BRCA1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSDLV02-11dox	BGRSDLV02-12dox
idx	0	0
TRCN#_or_BGC#	TRCN0000244986	TRCN0000244986
shRNA_or_gRNA_sequence	CCGGTTGCAACCTGAGGTCTATAAACTCGAGTTTATAGACCTCAGGTTGCAATTTTTG	CCGGTTGCAACCTGAGGTCTATAAACTCGAGTTTATAGACCTCAGGTTGCAATTTTTG
PAM
Name	BRCA1	BRCA1
Sample_ID	BGRSDLV02-11dox	BGRSDLV02-12dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	BRCA1	BRCA1
qPCR_result	64.5	69.2
Ave_qPCR	66.9
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	11270	11271

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-11dox	BGRSDLV02-12dox
Sample_ID	BGRSDLV02-11dox	BGRSDLV02-12dox
Sample Name
Sample Name	BRCA1-BGRSDLV02-11dox	BRCA1-BGRSDLV02-12dox
RBP	BRCA1	BRCA1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	12330	12331

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-11dox	BGRSDLV02-12dox
Sample #	11	12
Sample Name	BRCA1-BGRSDLV02-11dox	BRCA1-BGRSDLV02-12dox
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	297	289
Peak_Molarity	66.40	75.70
libSampleQC_DNA_Well	DNA_Library_set65/set1/C2.png	DNA_Library_set65/set1/D2.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set65/set1/C2.png	RNA_Library_set65/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-11dox	BGRSDLV02-12dox
RBP	BRCA1	BRCA1
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3932	3933

Sequencing Information

	BGRSDLV02-11dox	BGRSDLV02-12dox
Sample_ID	BGRSDLV02-11dox	BGRSDLV02-12dox
Sample Name	BRCA1-BGRSDLV02-11dox	BRCA1-BGRSDLV02-12dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	29,766,923	24,846,018
total_aligned_reads	26,316,626	22,016,787
unique_aligned_reads	24,493,662	20,365,433
percent_uniqueAligned	0.82285	0.81967
correlation_replicates	0.995811	0.995811
spikein_reads	7,920	4,894
percent_spikeins	0.00027	0.00020
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2679	2680

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
BRCA1-BGRSDLV02-11dox_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2679	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8743
BRCA1-BGRSDLV02-11dox_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2679	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8819
BRCA1-BGRSDLV02-11dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-11dox_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9308
BRCA1-BGRSDLV02-11dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	9384
BRCA1-BGRSDLV02-11dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	9460
BRCA1-BGRSDLV02-11dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	9536
BRCA1-BGRSDLV02-11dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox/Aligned.sortedByCoord.out.bam		ENCORE2	9612
BRCA1-BGRSDLV02-11dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2679					GRCh38	V40	BRCA1-BGRSDLV02-11dox_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-11dox_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9688
BRCA1-BGRSDLV02-12dox_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2680	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8744
BRCA1-BGRSDLV02-12dox_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2680	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8820
BRCA1-BGRSDLV02-12dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-12dox_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9309
BRCA1-BGRSDLV02-12dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	9385
BRCA1-BGRSDLV02-12dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	9461
BRCA1-BGRSDLV02-12dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	9537
BRCA1-BGRSDLV02-12dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox/Aligned.sortedByCoord.out.bam		ENCORE2	9613
BRCA1-BGRSDLV02-12dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2680					GRCh38	V40	BRCA1-BGRSDLV02-12dox_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-12dox_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9689