NXF1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-47	BGHcLV47-48
idx	1651	1652
TRCN#_or_BGC#	BGC#0000196	BGC#0000196
shRNA_or_gRNA_sequence	GTAGGTGGACTGGTCTCGGA	GTAGGTGGACTGGTCTCGGA
PAM	AGG	AGG
Name	NXF1-90F	NXF1-90F
Sample_ID	BGHcLV47-47	BGHcLV47-48
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	NXF1	NXF1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gctgtacaggctggatgaca
RT-qPCR_primer-R	aattcccgctcagacttcaa
protein_conc	2080	2294
WB_result	81.9	84.9
Ave_WB
WB_DONE_date	2/5/25
MW	70kd
IP
antibody_Cat#	A303-914A	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	9840	9841

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NXF1	Product_ID: A303-914A Lot_ID: 1 Source: Bethyl Labs Target Name: NXF1-human

Experiment Status

	BGHcLV47-47	BGHcLV47-48
Sample_ID	BGHcLV47-47	BGHcLV47-48
Sample Name
Sample Name	NXF1-BGHcLV47-47	NXF1-BGHcLV47-48
RBP	NXF1	NXF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14168	14169

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-47	BGHcLV47-48
Sample #	21	22
Sample Name	NXF1-BGHcLV47-47	NXF1-BGHcLV47-48
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	270	260
Peak_Molarity	52.60	49.00
libSampleQC_DNA_Well	DNA_Library_set78/set1/E8.png	DNA_Library_set78/set1/F8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set78/set1/E3.png	RNA_Library_set78/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-47	BGHcLV47-48
RBP	NXF1	NXF1
Batch_ID	BGHcLV47	BGHcLV47
WB_result	81.900	84.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4732	4733

Sequencing Information

	BGHcLV47-47	BGHcLV47-48
Sample_ID	BGHcLV47-47	BGHcLV47-48
Sample Name	NXF1-BGHcLV47-47	NXF1-BGHcLV47-48
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	13,109,367	14,643,332
total_aligned_reads	11,281,988	12,029,798
unique_aligned_reads	10,631,444	11,336,054
percent_uniqueAligned	0.81098	0.77414
correlation_replicates	0.995956	0.995956
spikein_reads	19,866	20,386
percent_spikeins	0.00152	0.00139
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3435	3436

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
NXF1-BGHcLV47-47_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3435	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32568
NXF1-BGHcLV47-47_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3435	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32602
NXF1-BGHcLV47-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGHcLV47-47_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32636
NXF1-BGHcLV47-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_Aligned.sortedByCoord.out.bam		ENCORE2	32670
NXF1-BGHcLV47-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_Aligned.sortedByCoord.out.bam		ENCORE2	32704
NXF1-BGHcLV47-47_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_Aligned.sortedByCoord.out.bam		ENCORE2	32738
NXF1-BGHcLV47-47_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_Aligned.sortedByCoord.out.bam		ENCORE2	32772
NXF1-BGHcLV47-47_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3435					GRCh38	V40	NXF1-BGHcLV47-47_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGHcLV47-47_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32806
NXF1-BGHcLV47-48_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3436	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32569
NXF1-BGHcLV47-48_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3436	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32603
NXF1-BGHcLV47-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGHcLV47-48_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32637
NXF1-BGHcLV47-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_Aligned.sortedByCoord.out.bam		ENCORE2	32671
NXF1-BGHcLV47-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_Aligned.sortedByCoord.out.bam		ENCORE2	32705
NXF1-BGHcLV47-48_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_Aligned.sortedByCoord.out.bam		ENCORE2	32739
NXF1-BGHcLV47-48_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_Aligned.sortedByCoord.out.bam		ENCORE2	32773
NXF1-BGHcLV47-48_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3436					GRCh38	V40	NXF1-BGHcLV47-48_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,NXF1-BGHcLV47-48_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32807