PAM	agg	agg
Name	EEF1G_76	EEF1G_76
Sample_ID	BGHcLV39-41	BGHcLV39-42
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EEF1G	EEF1G
qPCR_result	64.8	70.1
Ave_qPCR	67.4
RT-qPCR_primer-F	ggcgaagtgaaactgtgtga
RT-qPCR_primer-R	ctttccgtggtgtgtccttt
protein_conc	1145	1307
WB_result	67.5	67.1
Ave_WB	67.3
WB_DONE_date	7/5/23
MW	50kd
IP
antibody_Cat#	A300-734A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7434	7435

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

	BGHcLV39-41	BGHcLV39-42
Sample_ID	BGHcLV39-41	BGHcLV39-42
Sample Name
Sample Name	EEF1G-BGHcLV39-41	EEF1G-BGHcLV39-42
RBP	EEF1G	EEF1G
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11990	11991

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-41	BGHcLV39-42
Sample #	17	18
Sample Name	EEF1G-BGHcLV39-41	EEF1G-BGHcLV39-42
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	281	289
Peak_Molarity	36.30	18.40
libSampleQC_DNA_Well	DNA_Library_set63/set1/A11.png	DNA_Library_set63/set1/B11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set63/set1/A11.png	RNA_Library_set63/set1/B11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-41	BGHcLV39-42
RBP	EEF1G	EEF1G
Batch_ID	BGHcLV39	BGHcLV39
WB_result	67.500	67.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3760	3761

Sequencing Information

	BGHcLV39-41	BGHcLV39-42
Sample_ID	BGHcLV39-41	BGHcLV39-42
Sample Name	EEF1G-BGHcLV39-41	EEF1G-BGHcLV39-42
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	64,384,388	56,299,601
total_aligned_reads	50,038,552	41,376,303
unique_aligned_reads	47,279,343	39,061,206
percent_uniqueAligned	0.73433	0.69381
correlation_replicates	0.999829	0.999829
spikein_reads	78,070	119,566
percent_spikeins	0.00121	0.00212
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2659	2660

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-BGHcLV39-41_S11_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2659	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8644
EEF1G-BGHcLV39-41_S11_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2659	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8670
EEF1G-BGHcLV39-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41_S11_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGHcLV39-41_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9941
EEF1G-BGHcLV39-41_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41/Aligned.sortedByCoord.out.bam		ENCORE2	9967
EEF1G-BGHcLV39-41_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41/Aligned.sortedByCoord.out.bam		ENCORE2	9993
EEF1G-BGHcLV39-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41/Aligned.sortedByCoord.out.bam		ENCORE2	10019
EEF1G-BGHcLV39-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41/Aligned.sortedByCoord.out.bam		ENCORE2	10045
EEF1G-BGHcLV39-41_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2659					GRCh38	V40	EEF1G-BGHcLV39-41_S11_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGHcLV39-41_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10071
EEF1G-BGHcLV39-42_S12_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2660	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8645
EEF1G-BGHcLV39-42_S12_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2660	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8671
EEF1G-BGHcLV39-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42_S12_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGHcLV39-42_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9942
EEF1G-BGHcLV39-42_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42/Aligned.sortedByCoord.out.bam		ENCORE2	9968
EEF1G-BGHcLV39-42_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42/Aligned.sortedByCoord.out.bam		ENCORE2	9994
EEF1G-BGHcLV39-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42/Aligned.sortedByCoord.out.bam		ENCORE2	10020
EEF1G-BGHcLV39-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42/Aligned.sortedByCoord.out.bam		ENCORE2	10046
EEF1G-BGHcLV39-42_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2660					GRCh38	V40	EEF1G-BGHcLV39-42_S12_R1_001.filtered.trimmed.paired.fastq.gz,EEF1G-BGHcLV39-42_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10072