TTF2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-39	BGRSLV02-40
idx	0	0
TRCN#_or_BGC#	TRCN0000022230	TRCN0000022230
shRNA_or_gRNA_sequence	CCGGGCTCGAATCATATTGGATGAACTCGAGTTCATCCAATATGATTCGAGCTTTTT	CCGGGCTCGAATCATATTGGATGAACTCGAGTTCATCCAATATGATTCGAGCTTTTT
PAM
Name	TTF2	TTF2
Sample_ID	BGRSLV02-39	BGRSLV02-40
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	TTF2	TTF2
qPCR_result	53.6	67.4
Ave_qPCR	60.5
RT-qPCR_primer-F	GTGAAGCCATCGGTCAACTGCA
RT-qPCR_primer-R	TGTGGCTTCTGACTTTCTCGCC
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	8276	8277

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-39	BGRSLV02-40
Sample_ID	BGRSLV02-39	BGRSLV02-40
Sample Name
Sample Name	TTF2-BGRSLV02-39	TTF2-BGRSLV02-40
RBP	TTF2	TTF2
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	11326	11327

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-39	BGRSLV02-40
Sample #	29	30
Sample Name	TTF2-BGRSLV02-39	TTF2-BGRSLV02-40
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	297	296
Peak_Molarity	58.40	60.80
libSampleQC_DNA_Well	DNA_Library_set57/set1/E10.png	DNA_Library_set57/set1/F10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set57/set1/E4.png	RNA_Library_set57/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-39	BGRSLV02-40
RBP	TTF2	TTF2
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3490	3491

Sequencing Information

	BGRSLV02-39	BGRSLV02-40
Sample_ID	BGRSLV02-39	BGRSLV02-40
Sample Name	TTF2-BGRSLV02-39	TTF2-BGRSLV02-40
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	44,716,364	45,220,218
total_aligned_reads	41,765,266	42,058,648
unique_aligned_reads	38,977,270	39,070,207
percent_uniqueAligned	0.87166	0.86400
correlation_replicates	0.996269	0.996269
spikein_reads	16,938	19,078
percent_spikeins	0.00038	0.00042
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2361	2362

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
TTF2-BGRSLV02-39_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2361	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8234
TTF2-BGRSLV02-39_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2361	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8280
TTF2-BGRSLV02-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz,TTF2-BGRSLV02-39_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11523
TTF2-BGRSLV02-39_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39/Aligned.sortedByCoord.out.bam		ENCORE2	11569
TTF2-BGRSLV02-39_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39/Aligned.sortedByCoord.out.bam		ENCORE2	11615
TTF2-BGRSLV02-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39/Aligned.sortedByCoord.out.bam		ENCORE2	11661
TTF2-BGRSLV02-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39/Aligned.sortedByCoord.out.bam		ENCORE2	11707
TTF2-BGRSLV02-39_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2361					GRCh38	V40	TTF2-BGRSLV02-39_S117_L003_R1_001.filtered.trimmed.paired.fastq.gz,TTF2-BGRSLV02-39_S117_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11753
TTF2-BGRSLV02-40_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2362	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8235
TTF2-BGRSLV02-40_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2362	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8281
TTF2-BGRSLV02-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz,TTF2-BGRSLV02-40_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11524
TTF2-BGRSLV02-40_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40/Aligned.sortedByCoord.out.bam		ENCORE2	11570
TTF2-BGRSLV02-40_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40/Aligned.sortedByCoord.out.bam		ENCORE2	11616
TTF2-BGRSLV02-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40/Aligned.sortedByCoord.out.bam		ENCORE2	11662
TTF2-BGRSLV02-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40/Aligned.sortedByCoord.out.bam		ENCORE2	11708
TTF2-BGRSLV02-40_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2362					GRCh38	V40	TTF2-BGRSLV02-40_S118_L003_R1_001.filtered.trimmed.paired.fastq.gz,TTF2-BGRSLV02-40_S118_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11754