GRB2 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-17	BG293LV02-18
idx	0	0
TRCN#_or_BGC#	TRCN0000029369	TRCN0000029369
shRNA_or_gRNA_sequence	CCGGGCAGAAGAAATGCTTAGCAAACTCGAGTTTGCTAAGCATTTCTTCTGCTTTTT	CCGGGCAGAAGAAATGCTTAGCAAACTCGAGTTTGCTAAGCATTTCTTCTGCTTTTT
PAM
Name	GRB2	GRB2
Sample_ID	BG293LV02-17	BG293LV02-18
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	GRB2	GRB2
qPCR_result	84.1	87.4
Ave_qPCR	85.8
RT-qPCR_primer-F	x
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	9812	9813

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-17	BG293LV02-18
Sample_ID	BG293LV02-17	BG293LV02-18
Sample Name
Sample Name	GRB2-BG293LV02-17	GRB2-BG293LV02-18
RBP	GRB2	GRB2
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11572	11573

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-17	BG293LV02-18
Sample #	15	16
Sample Name	GRB2-BG293LV02-17	GRB2-BG293LV02-18
Sample_Name_Alias
Index Well Position	G02	H02
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	284	280
Peak_Molarity	94.10	66.40
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/G2.png	DNA_Library_set60-62/set2/H2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set60-62/set1/G2.png	RNA_Library_set60-62/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-17	BG293LV02-18
RBP	GRB2	GRB2
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	3602	3603

Sequencing Information

	BG293LV02-17	BG293LV02-18
Sample_ID	BG293LV02-17	BG293LV02-18
Sample Name	GRB2-BG293LV02-17	GRB2-BG293LV02-18
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	37,394,139	38,762,945
total_aligned_reads	32,035,983	29,338,287
unique_aligned_reads	29,844,549	27,315,356
percent_uniqueAligned	0.79811	0.70468
correlation_replicates	0.988085	0.988085
spikein_reads	59,654	66,906
percent_spikeins	0.00160	0.00173
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2473	2474

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
GRB2-BG293LV02-17_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2473	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	7974
GRB2-BG293LV02-17_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2473	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	8018
GRB2-BG293LV02-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2473					GRCh38	V40	GRB2-BG293LV02-17_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV02-17_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10767
GRB2-BG293LV02-17_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	2473					GRCh38	V40	GRB2-BG293LV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	10811
GRB2-BG293LV02-17_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	2473					GRCh38	V40	GRB2-BG293LV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	10855
GRB2-BG293LV02-17_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	2473					GRCh38	V40	GRB2-BG293LV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	10899
GRB2-BG293LV02-17_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	2473					GRCh38	V40	GRB2-BG293LV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	10943
GRB2-BG293LV02-17_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2473					GRCh38	V40	GRB2-BG293LV02-17_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV02-17_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10987
GRB2-BG293LV02-18_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2474	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	7975
GRB2-BG293LV02-18_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2474	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	8019
GRB2-BG293LV02-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2474					GRCh38	V40	GRB2-BG293LV02-18_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV02-18_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10768
GRB2-BG293LV02-18_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	2474					GRCh38	V40	GRB2-BG293LV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	10812
GRB2-BG293LV02-18_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	2474					GRCh38	V40	GRB2-BG293LV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	10856
GRB2-BG293LV02-18_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	2474					GRCh38	V40	GRB2-BG293LV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	10900
GRB2-BG293LV02-18_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	2474					GRCh38	V40	GRB2-BG293LV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	10944
GRB2-BG293LV02-18_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2474					GRCh38	V40	GRB2-BG293LV02-18_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV02-18_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10988