EFL1 RNA-Seq in K562

General Information


RBP	EFL1
Cell_Line	K562
Method	CRISPR
Exp_Name	EFL1-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	EFL1-BGKcLV38-37
Rep2	EFL1-BGKcLV38-38
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	57.7
Rep2_qPCR	64.5
Rep1_WB	81.6
Rep2_WB	76.2
Antibody Cat#	A305-854A-M
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1032

Experiment Information (Status: Submitting)

	BGKcLV38-37	BGKcLV38-38
idx	1454	1455
TRCN#_or_BGC#	BGC#0000953	BGC#0000953
shRNA_or_gRNA_sequence	TTAACAATAGACTTCAGCTA	TTAACAATAGACTTCAGCTA
PAM	TGG	TGG
Name	EFTUD1_71	EFTUD1_71
Sample_ID	BGKcLV38-37	BGKcLV38-38
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EFL1	EFL1
qPCR_result	57.7	64.5
Ave_qPCR	61.1
RT-qPCR_primer-F	cccatatcccatgctgttct
RT-qPCR_primer-R	tgcttgagtttctggtggaa
protein_conc	3638	3551
WB_result	81.6	76.2
Ave_WB	78.9
WB_DONE_date	11/4/22
MW	125KD
IP
antibody_Cat#	A305-854A-M	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	5632	5633

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EFL1	Product_ID: A305-854A-M Lot_ID: 1 Source: Bethyl Labs Target Name: EFL1-human

Experiment Status

	BGKcLV38-37	BGKcLV38-38
Sample_ID	BGKcLV38-37	BGKcLV38-38
Sample Name
Sample Name	EFL1-BGKcLV38-37	EFL1-BGKcLV38-38
RBP	EFL1	EFL1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11038	11039

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-37	BGKcLV38-38
Sample #	73	74
Sample Name	EFL1-BGKcLV38-37	EFL1-BGKcLV38-38
Sample_Name_Alias
Index Well Position	G10	H10
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	286	294
Peak_Molarity	80.50	86.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/G10.png	DNA_Library_set54-56/set2/H10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/A10.png	RNA_Library_set54-56/set1/B10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-37	BGKcLV38-38
RBP	EFL1	EFL1
Batch_ID	BGKcLV38	BGKcLV38
WB_result	81.600	76.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3444	3445

Sequencing Information

	BGKcLV38-37	BGKcLV38-38
Sample_ID	BGKcLV38-37	BGKcLV38-38
Sample Name	EFL1-BGKcLV38-37	EFL1-BGKcLV38-38
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	76,853,017	59,277,522
total_aligned_reads	72,061,052	55,664,136
unique_aligned_reads	67,087,274	51,658,645
percent_uniqueAligned	0.87293	0.87147
correlation_replicates	0.996897	0.996897
spikein_reads	16,166	14,866
percent_spikeins	0.00021	0.00025
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2315	2316

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
EFL1-BGKcLV38-37_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2315	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	8320
EFL1-BGKcLV38-37_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2315	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	8358
EFL1-BGKcLV38-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2315					GRCh38	V40	EFL1-BGKcLV38-37_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGKcLV38-37_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16972
EFL1-BGKcLV38-37_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	2315					GRCh38	V40	EFL1-BGKcLV38-37/Aligned.sortedByCoord.out.bam		ENCORE2	17010
EFL1-BGKcLV38-37_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	2315					GRCh38	V40	EFL1-BGKcLV38-37/Aligned.sortedByCoord.out.bam		ENCORE2	17048
EFL1-BGKcLV38-37_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	2315					GRCh38	V40	EFL1-BGKcLV38-37/Aligned.sortedByCoord.out.bam		ENCORE2	17086
EFL1-BGKcLV38-37_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	2315					GRCh38	V40	EFL1-BGKcLV38-37/Aligned.sortedByCoord.out.bam		ENCORE2	17124
EFL1-BGKcLV38-37_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2315					GRCh38	V40	EFL1-BGKcLV38-37_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGKcLV38-37_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17162
EFL1-BGKcLV38-38_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2316	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	8321
EFL1-BGKcLV38-38_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2316	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	8359
EFL1-BGKcLV38-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2316					GRCh38	V40	EFL1-BGKcLV38-38_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGKcLV38-38_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16973
EFL1-BGKcLV38-38_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	2316					GRCh38	V40	EFL1-BGKcLV38-38/Aligned.sortedByCoord.out.bam		ENCORE2	17011
EFL1-BGKcLV38-38_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	2316					GRCh38	V40	EFL1-BGKcLV38-38/Aligned.sortedByCoord.out.bam		ENCORE2	17049
EFL1-BGKcLV38-38_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	2316					GRCh38	V40	EFL1-BGKcLV38-38/Aligned.sortedByCoord.out.bam		ENCORE2	17087
EFL1-BGKcLV38-38_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	2316					GRCh38	V40	EFL1-BGKcLV38-38/Aligned.sortedByCoord.out.bam		ENCORE2	17125
EFL1-BGKcLV38-38_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2316					GRCh38	V40	EFL1-BGKcLV38-38_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGKcLV38-38_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17163