EIF4ENIF1 RNA-Seq in K562

General Information


RBP	EIF4ENIF1
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF4ENIF1-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF4ENIF1-BGKcLV38-61
Rep2	EIF4ENIF1-BGKcLV38-62
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	62.1
Rep2_qPCR	68.7
Rep1_WB	71.7
Rep2_WB	81.0
Antibody Cat#	A300-706A
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1040

Experiment Information (Status: Submitting)

	BGKcLV38-61	BGKcLV38-62
idx	1478	1479
TRCN#_or_BGC#	BGC#0000981	BGC#0000981
shRNA_or_gRNA_sequence	TGTATAGCGATGGGGGCATT	TGTATAGCGATGGGGGCATT
PAM	TGG	TGG
Name	EIF4ENIF1_83	EIF4ENIF1_83
Sample_ID	BGKcLV38-61	BGKcLV38-62
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EIF4ENIF1	EIF4ENIF1
qPCR_result	62.1	68.7
Ave_qPCR	65.4
RT-qPCR_primer-F	ctggaaaagcagctcttggt
RT-qPCR_primer-R	gagctggatgacaggaggtt
protein_conc	3492	3358
WB_result	71.7	81.0
Ave_WB	76.4
WB_DONE_date	11/4/22
MW	108KD
IP
antibody_Cat#	A300-706A	lot # 2
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	5662	5663

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4ENIF1	Product_ID: A300-706A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF4ENIF1-human

Experiment Status

	BGKcLV38-61	BGKcLV38-62
Sample_ID	BGKcLV38-61	BGKcLV38-62
Sample Name
Sample Name	EIF4ENIF1-BGKcLV38-61	EIF4ENIF1-BGKcLV38-62
RBP	EIF4ENIF1	EIF4ENIF1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11054	11055

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-61	BGKcLV38-62
Sample #	89	90
Sample Name	EIF4ENIF1-BGKcLV38-61	EIF4ENIF1-BGKcLV38-62
Sample_Name_Alias
Index Well Position	G12	H12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	294	289
Peak_Molarity	69.50	69.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/G12.png	DNA_Library_set54-56/set2/H12.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A12.png	RNA_Library_set54-56/set1/B12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-61	BGKcLV38-62
RBP	EIF4ENIF1	EIF4ENIF1
Batch_ID	BGKcLV38	BGKcLV38
WB_result	71.700	81.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3460	3461

Sequencing Information

	BGKcLV38-61	BGKcLV38-62
Sample_ID	BGKcLV38-61	BGKcLV38-62
Sample Name	EIF4ENIF1-BGKcLV38-61	EIF4ENIF1-BGKcLV38-62
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	53,031,517	55,810,608
total_aligned_reads	49,680,679	52,772,630
unique_aligned_reads	46,183,542	49,068,726
percent_uniqueAligned	0.87087	0.87920
correlation_replicates	0.998864	0.998864
spikein_reads	9,462	18,354
percent_spikeins	0.00018	0.00033
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2331	2332

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
EIF4ENIF1-BGKcLV38-61_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2331	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8336
EIF4ENIF1-BGKcLV38-61_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2331	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8374
EIF4ENIF1-BGKcLV38-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4ENIF1-BGKcLV38-61_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16988
EIF4ENIF1-BGKcLV38-61_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61/Aligned.sortedByCoord.out.bam		ENCORE2	17026
EIF4ENIF1-BGKcLV38-61_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61/Aligned.sortedByCoord.out.bam		ENCORE2	17064
EIF4ENIF1-BGKcLV38-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61/Aligned.sortedByCoord.out.bam		ENCORE2	17102
EIF4ENIF1-BGKcLV38-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61/Aligned.sortedByCoord.out.bam		ENCORE2	17140
EIF4ENIF1-BGKcLV38-61_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2331					GRCh38	V40	EIF4ENIF1-BGKcLV38-61_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4ENIF1-BGKcLV38-61_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17178
EIF4ENIF1-BGKcLV38-62_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2332	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8337
EIF4ENIF1-BGKcLV38-62_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2332	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8375
EIF4ENIF1-BGKcLV38-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4ENIF1-BGKcLV38-62_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16989
EIF4ENIF1-BGKcLV38-62_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62/Aligned.sortedByCoord.out.bam		ENCORE2	17027
EIF4ENIF1-BGKcLV38-62_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62/Aligned.sortedByCoord.out.bam		ENCORE2	17065
EIF4ENIF1-BGKcLV38-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62/Aligned.sortedByCoord.out.bam		ENCORE2	17103
EIF4ENIF1-BGKcLV38-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62/Aligned.sortedByCoord.out.bam		ENCORE2	17141
EIF4ENIF1-BGKcLV38-62_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2332					GRCh38	V40	EIF4ENIF1-BGKcLV38-62_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4ENIF1-BGKcLV38-62_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17179