LITAF RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-13	BGRSLV07-14
idx	0	0
TRCN#_or_BGC#	TRCN0000013459	TRCN0000013459
shRNA_or_gRNA_sequence	CCGGGCATGAATCCTCCTTCGTATTCTCGAGAATACGAAGGAGGATTCATGCTTTTT	CCGGGCATGAATCCTCCTTCGTATTCTCGAGAATACGAAGGAGGATTCATGCTTTTT
PAM
Name	LITAF	LITAF
Sample_ID	BGRSLV07-13	BGRSLV07-14
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	LITAF	LITAF
qPCR_result	67.1	67.4
Ave_qPCR	67.3
RT-qPCR_primer-F	ccatccccaataacaatcca
RT-qPCR_primer-R	gttgcaggaaggacaacaca
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	8595	8596

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-13	BGRSLV07-14
Sample_ID	BGRSLV07-13	BGRSLV07-14
Sample Name
Sample Name	LITAF-BGRSLV07-13	LITAF-BGRSLV07-14
RBP	LITAF	LITAF
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	11840	11841

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-13	BGRSLV07-14
Sample #	21	22
Sample Name	LITAF-BGRSLV07-13	LITAF-BGRSLV07-14
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	294	294
Peak_Molarity	77.60	83.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E3.png	DNA_Library_set60-62/set4/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/E3.png	RNA_Library_set60-62/set2/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-13	BGRSLV07-14
RBP	LITAF	LITAF
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3704	3705

Sequencing Information

	BGRSLV07-13	BGRSLV07-14
Sample_ID	BGRSLV07-13	BGRSLV07-14
Sample Name	LITAF-BGRSLV07-13	LITAF-BGRSLV07-14
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	37,019,220	29,004,877
total_aligned_reads	30,172,030	25,584,768
unique_aligned_reads	28,197,741	23,995,988
percent_uniqueAligned	0.76171	0.82731
correlation_replicates	0.995560	0.995560
spikein_reads	38,480	27,944
percent_spikeins	0.00104	0.00096
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2575	2576

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
LITAF-BGRSLV07-13_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2575	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7876
LITAF-BGRSLV07-13_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2575	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7920
LITAF-BGRSLV07-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz,LITAF-BGRSLV07-13_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10181
LITAF-BGRSLV07-13_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	10225
LITAF-BGRSLV07-13_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	10269
LITAF-BGRSLV07-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	10313
LITAF-BGRSLV07-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	10357
LITAF-BGRSLV07-13_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2575					GRCh38	V40	LITAF-BGRSLV07-13_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz,LITAF-BGRSLV07-13_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10401
LITAF-BGRSLV07-14_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2576	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7877
LITAF-BGRSLV07-14_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2576	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7921
LITAF-BGRSLV07-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz,LITAF-BGRSLV07-14_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10182
LITAF-BGRSLV07-14_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	10226
LITAF-BGRSLV07-14_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	10270
LITAF-BGRSLV07-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	10314
LITAF-BGRSLV07-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	10358
LITAF-BGRSLV07-14_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2576					GRCh38	V40	LITAF-BGRSLV07-14_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz,LITAF-BGRSLV07-14_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10402