EIF2AK4 RNA-Seq in K562

General Information


RBP	EIF2AK4
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2AK4-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF2AK4-BGKcLV42-31
Rep2	EIF2AK4-BGKcLV42-32
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	24.4
Rep2_qPCR	20.5
Rep1_WB	70.3
Rep2_WB	74.9
Antibody Cat#	65981S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1539

Experiment Information (Status: Submitting)

	BGKcLV42-31	BGKcLV42-32
idx	0	0
TRCN#_or_BGC#	BGC#0001134	BGC#0001134
shRNA_or_gRNA_sequence	CGCGCCGTAAATGGCCTCCA	CGCGCCGTAAATGGCCTCCA
PAM	GGG	GGG
Name	EIF2AK4_94	EIF2AK4_94
Sample_ID	BGKcLV42-31	BGKcLV42-32
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	EIF2AK4	EIF2AK4
qPCR_result	24.4	20.5
Ave_qPCR	22.4
RT-qPCR_primer-F	aatggtaaacatcgggcaaa
RT-qPCR_primer-R	gctgatcaggactccccata
protein_conc	3489	3548
WB_result	70.3	74.9
Ave_WB	72.6
WB_DONE_date	5/14/24
MW	220kd
IP
antibody_Cat#	65981S	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	5793	5794

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2AK4	Product_ID: 65981S Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF2AK4-human

Experiment Status

	BGKcLV42-31	BGKcLV42-32
Sample_ID	BGKcLV42-31	BGKcLV42-32
Sample Name
Sample Name	EIF2AK4-BGKcLV42-31	EIF2AK4-BGKcLV42-32
RBP	EIF2AK4	EIF2AK4
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13072	13073

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-31	BGKcLV42-32
Sample #	29	30
Sample Name	EIF2AK4-BGKcLV42-31	EIF2AK4-BGKcLV42-32
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	295	291
Peak_Molarity	101.00	102.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/E4.png	DNA_Library_set73/set1/F4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E4.png	RNA_Library_set73/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-31	BGKcLV42-32
RBP	EIF2AK4	EIF2AK4
Batch_ID	BGKcLV42	BGKcLV42
WB_result	70.300	74.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4298	4299

Sequencing Information

	BGKcLV42-31	BGKcLV42-32
Sample_ID	BGKcLV42-31	BGKcLV42-32
Sample Name	EIF2AK4-BGKcLV42-31	EIF2AK4-BGKcLV42-32
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	41,463,697	39,605,846
total_aligned_reads	37,403,941	37,173,492
unique_aligned_reads	34,514,776	34,272,966
percent_uniqueAligned	0.83241	0.86535
correlation_replicates	0.998498	0.998498
spikein_reads	2,554	3,468
percent_spikeins	0.00006	0.00009
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3165	3166

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
EIF2AK4-BGKcLV42-31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3165	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30366
EIF2AK4-BGKcLV42-31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3165	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30456
EIF2AK4-BGKcLV42-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK4-BGKcLV42-31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31298
EIF2AK4-BGKcLV42-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_Aligned.sortedByCoord.out.bam		ENCORE2	31388
EIF2AK4-BGKcLV42-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_Aligned.sortedByCoord.out.bam		ENCORE2	31478
EIF2AK4-BGKcLV42-31_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_Aligned.sortedByCoord.out.bam		ENCORE2	31568
EIF2AK4-BGKcLV42-31_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_Aligned.sortedByCoord.out.bam		ENCORE2	31658
EIF2AK4-BGKcLV42-31_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3165					GRCh38	V40	EIF2AK4-BGKcLV42-31_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK4-BGKcLV42-31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31748
EIF2AK4-BGKcLV42-32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3166	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30367
EIF2AK4-BGKcLV42-32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3166	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30457
EIF2AK4-BGKcLV42-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK4-BGKcLV42-32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31299
EIF2AK4-BGKcLV42-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_Aligned.sortedByCoord.out.bam		ENCORE2	31389
EIF2AK4-BGKcLV42-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_Aligned.sortedByCoord.out.bam		ENCORE2	31479
EIF2AK4-BGKcLV42-32_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_Aligned.sortedByCoord.out.bam		ENCORE2	31569
EIF2AK4-BGKcLV42-32_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_Aligned.sortedByCoord.out.bam		ENCORE2	31659
EIF2AK4-BGKcLV42-32_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3166					GRCh38	V40	EIF2AK4-BGKcLV42-32_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK4-BGKcLV42-32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31749