GRB2 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-7	BG293LV06-8
idx	0	0
TRCN#_or_BGC#	TRCN0000029369	TRCN0000029369
shRNA_or_gRNA_sequence	CCGGGCAGAAGAAATGCTTAGCAAACTCGAGTTTGCTAAGCATTTCTTCTGCTTTTT	CCGGGCAGAAGAAATGCTTAGCAAACTCGAGTTTGCTAAGCATTTCTTCTGCTTTTT
PAM
Name	GRB2	GRB2
Sample_ID	BG293LV06-7	BG293LV06-8
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	GRB2	GRB2
qPCR_result	64.9	53.6
Ave_qPCR	59.3
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	12142	12143

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-7	BG293LV06-8
Sample_ID	BG293LV06-7	BG293LV06-8
Sample Name
Sample Name	GRB2-BG293LV06-7	GRB2-BG293LV06-8
RBP	GRB2	GRB2
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13444	13445

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-7	BG293LV06-8
Sample #	11	12
Sample Name	GRB2-BG293LV06-7	GRB2-BG293LV06-8
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	298	298
Peak_Molarity	88.80	91.90
libSampleQC_DNA_Well	DNA_Library_set71/set1/C2.png	DNA_Library_set71/set1/D2.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C2.png	RNA_Library_set71/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-7	BG293LV06-8
RBP	GRB2	GRB2
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4436	4437

Sequencing Information

	BG293LV06-7	BG293LV06-8
Sample_ID	BG293LV06-7	BG293LV06-8
Sample Name	GRB2-BG293LV06-7	GRB2-BG293LV06-8
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	27,074,964	30,502,103
total_aligned_reads	24,875,733	27,768,484
unique_aligned_reads	23,339,976	26,024,753
percent_uniqueAligned	0.86205	0.85321
correlation_replicates	0.988759	0.988759
spikein_reads	78,934	103,282
percent_spikeins	0.00292	0.00339
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3005	3006

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-BG293LV06-7_S11_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3005	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29323
GRB2-BG293LV06-7_S11_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3005	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29387
GRB2-BG293LV06-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3005					GRCh38	V40	GRB2-BG293LV06-7_S11_L002_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV06-7_S11_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29452
GRB2-BG293LV06-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3005					GRCh38	V40	GRB2-BG293LV06-7_Aligned.sortedByCoord.out.bam		ENCORE2	29516
GRB2-BG293LV06-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3005					GRCh38	V40	GRB2-BG293LV06-7_Aligned.sortedByCoord.out.bam		ENCORE2	29580
GRB2-BG293LV06-7_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3005					GRCh38	V40	GRB2-BG293LV06-7_Aligned.sortedByCoord.out.bam		ENCORE2	29644
GRB2-BG293LV06-7_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3005					GRCh38	V40	GRB2-BG293LV06-7_S11_L002_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV06-7_S11_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29708
GRB2-BG293LV06-8_S12_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3006	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29324
GRB2-BG293LV06-8_S12_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3006	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29388
GRB2-BG293LV06-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3006					GRCh38	V40	GRB2-BG293LV06-8_S12_L002_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV06-8_S12_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29453
GRB2-BG293LV06-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3006					GRCh38	V40	GRB2-BG293LV06-8_Aligned.sortedByCoord.out.bam		ENCORE2	29517
GRB2-BG293LV06-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3006					GRCh38	V40	GRB2-BG293LV06-8_Aligned.sortedByCoord.out.bam		ENCORE2	29581
GRB2-BG293LV06-8_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3006					GRCh38	V40	GRB2-BG293LV06-8_Aligned.sortedByCoord.out.bam		ENCORE2	29645
GRB2-BG293LV06-8_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3006					GRCh38	V40	GRB2-BG293LV06-8_S12_L002_R1_001.filtered.trimmed.paired.fastq.gz,GRB2-BG293LV06-8_S12_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29709