F11R RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV50-51	BGHcLV50-52
idx	1870	1871
TRCN#_or_BGC#	BGC#0001008	BGC#0001008
shRNA_or_gRNA_sequence	AAGTTGTCCTGTGCCTACTC	AAGTTGTCCTGTGCCTACTC
PAM	GGG	GGG
Name	F11R_79	F11R_79
Sample_ID	BGHcLV50-51	BGHcLV50-52
transduction_Date	7/29/25	7/29/25
days	D6	D6
RBP_name	F11R	F11R
qPCR_result	72.6	72.0
Ave_qPCR	72.3
RT-qPCR_primer-F	gggacacccatgacttcaaa
RT-qPCR_primer-R	accagatgccaaaaaccaag
protein_conc	2624	2923
WB_result	90.9	96.0
Ave_WB
WB_DONE_date	8/8/25,8/14/25
MW	33kd
IP
antibody_Cat#	A302-891A	lot # 1
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	10059	10060

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-51	BGHcLV50-52
Sample_ID	BGHcLV50-51	BGHcLV50-52
Sample Name
Sample Name	F11R-BGHcLV50-51	F11R-BGHcLV50-52
RBP	F11R	F11R
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14458	14459

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-51	BGHcLV50-52
Sample #	11	12
Sample Name	F11R-BGHcLV50-51	F11R-BGHcLV50-52
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-10-01	2025-10-01
Lib_ID	Lib-251001	Lib-251001
Tecan_Location
Tecan
Tecan_date
Size_bp	287	294
Peak_Molarity	68.70	83.60
libSampleQC_DNA_Well	DNA_Library_set80/set1/C11.png	DNA_Library_set80/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set80/set1/C8.png	RNA_Library_set80/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-51	BGHcLV50-52
RBP	F11R	F11R
Batch_ID	BGHcLV50	BGHcLV50
WB_result	90.900	96.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4826	4827

Sequencing Information

	BGHcLV50-51	BGHcLV50-52
Sample_ID	BGHcLV50-51	BGHcLV50-52
Sample Name	F11R-BGHcLV50-51	F11R-BGHcLV50-52
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	23,694,973	20,768,512
total_aligned_reads	21,336,139	18,564,769
unique_aligned_reads	20,161,756	17,571,806
percent_uniqueAligned	0.85089	0.84608
correlation_replicates	0.992222	0.992222
spikein_reads	127,330	57,490
percent_spikeins	0.00537	0.00277
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3481	3482

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
F11R-BGHcLV50-51_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3481	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32982
F11R-BGHcLV50-51_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3481	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33006
F11R-BGHcLV50-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGHcLV50-51_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33030
F11R-BGHcLV50-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_Aligned.sortedByCoord.out.bam		ENCORE2	33054
F11R-BGHcLV50-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_Aligned.sortedByCoord.out.bam		ENCORE2	33078
F11R-BGHcLV50-51_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_Aligned.sortedByCoord.out.bam		ENCORE2	33102
F11R-BGHcLV50-51_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_Aligned.sortedByCoord.out.bam		ENCORE2	33126
F11R-BGHcLV50-51_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3481					GRCh38	V40	F11R-BGHcLV50-51_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGHcLV50-51_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33150
F11R-BGHcLV50-52_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3482	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32983
F11R-BGHcLV50-52_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3482	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33007
F11R-BGHcLV50-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGHcLV50-52_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33031
F11R-BGHcLV50-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_Aligned.sortedByCoord.out.bam		ENCORE2	33055
F11R-BGHcLV50-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_Aligned.sortedByCoord.out.bam		ENCORE2	33079
F11R-BGHcLV50-52_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_Aligned.sortedByCoord.out.bam		ENCORE2	33103
F11R-BGHcLV50-52_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_Aligned.sortedByCoord.out.bam		ENCORE2	33127
F11R-BGHcLV50-52_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3482					GRCh38	V40	F11R-BGHcLV50-52_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGHcLV50-52_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33151