TUT1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV06-47	BGRSLV06-48
idx	0	0
TRCN#_or_BGC#	TRCN0000150242	TRCN0000150242
shRNA_or_gRNA_sequence	CCGGCTCAAAGTAGATGGACAGAAACTCGAGTTTCTGTCCATCTACTTTGAGTTTTTTG	CCGGCTCAAAGTAGATGGACAGAAACTCGAGTTTCTGTCCATCTACTTTGAGTTTTTTG
PAM
Name	TUT1	TUT1
Sample_ID	BGRSLV06-47	BGRSLV06-48
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	TUT1	TUT1
qPCR_result	82.6	82.8
Ave_qPCR	82.7
RT-qPCR_primer-F	cttcaggtctccacggtgat
RT-qPCR_primer-R	tcaggaaacgggagttatgc
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	10622	10623

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-47	BGRSLV06-48
Sample_ID	BGRSLV06-47	BGRSLV06-48
Sample Name
Sample Name	TUT1-BGRSLV06-47	TUT1-BGRSLV06-48
RBP	TUT1	TUT1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	11708	11709

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-47	BGRSLV06-48
Sample #	91	92
Sample Name	TUT1-BGRSLV06-47	TUT1-BGRSLV06-48
Sample_Name_Alias
Index Well Position	C12	D12
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	301	301
Peak_Molarity	110.00	89.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G12.png	DNA_Library_set60-62/set1/H12.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set60-62/set1/C12.png	RNA_Library_set60-62/set1/D12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-47	BGRSLV06-48
RBP	TUT1	TUT1
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	3678	3679

Sequencing Information

	BGRSLV06-47	BGRSLV06-48
Sample_ID	BGRSLV06-47	BGRSLV06-48
Sample Name	TUT1-BGRSLV06-47	TUT1-BGRSLV06-48
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	45,397,203	25,172,798
total_aligned_reads	37,811,850	21,350,637
unique_aligned_reads	35,648,356	20,122,400
percent_uniqueAligned	0.78525	0.79937
correlation_replicates	0.993702	0.993702
spikein_reads	36,420	23,204
percent_spikeins	0.00080	0.00092
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2549	2550

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
TUT1-BGRSLV06-47_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2549	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	8610
TUT1-BGRSLV06-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2549					GRCh38	V40	TUT1-BGRSLV06-47_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,TUT1-BGRSLV06-47_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10475
TUT1-BGRSLV06-47_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	2549					GRCh38	V40	TUT1-BGRSLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	10527
TUT1-BGRSLV06-47_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	2549					GRCh38	V40	TUT1-BGRSLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	10579
TUT1-BGRSLV06-47_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	2549					GRCh38	V40	TUT1-BGRSLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	10631
TUT1-BGRSLV06-47_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	2549					GRCh38	V40	TUT1-BGRSLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	10683
TUT1-BGRSLV06-47_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2549					GRCh38	V40	TUT1-BGRSLV06-47_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,TUT1-BGRSLV06-47_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10735
TUT1-BGRSLV06-47_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2549	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	28877
TUT1-BGRSLV06-48_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2550	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	8611
TUT1-BGRSLV06-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2550					GRCh38	V40	TUT1-BGRSLV06-48_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,TUT1-BGRSLV06-48_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10476
TUT1-BGRSLV06-48_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	2550					GRCh38	V40	TUT1-BGRSLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	10528
TUT1-BGRSLV06-48_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	2550					GRCh38	V40	TUT1-BGRSLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	10580
TUT1-BGRSLV06-48_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	2550					GRCh38	V40	TUT1-BGRSLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	10632
TUT1-BGRSLV06-48_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	2550					GRCh38	V40	TUT1-BGRSLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	10684
TUT1-BGRSLV06-48_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2550					GRCh38	V40	TUT1-BGRSLV06-48_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,TUT1-BGRSLV06-48_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10736
TUT1-BGRSLV06-48_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2550	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	28878