AHNAK RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-77	BG293LV06-78
idx	0	0
TRCN#_or_BGC#	TRCN0000123212	TRCN0000123212
shRNA_or_gRNA_sequence	CCGGGCAGCTCTGAAGTGGTTCTGACTCGAGTCAGAACCACTTCAGAGCTGCTTTTTG	CCGGGCAGCTCTGAAGTGGTTCTGACTCGAGTCAGAACCACTTCAGAGCTGCTTTTTG
PAM
Name	AHNAK	AHNAK
Sample_ID	BG293LV06-77	BG293LV06-78
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	AHNAK	AHNAK
qPCR_result	91.3	92.7
Ave_qPCR	92.0
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	12212	12213

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-77	BG293LV06-78
Sample_ID	BG293LV06-77	BG293LV06-78
Sample Name
Sample Name	AHNAK-BG293LV06-77B	AHNAK-BG293LV06-78B
RBP	AHNAK	AHNAK
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13514	13515

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-77	BG293LV06-78
Sample #	77	78
Sample Name	AHNAK-BG293LV06-77B	AHNAK-BG293LV06-78B
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	283	281
Peak_Molarity	88.50	86.30
libSampleQC_DNA_Well	DNA_Library_set72/set1/E3.png	DNA_Library_set72/set1/F3.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set72/set1/E3.png	RNA_Library_set72/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-77	BG293LV06-78
RBP	AHNAK	AHNAK
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4502	4503

Sequencing Information

	BG293LV06-77	BG293LV06-78
Sample_ID	BG293LV06-77	BG293LV06-78
Sample Name	AHNAK-BG293LV06-77B	AHNAK-BG293LV06-78B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	49,245,910	37,890,019
total_aligned_reads	43,215,105	33,606,979
unique_aligned_reads	40,298,722	31,316,530
percent_uniqueAligned	0.81832	0.82651
correlation_replicates	0.997525	0.997525
spikein_reads	164,046	120,826
percent_spikeins	0.00333	0.00319
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3071	3072

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
AHNAK-BG293LV06-77B_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3071	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29764
AHNAK-BG293LV06-77B_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3071	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29836
AHNAK-BG293LV06-77B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV06-77B_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29908
AHNAK-BG293LV06-77B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_Aligned.sortedByCoord.out.bam		ENCORE2	29980
AHNAK-BG293LV06-77B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_Aligned.sortedByCoord.out.bam		ENCORE2	30052
AHNAK-BG293LV06-77B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_Aligned.sortedByCoord.out.bam		ENCORE2	30124
AHNAK-BG293LV06-77B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_Aligned.sortedByCoord.out.bam		ENCORE2	30196
AHNAK-BG293LV06-77B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3071					GRCh38	V40	AHNAK-BG293LV06-77B_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV06-77B_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30268
AHNAK-BG293LV06-78B_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3072	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29765
AHNAK-BG293LV06-78B_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3072	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29837
AHNAK-BG293LV06-78B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV06-78B_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29909
AHNAK-BG293LV06-78B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_Aligned.sortedByCoord.out.bam		ENCORE2	29981
AHNAK-BG293LV06-78B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_Aligned.sortedByCoord.out.bam		ENCORE2	30053
AHNAK-BG293LV06-78B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_Aligned.sortedByCoord.out.bam		ENCORE2	30125
AHNAK-BG293LV06-78B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_Aligned.sortedByCoord.out.bam		ENCORE2	30197
AHNAK-BG293LV06-78B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3072					GRCh38	V40	AHNAK-BG293LV06-78B_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV06-78B_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30269