NUFIP1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-27	BGRSLV04-28
idx	0	0
TRCN#_or_BGC#	TRCN0000336992	TRCN0000336992
shRNA_or_gRNA_sequence	CCGGGATGTCCAGACATTCACAAATCTCGAGATTTGTGAATGTCTGGACATCTTTTTG	CCGGGATGTCCAGACATTCACAAATCTCGAGATTTGTGAATGTCTGGACATCTTTTTG
PAM
Name	NUFIP1	NUFIP1
Sample_ID	BGRSLV04-27	BGRSLV04-28
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	NUFIP1	NUFIP1
qPCR_result	63.8	71.0
Ave_qPCR	67.4
RT-qPCR_primer-F	acccaaggaagtgacaccag
RT-qPCR_primer-R	gaacctggttttctgccaaa
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	8407	8408

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-27	BGRSLV04-28
Sample_ID	BGRSLV04-27	BGRSLV04-28
Sample Name
Sample Name	NUFIP1-BGRSLV04-27	NUFIP1-BGRSLV04-28
RBP	NUFIP1	NUFIP1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11448	11449

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-27	BGRSLV04-28
Sample #	13	14
Sample Name	NUFIP1-BGRSLV04-27	NUFIP1-BGRSLV04-28
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	289	292
Peak_Molarity	52.40	60.10
libSampleQC_DNA_Well	DNA_Library_set59/set1/E8.png	DNA_Library_set59/set1/F8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set59/set1/E3.png	RNA_Library_set59/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-27	BGRSLV04-28
RBP	NUFIP1	NUFIP1
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3562	3563

Sequencing Information

	BGRSLV04-27	BGRSLV04-28
Sample_ID	BGRSLV04-27	BGRSLV04-28
Sample Name	NUFIP1-BGRSLV04-27	NUFIP1-BGRSLV04-28
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	56,861,765	47,816,750
total_aligned_reads	47,412,898	41,216,470
unique_aligned_reads	43,660,877	38,184,078
percent_uniqueAligned	0.76784	0.79855
correlation_replicates	0.984780	0.984780
spikein_reads	233,180	188,098
percent_spikeins	0.00410	0.00393
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2433	2434

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
NUFIP1-BGRSLV04-27_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2433	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8062
NUFIP1-BGRSLV04-27_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2433	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8100
NUFIP1-BGRSLV04-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP1-BGRSLV04-27_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11031
NUFIP1-BGRSLV04-27_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27/Aligned.sortedByCoord.out.bam		ENCORE2	11069
NUFIP1-BGRSLV04-27_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27/Aligned.sortedByCoord.out.bam		ENCORE2	11107
NUFIP1-BGRSLV04-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27/Aligned.sortedByCoord.out.bam		ENCORE2	11145
NUFIP1-BGRSLV04-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27/Aligned.sortedByCoord.out.bam		ENCORE2	11183
NUFIP1-BGRSLV04-27_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2433					GRCh38	V40	NUFIP1-BGRSLV04-27_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP1-BGRSLV04-27_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11221
NUFIP1-BGRSLV04-28_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2434	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8063
NUFIP1-BGRSLV04-28_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2434	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8101
NUFIP1-BGRSLV04-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP1-BGRSLV04-28_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11032
NUFIP1-BGRSLV04-28_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28/Aligned.sortedByCoord.out.bam		ENCORE2	11070
NUFIP1-BGRSLV04-28_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28/Aligned.sortedByCoord.out.bam		ENCORE2	11108
NUFIP1-BGRSLV04-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28/Aligned.sortedByCoord.out.bam		ENCORE2	11146
NUFIP1-BGRSLV04-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28/Aligned.sortedByCoord.out.bam		ENCORE2	11184
NUFIP1-BGRSLV04-28_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2434					GRCh38	V40	NUFIP1-BGRSLV04-28_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUFIP1-BGRSLV04-28_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11222