RNF43 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-33	BGRSLV06-34
idx	0	0
TRCN#_or_BGC#	TRCN0000004218	TRCN0000004218
shRNA_or_gRNA_sequence	CCGGCCACCTCCAATCCACCTCACACTCGAGTGTGAGGTGGATTGGAGGTGGTTTTT	CCGGCCACCTCCAATCCACCTCACACTCGAGTGTGAGGTGGATTGGAGGTGGTTTTT
PAM
Name	RNF43	RNF43
Sample_ID	BGRSLV06-33	BGRSLV06-34
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	RNF43	RNF43
qPCR_result	76.9	71.9
Ave_qPCR	74.4
RT-qPCR_primer-F	gggtaatgacgctgagaagc
RT-qPCR_primer-R	gcccaccactgtcattagga
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	8560	8561

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-33	BGRSLV06-34
Sample_ID	BGRSLV06-33	BGRSLV06-34
Sample Name
Sample Name	RNF43-BGRSLV06-33	RNF43-BGRSLV06-34
RBP	RNF43	RNF43
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	11700	11701

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-33	BGRSLV06-34
Sample #	83	84
Sample Name	RNF43-BGRSLV06-33	RNF43-BGRSLV06-34
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	285	273
Peak_Molarity	76.70	74.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G11.png	DNA_Library_set60-62/set1/H11.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/C11.png	RNA_Library_set60-62/set1/D11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-33	BGRSLV06-34
RBP	RNF43	RNF43
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3670	3671

Sequencing Information

	BGRSLV06-33	BGRSLV06-34
Sample_ID	BGRSLV06-33	BGRSLV06-34
Sample Name	RNF43-BGRSLV06-33	RNF43-BGRSLV06-34
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	29,623,715	39,108,962
total_aligned_reads	24,793,180	33,405,441
unique_aligned_reads	23,311,770	31,429,864
percent_uniqueAligned	0.78693	0.80365
correlation_replicates	0.988122	0.988122
spikein_reads	18,504	38,884
percent_spikeins	0.00062	0.00099
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2541	2542

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
RNF43-BGRSLV06-33_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2541	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8598
RNF43-BGRSLV06-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF43-BGRSLV06-33_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10463
RNF43-BGRSLV06-33_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33/Aligned.sortedByCoord.out.bam		ENCORE2	10515
RNF43-BGRSLV06-33_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33/Aligned.sortedByCoord.out.bam		ENCORE2	10567
RNF43-BGRSLV06-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33/Aligned.sortedByCoord.out.bam		ENCORE2	10619
RNF43-BGRSLV06-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33/Aligned.sortedByCoord.out.bam		ENCORE2	10671
RNF43-BGRSLV06-33_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2541					GRCh38	V40	RNF43-BGRSLV06-33_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF43-BGRSLV06-33_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10723
RNF43-BGRSLV06-33_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2541	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28865
RNF43-BGRSLV06-34_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2542	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8599
RNF43-BGRSLV06-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF43-BGRSLV06-34_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10464
RNF43-BGRSLV06-34_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34/Aligned.sortedByCoord.out.bam		ENCORE2	10516
RNF43-BGRSLV06-34_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34/Aligned.sortedByCoord.out.bam		ENCORE2	10568
RNF43-BGRSLV06-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34/Aligned.sortedByCoord.out.bam		ENCORE2	10620
RNF43-BGRSLV06-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34/Aligned.sortedByCoord.out.bam		ENCORE2	10672
RNF43-BGRSLV06-34_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2542					GRCh38	V40	RNF43-BGRSLV06-34_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF43-BGRSLV06-34_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10724
RNF43-BGRSLV06-34_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2542	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28866