CAPRIN1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV50-13	BGHcLV50-14
idx	1832	1833
TRCN#_or_BGC#	BGC#0001403	BGC#0001403
shRNA_or_gRNA_sequence	CTCCCGGAGGAACCCGACGG	CTCCCGGAGGAACCCGACGG
PAM	CGG	CGG
Name	CAPRIN1_92	CAPRIN1_92
Sample_ID	BGHcLV50-13	BGHcLV50-14
transduction_Date	7/29/25	7/29/25
days	D6	D6
RBP_name	CAPRIN1	CAPRIN1
qPCR_result	7.4	18.0
Ave_qPCR	12.7
RT-qPCR_primer-F	ggcttgatgaatggataccg
RT-qPCR_primer-R	ggggagcactgaactgagac
protein_conc	3294	2855
WB_result	64.1	56.7
Ave_WB
WB_DONE_date	8/11/25
MW	78kDa
IP	Rabbit / I
antibody_Cat#	A303-882A	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	10021	10022

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-13	BGHcLV50-14
Sample_ID	BGHcLV50-13	BGHcLV50-14
Sample Name
Sample Name	CAPRIN1-BGHcLV50-13	CAPRIN1-BGHcLV50-14
RBP	CAPRIN1	CAPRIN1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14452	14453

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-13	BGHcLV50-14
Sample #	5	6
Sample Name	CAPRIN1-BGHcLV50-13	CAPRIN1-BGHcLV50-14
Sample_Name_Alias
Index Well Position	E10	F10
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	285	282
Peak_Molarity	56.20	45.90
libSampleQC_DNA_Well	DNA_Library_set80/set1/E10.png	DNA_Library_set80/set1/F10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set80/set1/E7.png	RNA_Library_set80/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-13	BGHcLV50-14
RBP	CAPRIN1	CAPRIN1
Batch_ID	BGHcLV50	BGHcLV50
WB_result	64.100	56.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4820	4821

Sequencing Information

	BGHcLV50-13	BGHcLV50-14
Sample_ID	BGHcLV50-13	BGHcLV50-14
Sample Name	CAPRIN1-BGHcLV50-13	CAPRIN1-BGHcLV50-14
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	16,751,146	19,726,980
total_aligned_reads	14,950,031	17,442,005
unique_aligned_reads	14,095,151	16,492,848
percent_uniqueAligned	0.84144	0.83606
correlation_replicates	0.991637	0.991637
spikein_reads	84,524	10,432
percent_spikeins	0.00505	0.00053
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3475	3476

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
CAPRIN1-BGHcLV50-13_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3475	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	32976
CAPRIN1-BGHcLV50-13_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3475	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	33000
CAPRIN1-BGHcLV50-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGHcLV50-13_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33024
CAPRIN1-BGHcLV50-13_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	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_Aligned.sortedByCoord.out.bam		ENCORE2	33048
CAPRIN1-BGHcLV50-13_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	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_Aligned.sortedByCoord.out.bam		ENCORE2	33072
CAPRIN1-BGHcLV50-13_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	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_Aligned.sortedByCoord.out.bam		ENCORE2	33096
CAPRIN1-BGHcLV50-13_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	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_Aligned.sortedByCoord.out.bam		ENCORE2	33120
CAPRIN1-BGHcLV50-13_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3475					GRCh38	V40	CAPRIN1-BGHcLV50-13_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGHcLV50-13_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33144
CAPRIN1-BGHcLV50-14_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3476	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	32977
CAPRIN1-BGHcLV50-14_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3476	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	33001
CAPRIN1-BGHcLV50-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGHcLV50-14_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33025
CAPRIN1-BGHcLV50-14_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	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_Aligned.sortedByCoord.out.bam		ENCORE2	33049
CAPRIN1-BGHcLV50-14_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	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_Aligned.sortedByCoord.out.bam		ENCORE2	33073
CAPRIN1-BGHcLV50-14_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	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_Aligned.sortedByCoord.out.bam		ENCORE2	33097
CAPRIN1-BGHcLV50-14_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	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_Aligned.sortedByCoord.out.bam		ENCORE2	33121
CAPRIN1-BGHcLV50-14_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3476					GRCh38	V40	CAPRIN1-BGHcLV50-14_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGHcLV50-14_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33145