EIF3B RNA-Seq in K562

General Information


RBP	EIF3B
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3B-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	EIF3B-BGKcLV38-47
Rep2	EIF3B-BGKcLV38-48
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	67.2
Rep2_qPCR	65.1
Rep1_WB	71.5
Rep2_WB	75.2
Antibody Cat#	A301-761A
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1036

Experiment Information (Status: Submitting)

	BGKcLV38-47	BGKcLV38-48
idx	1464	1465
TRCN#_or_BGC#	BGC#0000963	BGC#0000963
shRNA_or_gRNA_sequence	TATGACGATCAGTGACGAGT	TATGACGATCAGTGACGAGT
PAM	GGG	GGG
Name	EIF3B_95	EIF3B_95
Sample_ID	BGKcLV38-47	BGKcLV38-48
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EIF3B	EIF3B
qPCR_result	67.2	65.1
Ave_qPCR	66.1
RT-qPCR_primer-F	tcctgaagaggatgggaaga
RT-qPCR_primer-R	aagaggttgacccggaatgt
protein_conc	2927	3164
WB_result	71.5	75.2
Ave_WB	73.3
WB_DONE_date	10/28/22
MW	92KD
IP
antibody_Cat#	A301-761A	lot # 2
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	5646	5647

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3B	Product_ID: A301-761A Lot_ID: 2 Source: Bethyl Labs Target Name: EIF3B-human

Experiment Status

	BGKcLV38-47	BGKcLV38-48
Sample_ID	BGKcLV38-47	BGKcLV38-48
Sample Name
Sample Name	EIF3B-BGKcLV38-47	EIF3B-BGKcLV38-48
RBP	EIF3B	EIF3B
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11046	11047

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-47	BGKcLV38-48
Sample #	81	82
Sample Name	EIF3B-BGKcLV38-47	EIF3B-BGKcLV38-48
Sample_Name_Alias
Index Well Position	G11	H11
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	297	323
Peak_Molarity	72.70	79.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/G11.png	DNA_Library_set54-56/set2/H11.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/A11.png	RNA_Library_set54-56/set1/B11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-47	BGKcLV38-48
RBP	EIF3B	EIF3B
Batch_ID	BGKcLV38	BGKcLV38
WB_result	71.500	75.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3452	3453

Sequencing Information

	BGKcLV38-47	BGKcLV38-48
Sample_ID	BGKcLV38-47	BGKcLV38-48
Sample Name	EIF3B-BGKcLV38-47	EIF3B-BGKcLV38-48
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	80,375,990	56,882,571
total_aligned_reads	74,729,866	53,734,615
unique_aligned_reads	69,328,660	49,984,657
percent_uniqueAligned	0.86255	0.87873
correlation_replicates	0.997116	0.997116
spikein_reads	13,114	16,284
percent_spikeins	0.00016	0.00029
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2323	2324

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
EIF3B-BGKcLV38-47_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2323	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	8328
EIF3B-BGKcLV38-47_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2323	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	8366
EIF3B-BGKcLV38-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2323					GRCh38	V40	EIF3B-BGKcLV38-47_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3B-BGKcLV38-47_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16980
EIF3B-BGKcLV38-47_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	2323					GRCh38	V40	EIF3B-BGKcLV38-47/Aligned.sortedByCoord.out.bam		ENCORE2	17018
EIF3B-BGKcLV38-47_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	2323					GRCh38	V40	EIF3B-BGKcLV38-47/Aligned.sortedByCoord.out.bam		ENCORE2	17056
EIF3B-BGKcLV38-47_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	2323					GRCh38	V40	EIF3B-BGKcLV38-47/Aligned.sortedByCoord.out.bam		ENCORE2	17094
EIF3B-BGKcLV38-47_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	2323					GRCh38	V40	EIF3B-BGKcLV38-47/Aligned.sortedByCoord.out.bam		ENCORE2	17132
EIF3B-BGKcLV38-47_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2323					GRCh38	V40	EIF3B-BGKcLV38-47_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3B-BGKcLV38-47_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17170
EIF3B-BGKcLV38-48_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2324	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	8329
EIF3B-BGKcLV38-48_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2324	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	8367
EIF3B-BGKcLV38-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2324					GRCh38	V40	EIF3B-BGKcLV38-48_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3B-BGKcLV38-48_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16981
EIF3B-BGKcLV38-48_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	2324					GRCh38	V40	EIF3B-BGKcLV38-48/Aligned.sortedByCoord.out.bam		ENCORE2	17019
EIF3B-BGKcLV38-48_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	2324					GRCh38	V40	EIF3B-BGKcLV38-48/Aligned.sortedByCoord.out.bam		ENCORE2	17057
EIF3B-BGKcLV38-48_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	2324					GRCh38	V40	EIF3B-BGKcLV38-48/Aligned.sortedByCoord.out.bam		ENCORE2	17095
EIF3B-BGKcLV38-48_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	2324					GRCh38	V40	EIF3B-BGKcLV38-48/Aligned.sortedByCoord.out.bam		ENCORE2	17133
EIF3B-BGKcLV38-48_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2324					GRCh38	V40	EIF3B-BGKcLV38-48_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3B-BGKcLV38-48_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17171