HNRNPF RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-7	BG293LV05-8
idx	0	0
TRCN#_or_BGC#	TRCN0000001235	TRCN0000001235
shRNA_or_gRNA_sequence	CCGGGAGGTACATTGGCATCGTGAACTCGAGTTCACGATGCCAATGTACCTCTTTTT	CCGGGAGGTACATTGGCATCGTGAACTCGAGTTCACGATGCCAATGTACCTCTTTTT
PAM
Name	HNRNPF	HNRNPF
Sample_ID	BG293LV05-7	BG293LV05-8
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	HNRNPF	HNRNPF
qPCR_result	75.2	83.5
Ave_qPCR	79.35
RT-qPCR_primer-F	gcgagttgaggctgttgatt
RT-qPCR_primer-R	ttcctggaaaagcttgatgg
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	9979	9980

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-7	BG293LV05-8
Sample_ID	BG293LV05-7	BG293LV05-8
Sample Name
Sample Name	HNRNPF-BG293LV05-7	HNRNPF-BG293LV05-8
RBP	HNRNPF	HNRNPF
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12838	12839

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-7	BG293LV05-8
Sample #	5	6
Sample Name	HNRNPF-BG293LV05-7	HNRNPF-BG293LV05-8
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	282	283
Peak_Molarity	77.10	47.80
libSampleQC_DNA_Well	DNA_Library_set69/set1/E1.png	DNA_Library_set69/set1/F1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set69/set1/E6.png	RNA_Library_set69/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-7	BG293LV05-8
RBP	HNRNPF	HNRNPF
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4186	4187

Sequencing Information

	BG293LV05-7	BG293LV05-8
Sample_ID	BG293LV05-7	BG293LV05-8
Sample Name	HNRNPF-BG293LV05-7	HNRNPF-BG293LV05-8
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	21,353,944	25,199,115
total_aligned_reads	17,497,622	22,078,549
unique_aligned_reads	16,335,472	20,552,115
percent_uniqueAligned	0.76499	0.81559
correlation_replicates	0.994860	0.994860
spikein_reads	6,178	9,624
percent_spikeins	0.00029	0.00038
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2905	2906

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
HNRNPF-BG293LV05-7_S137_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2905	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28501
HNRNPF-BG293LV05-7_S137_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2905	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28545
HNRNPF-BG293LV05-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7_S137_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV05-7_S137_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28589
HNRNPF-BG293LV05-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7/Aligned.sortedByCoord.out.bam		ENCORE2	28633
HNRNPF-BG293LV05-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7/Aligned.sortedByCoord.out.bam		ENCORE2	28677
HNRNPF-BG293LV05-7_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7/Aligned.sortedByCoord.out.bam		ENCORE2	28721
HNRNPF-BG293LV05-7_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7/Aligned.sortedByCoord.out.bam		ENCORE2	28765
HNRNPF-BG293LV05-7_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2905					GRCh38	V40	HNRNPF-BG293LV05-7_S137_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV05-7_S137_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28809
HNRNPF-BG293LV05-8_S138_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2906	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28502
HNRNPF-BG293LV05-8_S138_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2906	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28546
HNRNPF-BG293LV05-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8_S138_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV05-8_S138_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28590
HNRNPF-BG293LV05-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8/Aligned.sortedByCoord.out.bam		ENCORE2	28634
HNRNPF-BG293LV05-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8/Aligned.sortedByCoord.out.bam		ENCORE2	28678
HNRNPF-BG293LV05-8_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8/Aligned.sortedByCoord.out.bam		ENCORE2	28722
HNRNPF-BG293LV05-8_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8/Aligned.sortedByCoord.out.bam		ENCORE2	28766
HNRNPF-BG293LV05-8_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2906					GRCh38	V40	HNRNPF-BG293LV05-8_S138_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV05-8_S138_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28810