EIF1 RNA-Seq in K562

General Information


RBP	EIF1
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF1-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	EIF1-BGKcLV42-29
Rep2	EIF1-BGKcLV42-30
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	46.8
Rep2_qPCR	59.7
Rep1_WB	89.8
Rep2_WB	96.0
Antibody Cat#	12496S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1538

Experiment Information (Status: Submitting)

	BGKcLV42-29	BGKcLV42-30
idx	0	0
TRCN#_or_BGC#	BGC#0001131	BGC#0001131
shRNA_or_gRNA_sequence	TGACTGAACTCACCTCTACG	TGACTGAACTCACCTCTACG
PAM	AGG	AGG
Name	EIF1_83	EIF1_83
Sample_ID	BGKcLV42-29	BGKcLV42-30
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	EIF1	EIF1
qPCR_result	46.8	59.7
Ave_qPCR	53.2
RT-qPCR_primer-F	agggatcgctgatgattacg
RT-qPCR_primer-R	tctccatattccggatgctc
protein_conc	3570	3233
WB_result	89.8	96.0
Ave_WB	92.9
WB_DONE_date	5/2/24
MW	13kd
IP
antibody_Cat#	12496S	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	5791	5792

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF1	Product_ID: 12496S Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF1-human

Experiment Status

	BGKcLV42-29	BGKcLV42-30
Sample_ID	BGKcLV42-29	BGKcLV42-30
Sample Name
Sample Name	EIF1-BGKcLV42-29	EIF1-BGKcLV42-30
RBP	EIF1	EIF1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13070	13071

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-29	BGKcLV42-30
Sample #	27	28
Sample Name	EIF1-BGKcLV42-29	EIF1-BGKcLV42-30
Sample_Name_Alias
Index Well Position	C04	D04
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	303	291
Peak_Molarity	113.00	95.10
libSampleQC_DNA_Well	DNA_Library_set73/set1/C4.png	DNA_Library_set73/set1/D4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C4.png	RNA_Library_set73/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-29	BGKcLV42-30
RBP	EIF1	EIF1
Batch_ID	BGKcLV42	BGKcLV42
WB_result	89.800	96.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4296	4297

Sequencing Information

	BGKcLV42-29	BGKcLV42-30
Sample_ID	BGKcLV42-29	BGKcLV42-30
Sample Name	EIF1-BGKcLV42-29	EIF1-BGKcLV42-30
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	43,960,894	41,638,920
total_aligned_reads	39,329,321	38,206,585
unique_aligned_reads	36,278,144	35,255,708
percent_uniqueAligned	0.82524	0.84670
correlation_replicates	0.997231	0.997231
spikein_reads	3,412	1,398
percent_spikeins	0.00008	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3163	3164

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
EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3163	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	30362
EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3163	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	30452
EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3163					GRCh38	V40	EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31294
EIF1-BGKcLV42-29_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	3163					GRCh38	V40	EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bam		ENCORE2	31384
EIF1-BGKcLV42-29_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	3163					GRCh38	V40	EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bam		ENCORE2	31474
EIF1-BGKcLV42-29_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	3163					GRCh38	V40	EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bam		ENCORE2	31564
EIF1-BGKcLV42-29_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	3163					GRCh38	V40	EIF1-BGKcLV42-29_Aligned.sortedByCoord.out.bam		ENCORE2	31654
EIF1-BGKcLV42-29_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3163					GRCh38	V40	EIF1-BGKcLV42-29_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31744
EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3164	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	30363
EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3164	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	30453
EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3164					GRCh38	V40	EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31295
EIF1-BGKcLV42-30_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	3164					GRCh38	V40	EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bam		ENCORE2	31385
EIF1-BGKcLV42-30_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	3164					GRCh38	V40	EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bam		ENCORE2	31475
EIF1-BGKcLV42-30_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	3164					GRCh38	V40	EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bam		ENCORE2	31565
EIF1-BGKcLV42-30_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	3164					GRCh38	V40	EIF1-BGKcLV42-30_Aligned.sortedByCoord.out.bam		ENCORE2	31655
EIF1-BGKcLV42-30_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3164					GRCh38	V40	EIF1-BGKcLV42-30_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGKcLV42-30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31745