RNF20 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-49	BGRSLV02-50
idx	0	0
TRCN#_or_BGC#	TRCN0000033876	TRCN0000033876
shRNA_or_gRNA_sequence	CCGGCCACTGATGATGCCTCACTATCTCGAGATAGTGAGGCATCATCAGTGGTTTTTG	CCGGCCACTGATGATGCCTCACTATCTCGAGATAGTGAGGCATCATCAGTGGTTTTTG
PAM
Name	RNF20	RNF20
Sample_ID	BGRSLV02-49	BGRSLV02-50
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	RNF20	RNF20
qPCR_result	51.3	48.6
Ave_qPCR	49.9
RT-qPCR_primer-F	GCTGGAGAAACTTCGGCAAGAC
RT-qPCR_primer-R	CAAGACGGAGAACTGTGACTGC
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	8286	8287

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-49	BGRSLV02-50
Sample_ID	BGRSLV02-49	BGRSLV02-50
Sample Name
Sample Name	RNF20-BGRSLV02-49	RNF20-BGRSLV02-50
RBP	RNF20	RNF20
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	11334	11335

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-49	BGRSLV02-50
Sample #	37	38
Sample Name	RNF20-BGRSLV02-49	RNF20-BGRSLV02-50
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	305	305
Peak_Molarity	28.50	62.60
libSampleQC_DNA_Well	DNA_Library_set57/set1/E11.png	DNA_Library_set57/set1/F11.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set57/set1/E5.png	RNA_Library_set57/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-49	BGRSLV02-50
RBP	RNF20	RNF20
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3498	3499

Sequencing Information

	BGRSLV02-49	BGRSLV02-50
Sample_ID	BGRSLV02-49	BGRSLV02-50
Sample Name	RNF20-BGRSLV02-49	RNF20-BGRSLV02-50
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	100,497,537	38,387,139
total_aligned_reads	93,585,648	35,642,617
unique_aligned_reads	87,999,879	33,367,711
percent_uniqueAligned	0.87564	0.86924
correlation_replicates	0.997514	0.997514
spikein_reads	35,028	17,998
percent_spikeins	0.00035	0.00047
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2369	2370

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
RNF20-BGRSLV02-49_S125_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2369	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8228
RNF20-BGRSLV02-49_S125_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2369	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8274
RNF20-BGRSLV02-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49_S125_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF20-BGRSLV02-49_S125_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11517
RNF20-BGRSLV02-49_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	11563
RNF20-BGRSLV02-49_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	11609
RNF20-BGRSLV02-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	11655
RNF20-BGRSLV02-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	11701
RNF20-BGRSLV02-49_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2369					GRCh38	V40	RNF20-BGRSLV02-49_S125_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF20-BGRSLV02-49_S125_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11747
RNF20-BGRSLV02-50_S126_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2370	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8229
RNF20-BGRSLV02-50_S126_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2370	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8275
RNF20-BGRSLV02-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50_S126_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF20-BGRSLV02-50_S126_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11518
RNF20-BGRSLV02-50_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	11564
RNF20-BGRSLV02-50_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	11610
RNF20-BGRSLV02-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	11656
RNF20-BGRSLV02-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	11702
RNF20-BGRSLV02-50_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2370					GRCh38	V40	RNF20-BGRSLV02-50_S126_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF20-BGRSLV02-50_S126_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11748