EIF2B4 RNA-Seq in K562

General Information


RBP	EIF2B4
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2B4-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	EIF2B4-BGKcLV38-41
Rep2	EIF2B4-BGKcLV38-42
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	37.0
Rep2_qPCR	33.0
Rep1_WB	58.1
Rep2_WB	52.3
Antibody Cat#	A302-983A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1033

Experiment Information (Status: Submitting)

	BGKcLV38-41	BGKcLV38-41	BGKcLV38-42	BGKcLV38-42
idx	1458	1458	1459	1459
TRCN#_or_BGC#	BGC#0000958	BGC#0000958	BGC#0000958	BGC#0000958
shRNA_or_gRNA_sequence	ACGAAGCAGGGCAATACACC	ACGAAGCAGGGCAATACACC	ACGAAGCAGGGCAATACACC	ACGAAGCAGGGCAATACACC
PAM	ggg	ggg	ggg	ggg
Name	EIF2B4_89	EIF2B4_89	EIF2B4_89	EIF2B4_89
Sample_ID	BGKcLV38-41	BGKcLV38-41	BGKcLV38-42	BGKcLV38-42
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	EIF2B4	EIF2B4	EIF2B4	EIF2B4
qPCR_result	37.0	37.0	33.0	33.0
Ave_qPCR	35.0	35.0
RT-qPCR_primer-F	tatctgcagcccaatgtcaa	tatctgcagcccaatgtcaa
RT-qPCR_primer-R	cgaccagctggaactttctc	cgaccagctggaactttctc
protein_conc	3429	3429	2873	2873
WB_result	58.1	68.5	52.3	71.3926
Ave_WB	55.2	69.9
WB_DONE_date	11/4/22	7/19/23
MW	58KD	58KD
IP
antibody_Cat#	A302-983A	A302-982A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5636	5638	5637	5639

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2B4	Product_ID: A302-982A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2B4-human
EIF2B4	Product_ID: A302-983A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2B4-human

Experiment Status

	BGKcLV38-41	BGKcLV38-42
Sample_ID	BGKcLV38-41	BGKcLV38-42
Sample Name
Sample Name	EIF2B4-BGKcLV38-41	EIF2B4-BGKcLV38-42
RBP	EIF2B4	EIF2B4
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11040	11041

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-41	BGKcLV38-42
Sample #	75	76
Sample Name	EIF2B4-BGKcLV38-41	EIF2B4-BGKcLV38-42
Sample_Name_Alias
Index Well Position	A11	B11
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	303	287
Peak_Molarity	36.20	68.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/A11.png	DNA_Library_set54-56/set2/B11.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/C10.png	RNA_Library_set54-56/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-41	BGKcLV38-42
RBP	EIF2B4	EIF2B4
Batch_ID	BGKcLV38	BGKcLV38
WB_result	58.100	52.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3446	3447

Sequencing Information

	BGKcLV38-41	BGKcLV38-42
Sample_ID	BGKcLV38-41	BGKcLV38-42
Sample Name	EIF2B4-BGKcLV38-41	EIF2B4-BGKcLV38-42
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	48,176,266	47,369,524
total_aligned_reads	44,683,350	44,369,417
unique_aligned_reads	41,681,014	41,316,515
percent_uniqueAligned	0.86518	0.87222
correlation_replicates	0.998751	0.998751
spikein_reads	15,632	11,594
percent_spikeins	0.00032	0.00024
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2317	2318

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
EIF2B4-BGKcLV38-41_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2317	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	8322
EIF2B4-BGKcLV38-41_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2317	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	8360
EIF2B4-BGKcLV38-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2317					GRCh38	V40	EIF2B4-BGKcLV38-41_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGKcLV38-41_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16974
EIF2B4-BGKcLV38-41_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	2317					GRCh38	V40	EIF2B4-BGKcLV38-41/Aligned.sortedByCoord.out.bam		ENCORE2	17012
EIF2B4-BGKcLV38-41_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	2317					GRCh38	V40	EIF2B4-BGKcLV38-41/Aligned.sortedByCoord.out.bam		ENCORE2	17050
EIF2B4-BGKcLV38-41_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	2317					GRCh38	V40	EIF2B4-BGKcLV38-41/Aligned.sortedByCoord.out.bam		ENCORE2	17088
EIF2B4-BGKcLV38-41_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	2317					GRCh38	V40	EIF2B4-BGKcLV38-41/Aligned.sortedByCoord.out.bam		ENCORE2	17126
EIF2B4-BGKcLV38-41_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2317					GRCh38	V40	EIF2B4-BGKcLV38-41_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGKcLV38-41_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17164
EIF2B4-BGKcLV38-42_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2318	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	8323
EIF2B4-BGKcLV38-42_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2318	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	8361
EIF2B4-BGKcLV38-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2318					GRCh38	V40	EIF2B4-BGKcLV38-42_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGKcLV38-42_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16975
EIF2B4-BGKcLV38-42_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	2318					GRCh38	V40	EIF2B4-BGKcLV38-42/Aligned.sortedByCoord.out.bam		ENCORE2	17013
EIF2B4-BGKcLV38-42_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	2318					GRCh38	V40	EIF2B4-BGKcLV38-42/Aligned.sortedByCoord.out.bam		ENCORE2	17051
EIF2B4-BGKcLV38-42_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	2318					GRCh38	V40	EIF2B4-BGKcLV38-42/Aligned.sortedByCoord.out.bam		ENCORE2	17089
EIF2B4-BGKcLV38-42_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	2318					GRCh38	V40	EIF2B4-BGKcLV38-42/Aligned.sortedByCoord.out.bam		ENCORE2	17127
EIF2B4-BGKcLV38-42_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2318					GRCh38	V40	EIF2B4-BGKcLV38-42_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGKcLV38-42_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17165