EIF3L RNA-Seq in K562

General Information


RBP	EIF3L
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3L-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	EIF3L-BGKcLV38-55
Rep2	EIF3L-BGKcLV38-56
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	61.0
Rep2_qPCR	60.5
Rep1_WB	77.2
Rep2_WB	79.6
Antibody Cat#	A304-754A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1038

Experiment Information (Status: Submitting)

	BGKcLV38-55	BGKcLV38-55	BGKcLV38-56	BGKcLV38-56
idx	1472	1472	1473	1473
TRCN#_or_BGC#	BGC#0000975	BGC#0000975	BGC#0000975	BGC#0000975
shRNA_or_gRNA_sequence	GCAGGCGGAGAAGCCCGACC	GCAGGCGGAGAAGCCCGACC	GCAGGCGGAGAAGCCCGACC	GCAGGCGGAGAAGCCCGACC
PAM	AGG	AGG	AGG	AGG
Name	EIF3L_83	EIF3L_83	EIF3L_83	EIF3L_83
Sample_ID	BGKcLV38-55	BGKcLV38-55	BGKcLV38-56	BGKcLV38-56
transduction_Date	10/18/22	10/18/22	10/18/22	10/18/22
days	D6	D6	D6	D6
RBP_name	EIF3L	EIF3L	EIF3L	EIF3L
qPCR_result	61.0	61.0	60.5	60.5
Ave_qPCR	60.7	60.7
RT-qPCR_primer-F	gctacaggccagtcgtgtct	gctacaggccagtcgtgtct
RT-qPCR_primer-R	gggccaaggtgtattcttga	gggccaaggtgtattcttga
protein_conc	3218	3218	3284	3284
WB_result	77.2	67.9	79.6	69.1908
Ave_WB	78.4	68.5
WB_DONE_date	10/28/22	11/3/22
MW	67KD	67KD
IP
antibody_Cat#	A304-754A	A304-753A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5654	5656	5655	5657

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3L	Product_ID: A304-753A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3L-human
EIF3L	Product_ID: A304-754A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3L-human

Experiment Status

	BGKcLV38-55	BGKcLV38-55	BGKcLV38-56	BGKcLV38-56
Sample_ID	BGKcLV38-55	BGKcLV38-55	BGKcLV38-56	BGKcLV38-56
Sample Name
Sample Name	EIF3L-BGKcLV38-55		EIF3L-BGKcLV38-56
RBP	EIF3L	EIF3L	EIF3L	EIF3L
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2023-01-03	2023-04-14	2023-01-03
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	11050	11076	11051	11077

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-55	BGKcLV38-56
Sample #	85	86
Sample Name	EIF3L-BGKcLV38-55	EIF3L-BGKcLV38-56
Sample_Name_Alias
Index Well Position	C12	D12
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	298	300
Peak_Molarity	60.50	65.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/C12.png	DNA_Library_set54-56/set2/D12.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set54-56/set1/E11.png	RNA_Library_set54-56/set1/F11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-55	BGKcLV38-56
RBP	EIF3L	EIF3L
Batch_ID	BGKcLV38	BGKcLV38
WB_result	77.200	79.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3456	3457

Sequencing Information

	BGKcLV38-55	BGKcLV38-56
Sample_ID	BGKcLV38-55	BGKcLV38-56
Sample Name	EIF3L-BGKcLV38-55	EIF3L-BGKcLV38-56
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	80,989,919	62,312,977
total_aligned_reads	76,424,541	59,127,341
unique_aligned_reads	71,042,424	54,992,521
percent_uniqueAligned	0.87718	0.88252
correlation_replicates	0.997081	0.997081
spikein_reads	11,764	7,936
percent_spikeins	0.00015	0.00013
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2327	2328

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
EIF3L-BGKcLV38-55_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2327	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	8332
EIF3L-BGKcLV38-55_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2327	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	8370
EIF3L-BGKcLV38-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2327					GRCh38	V40	EIF3L-BGKcLV38-55_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGKcLV38-55_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16984
EIF3L-BGKcLV38-55_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	2327					GRCh38	V40	EIF3L-BGKcLV38-55/Aligned.sortedByCoord.out.bam		ENCORE2	17022
EIF3L-BGKcLV38-55_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	2327					GRCh38	V40	EIF3L-BGKcLV38-55/Aligned.sortedByCoord.out.bam		ENCORE2	17060
EIF3L-BGKcLV38-55_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	2327					GRCh38	V40	EIF3L-BGKcLV38-55/Aligned.sortedByCoord.out.bam		ENCORE2	17098
EIF3L-BGKcLV38-55_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	2327					GRCh38	V40	EIF3L-BGKcLV38-55/Aligned.sortedByCoord.out.bam		ENCORE2	17136
EIF3L-BGKcLV38-55_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2327					GRCh38	V40	EIF3L-BGKcLV38-55_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGKcLV38-55_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17174
EIF3L-BGKcLV38-56_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2328	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	8333
EIF3L-BGKcLV38-56_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2328	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	8371
EIF3L-BGKcLV38-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2328					GRCh38	V40	EIF3L-BGKcLV38-56_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGKcLV38-56_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16985
EIF3L-BGKcLV38-56_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	2328					GRCh38	V40	EIF3L-BGKcLV38-56/Aligned.sortedByCoord.out.bam		ENCORE2	17023
EIF3L-BGKcLV38-56_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	2328					GRCh38	V40	EIF3L-BGKcLV38-56/Aligned.sortedByCoord.out.bam		ENCORE2	17061
EIF3L-BGKcLV38-56_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	2328					GRCh38	V40	EIF3L-BGKcLV38-56/Aligned.sortedByCoord.out.bam		ENCORE2	17099
EIF3L-BGKcLV38-56_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	2328					GRCh38	V40	EIF3L-BGKcLV38-56/Aligned.sortedByCoord.out.bam		ENCORE2	17137
EIF3L-BGKcLV38-56_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2328					GRCh38	V40	EIF3L-BGKcLV38-56_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGKcLV38-56_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17175