NUFIP2 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-71	BGHcLV49-72
idx	1772	1773
TRCN#_or_BGC#	BGC#0001036	BGC#0001036
shRNA_or_gRNA_sequence	GTCCCAGCCGCTTTCAATGG	GTCCCAGCCGCTTTCAATGG
PAM	AGG	AGG
Name	NUFIP2_88	NUFIP2_88
Sample_ID	BGHcLV49-71	BGHcLV49-72
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	NUFIP2	NUFIP2
qPCR_result	22.8	21.9
Ave_qPCR	22.3
RT-qPCR_primer-F	AGCACCAGGAAACGCCGAAGAA
RT-qPCR_primer-R	CTTGCTGGTTGCCATTGAGGAC
protein_conc	4430	5335
WB_result	80.5	83.8
Ave_WB
WB_DONE_date	7/3/25
MW	76kd
IP
antibody_Cat#	A301-600A	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	9961	9962

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV49-71	BGHcLV49-72
Sample_ID	BGHcLV49-71	BGHcLV49-72
Sample Name
Sample Name	NUFIP2-BGHcLV49-71	NUFIP2-BGHcLV49-72
RBP	NUFIP2	NUFIP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14356	14357

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-71	BGHcLV49-72
Sample #	53	54
Sample Name	NUFIP2-BGHcLV49-71	NUFIP2-BGHcLV49-72
Sample_Name_Alias
Index Well Position	G07	H07
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	268	261
Peak_Molarity	82.50	59.60
libSampleQC_DNA_Well	DNA_Library_set81/set1/G4.png	DNA_Library_set81/set1/H4.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set81/set1/G7.png	RNA_Library_set81/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-71	BGHcLV49-72
RBP	NUFIP2	NUFIP2
Batch_ID	BGHcLV49	BGHcLV49
WB_result	80.500	83.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4798	4799

Sequencing Information

	BGHcLV49-71	BGHcLV49-72
Sample_ID	BGHcLV49-71	BGHcLV49-72
Sample Name	NUFIP2-BGHcLV49-71	NUFIP2-BGHcLV49-72
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	39,724,639	28,729,706
total_aligned_reads	33,910,891	25,045,561
unique_aligned_reads	31,895,478	23,600,996
percent_uniqueAligned	0.80291	0.82148
correlation_replicates	0.998432	0.998432
spikein_reads	150,328	76,998
percent_spikeins	0.00378	0.00268
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3525	3526

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
NUFIP2-BGHcLV49-71_S127_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3525	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	33198
NUFIP2-BGHcLV49-71_S127_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3525	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	33244
NUFIP2-BGHcLV49-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_S127_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP2-BGHcLV49-71_S127_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33290
NUFIP2-BGHcLV49-71_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	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_Aligned.sortedByCoord.out.bam		ENCORE2	33336
NUFIP2-BGHcLV49-71_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	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_Aligned.sortedByCoord.out.bam		ENCORE2	33382
NUFIP2-BGHcLV49-71_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	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_Aligned.sortedByCoord.out.bam		ENCORE2	33428
NUFIP2-BGHcLV49-71_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	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_Aligned.sortedByCoord.out.bam		ENCORE2	33474
NUFIP2-BGHcLV49-71_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3525					GRCh38	V40	NUFIP2-BGHcLV49-71_S127_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP2-BGHcLV49-71_S127_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33520
NUFIP2-BGHcLV49-72_S129_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3526	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	33199
NUFIP2-BGHcLV49-72_S129_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3526	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	33245
NUFIP2-BGHcLV49-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_S129_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP2-BGHcLV49-72_S129_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33291
NUFIP2-BGHcLV49-72_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	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_Aligned.sortedByCoord.out.bam		ENCORE2	33337
NUFIP2-BGHcLV49-72_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	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_Aligned.sortedByCoord.out.bam		ENCORE2	33383
NUFIP2-BGHcLV49-72_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	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_Aligned.sortedByCoord.out.bam		ENCORE2	33429
NUFIP2-BGHcLV49-72_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	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_Aligned.sortedByCoord.out.bam		ENCORE2	33475
NUFIP2-BGHcLV49-72_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3526					GRCh38	V40	NUFIP2-BGHcLV49-72_S129_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP2-BGHcLV49-72_S129_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33521