HNRNPF RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-55	BG293LV06-56
idx	0	0
TRCN#_or_BGC#	TRCN0000001235	TRCN0000001235
shRNA_or_gRNA_sequence	CCGGGAGGTACATTGGCATCGTGAACTCGAGTTCACGATGCCAATGTACCTCTTTTT	CCGGGAGGTACATTGGCATCGTGAACTCGAGTTCACGATGCCAATGTACCTCTTTTT
PAM
Name	HNRNPF	HNRNPF
Sample_ID	BG293LV06-55	BG293LV06-56
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	HNRNPF	HNRNPF
qPCR_result	68.9	69.7
Ave_qPCR	69.3
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	12190	12191

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-55	BG293LV06-56
Sample_ID	BG293LV06-55	BG293LV06-56
Sample Name
Sample Name	HNRNPF-BG293LV06-55	HNRNPF-BG293LV06-56
RBP	HNRNPF	HNRNPF
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13492	13493

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-55	BG293LV06-56
Sample #	57	58
Sample Name	HNRNPF-BG293LV06-55	HNRNPF-BG293LV06-56
Sample_Name_Alias
Index Well Position	A08	B08
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	276	280
Peak_Molarity	92.90	100.00
libSampleQC_DNA_Well	DNA_Library_set71/set1/A8.png	DNA_Library_set71/set1/B8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/A8.png	RNA_Library_set71/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-55	BG293LV06-56
RBP	HNRNPF	HNRNPF
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	4482	4483

Sequencing Information

	BG293LV06-55	BG293LV06-56
Sample_ID	BG293LV06-55	BG293LV06-56
Sample Name	HNRNPF-BG293LV06-55	HNRNPF-BG293LV06-56
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	34,738,368	34,713,251
total_aligned_reads	31,638,474	31,812,601
unique_aligned_reads	29,880,122	30,018,025
percent_uniqueAligned	0.86015	0.86474
correlation_replicates	0.994143	0.994143
spikein_reads	142,592	117,916
percent_spikeins	0.00410	0.00340
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3051	3052

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-BG293LV06-55_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3051	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	29327
HNRNPF-BG293LV06-55_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3051	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	29391
HNRNPF-BG293LV06-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3051					GRCh38	V40	HNRNPF-BG293LV06-55_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV06-55_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29456
HNRNPF-BG293LV06-55_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	3051					GRCh38	V40	HNRNPF-BG293LV06-55_Aligned.sortedByCoord.out.bam		ENCORE2	29520
HNRNPF-BG293LV06-55_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	3051					GRCh38	V40	HNRNPF-BG293LV06-55_Aligned.sortedByCoord.out.bam		ENCORE2	29584
HNRNPF-BG293LV06-55_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	3051					GRCh38	V40	HNRNPF-BG293LV06-55_Aligned.sortedByCoord.out.bam		ENCORE2	29648
HNRNPF-BG293LV06-55_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3051					GRCh38	V40	HNRNPF-BG293LV06-55_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV06-55_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29712
HNRNPF-BG293LV06-56_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3052	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	29328
HNRNPF-BG293LV06-56_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3052	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	29392
HNRNPF-BG293LV06-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3052					GRCh38	V40	HNRNPF-BG293LV06-56_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV06-56_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29457
HNRNPF-BG293LV06-56_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	3052					GRCh38	V40	HNRNPF-BG293LV06-56_Aligned.sortedByCoord.out.bam		ENCORE2	29521
HNRNPF-BG293LV06-56_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	3052					GRCh38	V40	HNRNPF-BG293LV06-56_Aligned.sortedByCoord.out.bam		ENCORE2	29585
HNRNPF-BG293LV06-56_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	3052					GRCh38	V40	HNRNPF-BG293LV06-56_Aligned.sortedByCoord.out.bam		ENCORE2	29649
HNRNPF-BG293LV06-56_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3052					GRCh38	V40	HNRNPF-BG293LV06-56_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPF-BG293LV06-56_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29713