EIF2B5 RNA-Seq in K562

General Information


RBP	EIF2B5
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2B5-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	EIF2B5-BGKcLV38-43
Rep2	EIF2B5-BGKcLV38-44
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	68.4
Rep2_qPCR	62.8
Rep1_WB	62.9
Rep2_WB	73.4
Antibody Cat#	A302-557A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1034

Experiment Information (Status: Submitting)

	BGKcLV38-43	BGKcLV38-43	BGKcLV38-44	BGKcLV38-44
idx	1460	1460	1461	1461
TRCN#_or_BGC#	BGC#0000960	BGC#0000960	BGC#0000960	BGC#0000960
shRNA_or_gRNA_sequence	GAAGCGGCGATCGAAGCTAT	GAAGCGGCGATCGAAGCTAT	GAAGCGGCGATCGAAGCTAT	GAAGCGGCGATCGAAGCTAT
PAM	CGG	CGG	CGG	CGG
Name	EIF2B5_98	EIF2B5_98	EIF2B5_98	EIF2B5_98
Sample_ID	BGKcLV38-43	BGKcLV38-43	BGKcLV38-44	BGKcLV38-44
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	EIF2B5	EIF2B5	EIF2B5	EIF2B5
qPCR_result	68.4	68.4	62.8	62.8
Ave_qPCR	65.6	65.6
RT-qPCR_primer-F	gctggaaagctgctcaaatc	gctggaaagctgctcaaatc
RT-qPCR_primer-R	aggacatctcccagtgatcg	aggacatctcccagtgatcg
protein_conc	3446	3446	3721	3721
WB_result	62.9	50.7	73.4	48.4771
Ave_WB	68.2	49.6
WB_DONE_date	10/28/22	7/19/23
MW	80KD	80KD
IP
antibody_Cat#	A302-557A	A302-556A	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	5640	5642	5641	5643

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2B5	Product_ID: A302-557A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2B5-human
EIF2B5	Product_ID: A302-556A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2B5-human

Experiment Status

	BGKcLV38-43	BGKcLV38-44
Sample_ID	BGKcLV38-43	BGKcLV38-44
Sample Name
Sample Name	EIF2B5-BGKcLV38-43	EIF2B5-BGKcLV38-44
RBP	EIF2B5	EIF2B5
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11042	11043

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-43	BGKcLV38-44
Sample #	77	78
Sample Name	EIF2B5-BGKcLV38-43	EIF2B5-BGKcLV38-44
Sample_Name_Alias
Index Well Position	C11	D11
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	291	289
Peak_Molarity	78.90	76.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/C11.png	DNA_Library_set54-56/set2/D11.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/E10.png	RNA_Library_set54-56/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-43	BGKcLV38-44
RBP	EIF2B5	EIF2B5
Batch_ID	BGKcLV38	BGKcLV38
WB_result	62.900	73.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3448	3449

Sequencing Information

	BGKcLV38-43	BGKcLV38-44
Sample_ID	BGKcLV38-43	BGKcLV38-44
Sample Name	EIF2B5-BGKcLV38-43	EIF2B5-BGKcLV38-44
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	64,360,545	89,827,167
total_aligned_reads	60,414,308	84,658,099
unique_aligned_reads	56,218,631	78,862,667
percent_uniqueAligned	0.87350	0.87794
correlation_replicates	0.999492	0.999492
spikein_reads	6,636	9,532
percent_spikeins	0.00010	0.00011
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2319	2320

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
EIF2B5-BGKcLV38-43_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2319	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	8324
EIF2B5-BGKcLV38-43_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2319	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	8362
EIF2B5-BGKcLV38-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2319					GRCh38	V40	EIF2B5-BGKcLV38-43_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGKcLV38-43_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16976
EIF2B5-BGKcLV38-43_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	2319					GRCh38	V40	EIF2B5-BGKcLV38-43/Aligned.sortedByCoord.out.bam		ENCORE2	17014
EIF2B5-BGKcLV38-43_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	2319					GRCh38	V40	EIF2B5-BGKcLV38-43/Aligned.sortedByCoord.out.bam		ENCORE2	17052
EIF2B5-BGKcLV38-43_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	2319					GRCh38	V40	EIF2B5-BGKcLV38-43/Aligned.sortedByCoord.out.bam		ENCORE2	17090
EIF2B5-BGKcLV38-43_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	2319					GRCh38	V40	EIF2B5-BGKcLV38-43/Aligned.sortedByCoord.out.bam		ENCORE2	17128
EIF2B5-BGKcLV38-43_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2319					GRCh38	V40	EIF2B5-BGKcLV38-43_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGKcLV38-43_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17166
EIF2B5-BGKcLV38-44_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2320	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	8325
EIF2B5-BGKcLV38-44_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2320	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	8363
EIF2B5-BGKcLV38-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2320					GRCh38	V40	EIF2B5-BGKcLV38-44_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGKcLV38-44_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16977
EIF2B5-BGKcLV38-44_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	2320					GRCh38	V40	EIF2B5-BGKcLV38-44/Aligned.sortedByCoord.out.bam		ENCORE2	17015
EIF2B5-BGKcLV38-44_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	2320					GRCh38	V40	EIF2B5-BGKcLV38-44/Aligned.sortedByCoord.out.bam		ENCORE2	17053
EIF2B5-BGKcLV38-44_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	2320					GRCh38	V40	EIF2B5-BGKcLV38-44/Aligned.sortedByCoord.out.bam		ENCORE2	17091
EIF2B5-BGKcLV38-44_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	2320					GRCh38	V40	EIF2B5-BGKcLV38-44/Aligned.sortedByCoord.out.bam		ENCORE2	17129
EIF2B5-BGKcLV38-44_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2320					GRCh38	V40	EIF2B5-BGKcLV38-44_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGKcLV38-44_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17167