EIF2AK2 RNA-Seq in K562

General Information


RBP	EIF2AK2
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2AK2-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	EIF2AK2-BGKcLV42-27
Rep2	EIF2AK2-BGKcLV42-28
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	76.9
Rep2_qPCR	80.4
Rep1_WB	70.6
Rep2_WB	69.3
Antibody Cat#	12297S
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1537

Experiment Information (Status: Submitting)

	BGKcLV42-27	BGKcLV42-28
idx	0	0
TRCN#_or_BGC#	BGC#0001130	BGC#0001130
shRNA_or_gRNA_sequence	ATTATGAACAGTGTGCATCG	ATTATGAACAGTGTGCATCG
PAM	GGG	GGG
Name	E2AK2_90	E2AK2_90
Sample_ID	BGKcLV42-27	BGKcLV42-28
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	EIF2AK2	EIF2AK2
qPCR_result	76.9	80.4
Ave_qPCR	78.6
RT-qPCR_primer-F	aatgccgcagccaaatta
RT-qPCR_primer-R	ttccccatggataatccttct
protein_conc	2845	2846
WB_result	70.6	69.3
Ave_WB	70.0
WB_DONE_date	5/6/24
MW	74kd
IP
antibody_Cat#	12297S	lot # 3
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	5789	5790

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2AK2	Product_ID: 12297S Lot_ID: 3 Source: Cell Signaling Technology Target Name: EIF2AK2-human

Experiment Status

	BGKcLV42-27	BGKcLV42-28
Sample_ID	BGKcLV42-27	BGKcLV42-28
Sample Name
Sample Name	EIF2AK2-BGKcLV42-27	EIF2AK2-BGKcLV42-28
RBP	EIF2AK2	EIF2AK2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13068	13069

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-27	BGKcLV42-28
Sample #	25	26
Sample Name	EIF2AK2-BGKcLV42-27	EIF2AK2-BGKcLV42-28
Sample_Name_Alias
Index Well Position	A04	B04
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	296	296
Peak_Molarity	114.00	104.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/A4.png	DNA_Library_set73/set1/B4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A4.png	RNA_Library_set73/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-27	BGKcLV42-28
RBP	EIF2AK2	EIF2AK2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	70.600	69.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4294	4295

Sequencing Information

	BGKcLV42-27	BGKcLV42-28
Sample_ID	BGKcLV42-27	BGKcLV42-28
Sample Name	EIF2AK2-BGKcLV42-27	EIF2AK2-BGKcLV42-28
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	44,471,723	28,963,620
total_aligned_reads	37,197,707	26,039,477
unique_aligned_reads	34,201,441	23,981,831
percent_uniqueAligned	0.76906	0.82800
correlation_replicates	0.995631	0.995631
spikein_reads	5,308	936
percent_spikeins	0.00012	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3161	3162

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
EIF2AK2-BGKcLV42-27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3161	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	30364
EIF2AK2-BGKcLV42-27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3161	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	30454
EIF2AK2-BGKcLV42-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGKcLV42-27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31296
EIF2AK2-BGKcLV42-27_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	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_Aligned.sortedByCoord.out.bam		ENCORE2	31386
EIF2AK2-BGKcLV42-27_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	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_Aligned.sortedByCoord.out.bam		ENCORE2	31476
EIF2AK2-BGKcLV42-27_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	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_Aligned.sortedByCoord.out.bam		ENCORE2	31566
EIF2AK2-BGKcLV42-27_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	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_Aligned.sortedByCoord.out.bam		ENCORE2	31656
EIF2AK2-BGKcLV42-27_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3161					GRCh38	V40	EIF2AK2-BGKcLV42-27_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGKcLV42-27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31746
EIF2AK2-BGKcLV42-28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3162	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	30365
EIF2AK2-BGKcLV42-28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3162	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	30455
EIF2AK2-BGKcLV42-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGKcLV42-28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31297
EIF2AK2-BGKcLV42-28_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	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_Aligned.sortedByCoord.out.bam		ENCORE2	31387
EIF2AK2-BGKcLV42-28_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	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_Aligned.sortedByCoord.out.bam		ENCORE2	31477
EIF2AK2-BGKcLV42-28_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	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_Aligned.sortedByCoord.out.bam		ENCORE2	31567
EIF2AK2-BGKcLV42-28_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	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_Aligned.sortedByCoord.out.bam		ENCORE2	31657
EIF2AK2-BGKcLV42-28_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3162					GRCh38	V40	EIF2AK2-BGKcLV42-28_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGKcLV42-28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31747