RYBP RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-35	BGRSLV06-36
idx	0	0
TRCN#_or_BGC#	TRCN0000007945	TRCN0000007945
shRNA_or_gRNA_sequence	CCGGCACCGTCATTATCACAGACTTCTCGAGAAGTCTGTGATAATGACGGTGTTTTT	CCGGCACCGTCATTATCACAGACTTCTCGAGAAGTCTGTGATAATGACGGTGTTTTT
PAM
Name	RYBP	RYBP
Sample_ID	BGRSLV06-35	BGRSLV06-36
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	RYBP	RYBP
qPCR_result	95.4	89.6
Ave_qPCR	92.5
RT-qPCR_primer-F	GGATTGTAGCGTCTGCACCT
RT-qPCR_primer-R	ACCAGCTGAGAATTGATCCG
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	8562	8563

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-35	BGRSLV06-36
Sample_ID	BGRSLV06-35	BGRSLV06-36
Sample Name
Sample Name	RYBP-BGRSLV06-35	RYBP-BGRSLV06-36
RBP	RYBP	RYBP
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	11702	11703

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-35	BGRSLV06-36
Sample #	85	86
Sample Name	RYBP-BGRSLV06-35	RYBP-BGRSLV06-36
Sample_Name_Alias
Index Well Position	E11	F11
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	295	289
Peak_Molarity	90.80	91.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A12.png	DNA_Library_set60-62/set1/B12.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set60-62/set1/E11.png	RNA_Library_set60-62/set1/F11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-35	BGRSLV06-36
RBP	RYBP	RYBP
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	3672	3673

Sequencing Information

	BGRSLV06-35	BGRSLV06-36
Sample_ID	BGRSLV06-35	BGRSLV06-36
Sample Name	RYBP-BGRSLV06-35	RYBP-BGRSLV06-36
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	29,807,058	45,539,752
total_aligned_reads	26,350,564	36,508,007
unique_aligned_reads	24,837,026	34,347,226
percent_uniqueAligned	0.83326	0.75423
correlation_replicates	0.985372	0.985372
spikein_reads	65,248	74,438
percent_spikeins	0.00219	0.00163
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2543	2544

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
RYBP-BGRSLV06-35_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2543	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	8600
RYBP-BGRSLV06-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2543					GRCh38	V40	RYBP-BGRSLV06-35_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGRSLV06-35_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10465
RYBP-BGRSLV06-35_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	2543					GRCh38	V40	RYBP-BGRSLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	10517
RYBP-BGRSLV06-35_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	2543					GRCh38	V40	RYBP-BGRSLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	10569
RYBP-BGRSLV06-35_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	2543					GRCh38	V40	RYBP-BGRSLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	10621
RYBP-BGRSLV06-35_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	2543					GRCh38	V40	RYBP-BGRSLV06-35/Aligned.sortedByCoord.out.bam		ENCORE2	10673
RYBP-BGRSLV06-35_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2543					GRCh38	V40	RYBP-BGRSLV06-35_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGRSLV06-35_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10725
RYBP-BGRSLV06-35_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2543	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	28867
RYBP-BGRSLV06-36_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2544	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	8601
RYBP-BGRSLV06-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2544					GRCh38	V40	RYBP-BGRSLV06-36_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGRSLV06-36_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10466
RYBP-BGRSLV06-36_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	2544					GRCh38	V40	RYBP-BGRSLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	10518
RYBP-BGRSLV06-36_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	2544					GRCh38	V40	RYBP-BGRSLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	10570
RYBP-BGRSLV06-36_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	2544					GRCh38	V40	RYBP-BGRSLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	10622
RYBP-BGRSLV06-36_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	2544					GRCh38	V40	RYBP-BGRSLV06-36/Aligned.sortedByCoord.out.bam		ENCORE2	10674
RYBP-BGRSLV06-36_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2544					GRCh38	V40	RYBP-BGRSLV06-36_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGRSLV06-36_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10726
RYBP-BGRSLV06-36_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2544	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	28868