EIF2S1 RNA-Seq in K562

General Information


RBP	EIF2S1
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2S1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF2S1-BGKcLV44-23
Rep2	EIF2S1-BGKcLV44-24
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	83.0
Rep2_qPCR	79.2
Rep1_WB	60.1
Rep2_WB	60.9
Antibody Cat#	5324S
Antibody Lot#	lot # 9
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1599

Experiment Information (Status: Submitting)

	BGKcLV44-23	BGKcLV44-24
idx	0	0
TRCN#_or_BGC#	BGC#0001138	BGC#0001138
shRNA_or_gRNA_sequence	TGAGGTGTTAGAATACACCA	TGAGGTGTTAGAATACACCA
PAM	AGG	AGG
Name	EIF2S1_77	EIF2S1_77
Sample_ID	BGKcLV44-23	BGKcLV44-24
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	EIF2S1	EIF2S1
qPCR_result	83.0	79.2
Ave_qPCR	81.1
RT-qPCR_primer-F	TTGAATGAAGATGAACGGGAA
RT-qPCR_primer-R	GCATCAATGCCTTCATAACCA
protein_conc	4830	4557
WB_result	60.1	60.9
Ave_WB	60.5
WB_DONE_date	8/8/24
MW	38kd
IP
antibody_Cat#	5324S	lot # 9
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	5913	5914

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2S1	Product_ID: 5324S Lot_ID: 9 Source: Cell Signaling Technology Target Name: EIF2S1-human

Experiment Status

	BGKcLV44-23	BGKcLV44-24
Sample_ID	BGKcLV44-23	BGKcLV44-24
Sample Name
Sample Name	EIF2S1-BGKcLV44-23	EIF2S1-BGKcLV44-24
RBP	EIF2S1	EIF2S1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13590	13591

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-23	BGKcLV44-24
Sample #	19	20
Sample Name	EIF2S1-BGKcLV44-23	EIF2S1-BGKcLV44-24
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	292	292
Peak_Molarity	102.00	70.30
libSampleQC_DNA_Well	DNA_Library_set75/set1/C8.png	DNA_Library_set75/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/C2.png	RNA_Library_set75/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-23	BGKcLV44-24
RBP	EIF2S1	EIF2S1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	60.100	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4578	4579

Sequencing Information

	BGKcLV44-23	BGKcLV44-24
Sample_ID	BGKcLV44-23	BGKcLV44-24
Sample Name	EIF2S1-BGKcLV44-23	EIF2S1-BGKcLV44-24
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	46,895,755	45,633,725
total_aligned_reads	43,986,269	42,930,891
unique_aligned_reads	40,769,334	39,829,984
percent_uniqueAligned	0.86936	0.87282
correlation_replicates	0.999210	0.999210
spikein_reads	93,272	83,126
percent_spikeins	0.00199	0.00182
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3289	3290

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
EIF2S1-BGKcLV44-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3289	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30942
EIF2S1-BGKcLV44-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3289	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30984
EIF2S1-BGKcLV44-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2S1-BGKcLV44-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31026
EIF2S1-BGKcLV44-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_Aligned.sortedByCoord.out.bam		ENCORE2	31068
EIF2S1-BGKcLV44-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_Aligned.sortedByCoord.out.bam		ENCORE2	31110
EIF2S1-BGKcLV44-23_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_Aligned.sortedByCoord.out.bam		ENCORE2	31152
EIF2S1-BGKcLV44-23_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_Aligned.sortedByCoord.out.bam		ENCORE2	31194
EIF2S1-BGKcLV44-23_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3289					GRCh38	V40	EIF2S1-BGKcLV44-23_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2S1-BGKcLV44-23_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31236
EIF2S1-BGKcLV44-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3290	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30943
EIF2S1-BGKcLV44-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3290	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30985
EIF2S1-BGKcLV44-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2S1-BGKcLV44-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31027
EIF2S1-BGKcLV44-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_Aligned.sortedByCoord.out.bam		ENCORE2	31069
EIF2S1-BGKcLV44-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_Aligned.sortedByCoord.out.bam		ENCORE2	31111
EIF2S1-BGKcLV44-24_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_Aligned.sortedByCoord.out.bam		ENCORE2	31153
EIF2S1-BGKcLV44-24_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_Aligned.sortedByCoord.out.bam		ENCORE2	31195
EIF2S1-BGKcLV44-24_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3290					GRCh38	V40	EIF2S1-BGKcLV44-24_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF2S1-BGKcLV44-24_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31237