EIF2AK2 RNA-Seq in HepG2

General Information


RBP	EIF2AK2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF2AK2-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF2AK2-BGHcLV43-15
Rep2	EIF2AK2-BGHcLV43-16
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	81.8
Rep2_WB	87.1
Antibody Cat#	12297S
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1574

Experiment Information (Status: Submitting)

	BGHcLV43-15	BGHcLV43-16
idx	1383	1384
TRCN#_or_BGC#	BGC#0001131	BGC#0001131
shRNA_or_gRNA_sequence	AATACATACCGTCAGAAGCA	AATACATACCGTCAGAAGCA
PAM	GGG	GGG
Name	E2AK2_84	E2AK2_84
Sample_ID	BGHcLV43-15	BGHcLV43-16
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	EIF2AK2	EIF2AK2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TTCACAGACCTACGGGATGG
RT-qPCR_primer-R	GGTCGATCCTCAGGTTTCTTT
protein_conc	3017	3241
WB_result	81.8	87.1
Ave_WB	84.4
WB_DONE_date	6/13/24
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	9636	9637

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

	BGHcLV43-15	BGHcLV43-16
Sample_ID	BGHcLV43-15	BGHcLV43-16
Sample Name
Sample Name	EIF2AK2-BGHcLV43-15	EIF2AK2-BGHcLV43-16
RBP	EIF2AK2	EIF2AK2
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13238	13239

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-15	BGHcLV43-16
Sample #	11	12
Sample Name	EIF2AK2-BGHcLV43-15	EIF2AK2-BGHcLV43-16
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	301	310
Peak_Molarity	94.80	88.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/C2.png	DNA_Library_set74/set1/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G7.png	RNA_Library_set74/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-15	BGHcLV43-16
RBP	EIF2AK2	EIF2AK2
Batch_ID	BGHcLV43	BGHcLV43
WB_result	81.800	87.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4370	4371

Sequencing Information

	BGHcLV43-15	BGHcLV43-16
Sample_ID	BGHcLV43-15	BGHcLV43-16
Sample Name	EIF2AK2-BGHcLV43-15	EIF2AK2-BGHcLV43-16
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	42,108,574	45,121,344
total_aligned_reads	38,095,772	41,787,418
unique_aligned_reads	35,834,431	39,324,245
percent_uniqueAligned	0.85100	0.87152
correlation_replicates	0.997377	0.997377
spikein_reads	32,258	11,068
percent_spikeins	0.00077	0.00025
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3237	3238

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-BGHcLV43-15_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3237	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30530
EIF2AK2-BGHcLV43-15_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3237	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30582
EIF2AK2-BGHcLV43-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGHcLV43-15_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30634
EIF2AK2-BGHcLV43-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_Aligned.sortedByCoord.out.bam		ENCORE2	30686
EIF2AK2-BGHcLV43-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_Aligned.sortedByCoord.out.bam		ENCORE2	30738
EIF2AK2-BGHcLV43-15_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_Aligned.sortedByCoord.out.bam		ENCORE2	30790
EIF2AK2-BGHcLV43-15_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_Aligned.sortedByCoord.out.bam		ENCORE2	30842
EIF2AK2-BGHcLV43-15_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3237					GRCh38	V40	EIF2AK2-BGHcLV43-15_S101_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGHcLV43-15_S101_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30894
EIF2AK2-BGHcLV43-16_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3238	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30531
EIF2AK2-BGHcLV43-16_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3238	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30583
EIF2AK2-BGHcLV43-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGHcLV43-16_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30635
EIF2AK2-BGHcLV43-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_Aligned.sortedByCoord.out.bam		ENCORE2	30687
EIF2AK2-BGHcLV43-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_Aligned.sortedByCoord.out.bam		ENCORE2	30739
EIF2AK2-BGHcLV43-16_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_Aligned.sortedByCoord.out.bam		ENCORE2	30791
EIF2AK2-BGHcLV43-16_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_Aligned.sortedByCoord.out.bam		ENCORE2	30843
EIF2AK2-BGHcLV43-16_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3238					GRCh38	V40	EIF2AK2-BGHcLV43-16_S102_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK2-BGHcLV43-16_S102_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30895