RBBP6 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-19	BGRSLV06-20
idx	0	0
TRCN#_or_BGC#	TRCN0000034214	TRCN0000034214
shRNA_or_gRNA_sequence	CCGGCGACTTAAAGAAGCAGATTATCTCGAGATAATCTGCTTCTTTAAGTCGTTTTTG	CCGGCGACTTAAAGAAGCAGATTATCTCGAGATAATCTGCTTCTTTAAGTCGTTTTTG
PAM
Name	RBBP6	RBBP6
Sample_ID	BGRSLV06-19	BGRSLV06-20
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	RBBP6	RBBP6
qPCR_result	64.5	63.1
Ave_qPCR	63.8
RT-qPCR_primer-F	tggaggtgttaaatctacaagcaa
RT-qPCR_primer-R	gtagttgccatcgctggttc
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	8546	8547

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-19	BGRSLV06-20
Sample_ID	BGRSLV06-19	BGRSLV06-20
Sample Name
Sample Name	RBBP6-BGRSLV06-19	RBBP6-BGRSLV06-20
RBP	RBBP6	RBBP6
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	11694	11695

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-19	BGRSLV06-20
Sample #	77	78
Sample Name	RBBP6-BGRSLV06-19	RBBP6-BGRSLV06-20
Sample_Name_Alias
Index Well Position	E10	F10
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	288	293
Peak_Molarity	94.70	80.60
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A11.png	DNA_Library_set60-62/set1/B11.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set60-62/set1/E10.png	RNA_Library_set60-62/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-19	BGRSLV06-20
RBP	RBBP6	RBBP6
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	3664	3665

Sequencing Information

	BGRSLV06-19	BGRSLV06-20
Sample_ID	BGRSLV06-19	BGRSLV06-20
Sample Name	RBBP6-BGRSLV06-19	RBBP6-BGRSLV06-20
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	29,587,156	33,551,508
total_aligned_reads	25,312,438	28,433,842
unique_aligned_reads	23,776,540	26,699,353
percent_uniqueAligned	0.80361	0.79577
correlation_replicates	0.998465	0.998465
spikein_reads	45,496	58,732
percent_spikeins	0.00154	0.00175
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2535	2536

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
RBBP6-BGRSLV06-19_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2535	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	8590
RBBP6-BGRSLV06-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2535					GRCh38	V40	RBBP6-BGRSLV06-19_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBBP6-BGRSLV06-19_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10455
RBBP6-BGRSLV06-19_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	2535					GRCh38	V40	RBBP6-BGRSLV06-19/Aligned.sortedByCoord.out.bam		ENCORE2	10507
RBBP6-BGRSLV06-19_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	2535					GRCh38	V40	RBBP6-BGRSLV06-19/Aligned.sortedByCoord.out.bam		ENCORE2	10559
RBBP6-BGRSLV06-19_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	2535					GRCh38	V40	RBBP6-BGRSLV06-19/Aligned.sortedByCoord.out.bam		ENCORE2	10611
RBBP6-BGRSLV06-19_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	2535					GRCh38	V40	RBBP6-BGRSLV06-19/Aligned.sortedByCoord.out.bam		ENCORE2	10663
RBBP6-BGRSLV06-19_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2535					GRCh38	V40	RBBP6-BGRSLV06-19_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBBP6-BGRSLV06-19_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10715
RBBP6-BGRSLV06-19_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2535	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	28857
RBBP6-BGRSLV06-20_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2536	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	8591
RBBP6-BGRSLV06-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2536					GRCh38	V40	RBBP6-BGRSLV06-20_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBBP6-BGRSLV06-20_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10456
RBBP6-BGRSLV06-20_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	2536					GRCh38	V40	RBBP6-BGRSLV06-20/Aligned.sortedByCoord.out.bam		ENCORE2	10508
RBBP6-BGRSLV06-20_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	2536					GRCh38	V40	RBBP6-BGRSLV06-20/Aligned.sortedByCoord.out.bam		ENCORE2	10560
RBBP6-BGRSLV06-20_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	2536					GRCh38	V40	RBBP6-BGRSLV06-20/Aligned.sortedByCoord.out.bam		ENCORE2	10612
RBBP6-BGRSLV06-20_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	2536					GRCh38	V40	RBBP6-BGRSLV06-20/Aligned.sortedByCoord.out.bam		ENCORE2	10664
RBBP6-BGRSLV06-20_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2536					GRCh38	V40	RBBP6-BGRSLV06-20_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBBP6-BGRSLV06-20_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10716
RBBP6-BGRSLV06-20_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2536	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	28858