TIAL1 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-49	BG293LV02-50
idx	0	0
TRCN#_or_BGC#	TRCN0000017211	TRCN0000017211
shRNA_or_gRNA_sequence	CGGATATGGTATGGCAAGTTA	CGGATATGGTATGGCAAGTTA
PAM
Name	TIAL1	TIAL1
Sample_ID	BG293LV02-49	BG293LV02-50
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	TIAL1	TIAL1
qPCR_result	81.3	77.8
Ave_qPCR	79.5
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	9844	9845

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-49	BG293LV02-50
Sample_ID	BG293LV02-49	BG293LV02-50
Sample Name
Sample Name	TIAL1-BG293LV02-49	TIAL1-BG293LV02-50
RBP	TIAL1	TIAL1
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11598	11599

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-49	BG293LV02-50
Sample #	41	42
Sample Name	TIAL1-BG293LV02-49	TIAL1-BG293LV02-50
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	285	290
Peak_Molarity	70.10	85.40
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/A6.png	DNA_Library_set60-62/set2/B6.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/A6.png	RNA_Library_set60-62/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-49	BG293LV02-50
RBP	TIAL1	TIAL1
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3628	3629

Sequencing Information

	BG293LV02-49	BG293LV02-50
Sample_ID	BG293LV02-49	BG293LV02-50
Sample Name	TIAL1-BG293LV02-49	TIAL1-BG293LV02-50
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	34,598,408	40,681,955
total_aligned_reads	26,662,028	35,227,207
unique_aligned_reads	24,981,638	33,083,144
percent_uniqueAligned	0.72205	0.81321
correlation_replicates	0.994692	0.994692
spikein_reads	97,436	61,302
percent_spikeins	0.00282	0.00151
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2499	2500

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
TIAL1-BG293LV02-49_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2499	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8002
TIAL1-BG293LV02-49_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2499	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8046
TIAL1-BG293LV02-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,TIAL1-BG293LV02-49_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10795
TIAL1-BG293LV02-49_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	10839
TIAL1-BG293LV02-49_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	10883
TIAL1-BG293LV02-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	10927
TIAL1-BG293LV02-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	10971
TIAL1-BG293LV02-49_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2499					GRCh38	V40	TIAL1-BG293LV02-49_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,TIAL1-BG293LV02-49_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11015
TIAL1-BG293LV02-50_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2500	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8003
TIAL1-BG293LV02-50_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2500	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8047
TIAL1-BG293LV02-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,TIAL1-BG293LV02-50_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10796
TIAL1-BG293LV02-50_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	10840
TIAL1-BG293LV02-50_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	10884
TIAL1-BG293LV02-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	10928
TIAL1-BG293LV02-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	10972
TIAL1-BG293LV02-50_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2500					GRCh38	V40	TIAL1-BG293LV02-50_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,TIAL1-BG293LV02-50_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11016