EFL1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-49	BGHcLV49-50
idx	1748	1749
TRCN#_or_BGC#	BGC#0000953	BGC#0000953
shRNA_or_gRNA_sequence	TTAACAATAGACTTCAGCTA	TTAACAATAGACTTCAGCTA
PAM	TGG	TGG
Name	EFTUD1_71	EFTUD1_71
Sample_ID	BGHcLV49-49	BGHcLV49-50
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	EFL1	EFL1
qPCR_result	63.6	63.2
Ave_qPCR	63.4
RT-qPCR_primer-F	cccatatcccatgctgttct
RT-qPCR_primer-R	tgcttgagtttctggtggaa
protein_conc	4899	3845
WB_result	82.6	92.9
Ave_WB
WB_DONE_date	6/23/25
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	9937	9938

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

	BGHcLV49-49	BGHcLV49-50
Sample_ID	BGHcLV49-49	BGHcLV49-50
Sample Name
Sample Name	EFL1-BGHcLV49-49	EFL1-BGHcLV49-50
RBP	EFL1	EFL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14346	14347

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-49	BGHcLV49-50
Sample #	43	44
Sample Name	EFL1-BGHcLV49-49	EFL1-BGHcLV49-50
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	277	266
Peak_Molarity	90.00	75.70
libSampleQC_DNA_Well	DNA_Library_set81/set1/E3.png	DNA_Library_set81/set1/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/E6.png	RNA_Library_set81/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-49	BGHcLV49-50
RBP	EFL1	EFL1
Batch_ID	BGHcLV49	BGHcLV49
WB_result	82.600	92.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4788	4789

Sequencing Information

	BGHcLV49-49	BGHcLV49-50
Sample_ID	BGHcLV49-49	BGHcLV49-50
Sample Name	EFL1-BGHcLV49-49	EFL1-BGHcLV49-50
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	28,322,609	22,425,838
total_aligned_reads	24,656,199	17,895,981
unique_aligned_reads	23,243,801	16,819,930
percent_uniqueAligned	0.82068	0.75002
correlation_replicates	0.997176	0.997176
spikein_reads	55,514	44,574
percent_spikeins	0.00196	0.00199
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3515	3516

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-BGHcLV49-49_S140_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3515	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33184
EFL1-BGHcLV49-49_S140_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3515	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33230
EFL1-BGHcLV49-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_S140_L008_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGHcLV49-49_S140_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33276
EFL1-BGHcLV49-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_Aligned.sortedByCoord.out.bam		ENCORE2	33322
EFL1-BGHcLV49-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_Aligned.sortedByCoord.out.bam		ENCORE2	33368
EFL1-BGHcLV49-49_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_Aligned.sortedByCoord.out.bam		ENCORE2	33414
EFL1-BGHcLV49-49_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_Aligned.sortedByCoord.out.bam		ENCORE2	33460
EFL1-BGHcLV49-49_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3515					GRCh38	V40	EFL1-BGHcLV49-49_S140_L008_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGHcLV49-49_S140_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33506
EFL1-BGHcLV49-50_S145_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3516	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33185
EFL1-BGHcLV49-50_S145_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3516	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33231
EFL1-BGHcLV49-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_S145_L008_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGHcLV49-50_S145_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33277
EFL1-BGHcLV49-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_Aligned.sortedByCoord.out.bam		ENCORE2	33323
EFL1-BGHcLV49-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_Aligned.sortedByCoord.out.bam		ENCORE2	33369
EFL1-BGHcLV49-50_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_Aligned.sortedByCoord.out.bam		ENCORE2	33415
EFL1-BGHcLV49-50_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_Aligned.sortedByCoord.out.bam		ENCORE2	33461
EFL1-BGHcLV49-50_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3516					GRCh38	V40	EFL1-BGHcLV49-50_S145_L008_R1_001.filtered.trimmed.paired.fastq.gz,EFL1-BGHcLV49-50_S145_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33507