TEX13A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-91dox	BGRSDLV04-92dox
idx	0	0
TRCN#_or_BGC#	TRCN0000135125	TRCN0000135125
shRNA_or_gRNA_sequence	CCGGCCCGAGTTCTATCTTGAGAATCTCGAGATTCTCAAGATAGAACTCGGGTTTTTTG	CCGGCCCGAGTTCTATCTTGAGAATCTCGAGATTCTCAAGATAGAACTCGGGTTTTTTG
PAM
Name	TEX13A	TEX13A
Sample_ID	BGRSDLV04-91dox	BGRSDLV04-92dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	TEX13A	TEX13A
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9455	9456

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-91dox	BGRSDLV04-92dox
Sample_ID	BGRSDLV04-91dox	BGRSDLV04-92dox
Sample Name
Sample Name	TEX13A-BGRSDLV04-91dox	TEX13A-BGRSDLV04-92dox
RBP	TEX13A	TEX13A
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12692	12693

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-91dox	BGRSDLV04-92dox
Sample #	47	48
Sample Name	TEX13A-BGRSDLV04-91dox	TEX13A-BGRSDLV04-92dox
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	296	296
Peak_Molarity	50.20	62.40
libSampleQC_DNA_Well	DNA_Library_set68/set1/G6.png	DNA_Library_set68/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G6.png	RNA_Library_set68/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-91dox	BGRSDLV04-92dox
RBP	TEX13A	TEX13A
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4120	4121

Sequencing Information

	BGRSDLV04-91dox	BGRSDLV04-92dox
Sample_ID	BGRSDLV04-91dox	BGRSDLV04-92dox
Sample Name	TEX13A-BGRSDLV04-91dox	TEX13A-BGRSDLV04-92dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	38,255,274	30,545,182
total_aligned_reads	34,155,921	27,016,635
unique_aligned_reads	32,076,848	25,306,492
percent_uniqueAligned	0.83849	0.82849
correlation_replicates	0.996037	0.996037
spikein_reads	5,112	6,302
percent_spikeins	0.00013	0.00021
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2883	2884

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
TEX13A-BGRSDLV04-91dox_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2883	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27655
TEX13A-BGRSDLV04-91dox_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2883	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27719
TEX13A-BGRSDLV04-91dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-91dox_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27783
TEX13A-BGRSDLV04-91dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	27847
TEX13A-BGRSDLV04-91dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	27911
TEX13A-BGRSDLV04-91dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	27975
TEX13A-BGRSDLV04-91dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	28039
TEX13A-BGRSDLV04-91dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2883					GRCh38	V40	TEX13A-BGRSDLV04-91dox_S47_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-91dox_S47_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28103
TEX13A-BGRSDLV04-92dox_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2884	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27656
TEX13A-BGRSDLV04-92dox_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2884	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27720
TEX13A-BGRSDLV04-92dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-92dox_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27784
TEX13A-BGRSDLV04-92dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	27848
TEX13A-BGRSDLV04-92dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	27912
TEX13A-BGRSDLV04-92dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	27976
TEX13A-BGRSDLV04-92dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	28040
TEX13A-BGRSDLV04-92dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2884					GRCh38	V40	TEX13A-BGRSDLV04-92dox_S48_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-92dox_S48_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28104