RC3H1 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV51-85	BGKcLV51-86
idx	0	0
TRCN#_or_BGC#	BGC#0001479	BGC#0001479
shRNA_or_gRNA_sequence	AGGCAGGATTCGTGCCATGA	AGGCAGGATTCGTGCCATGA
PAM	GGG	GGG
Name	RC3H1_79B	RC3H1_79B
Sample_ID	BGKcLV51-85	BGKcLV51-86
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	RC3H1	RC3H1
qPCR_result	0.0	14.0
Ave_qPCR	0
RT-qPCR_primer-F	tatccagtggctcctcatcc
RT-qPCR_primer-R	agctgggccattatttcctt
protein_conc	2184	2200
WB_result	67.5	64.7
Ave_WB
WB_DONE_date	1/23/26
MW	126kd
IP
antibody_Cat#	A300-515A	lot# 2
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	6326	6327

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RC3H1	Product_ID: A300-515A Lot_ID: 1 Source: Bethyl Labs Target Name: RC3H1-human

Experiment Status

	BGKcLV51-85	BGKcLV51-86
Sample_ID	BGKcLV51-85	BGKcLV51-86
Sample Name
Sample Name	RC3H1-BGKcLV51-85	RC3H1-BGKcLV51-86
RBP	RC3H1	RC3H1
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14580	14581

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-85	BGKcLV51-86
Sample #	15	16
Sample Name	RC3H1-BGKcLV51-85	RC3H1-BGKcLV51-86
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-18	2026-05-18
Lib_ID	Lib-260518	Lib-260518
Tecan_Location
Tecan
Tecan_date
Size_bp	284	282
Peak_Molarity	50.60	41.80
libSampleQC_DNA_Well	DNA_Library_set82/set1/G9.png	DNA_Library_set82/set1/H9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set82/set1/G2.png	RNA_Library_set82/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-85	BGKcLV51-86
RBP	RC3H1	RC3H1
Batch_ID	BGKcLV51	BGKcLV51
WB_result	67.500	64.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4854	4855

Sequencing Information

	BGKcLV51-85	BGKcLV51-86
Sample_ID	BGKcLV51-85	BGKcLV51-86
Sample Name	RC3H1-BGKcLV51-85	RC3H1-BGKcLV51-86
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	16,850,496	17,108,424
total_aligned_reads	13,025,076	13,886,770
unique_aligned_reads	12,128,718	12,977,036
percent_uniqueAligned	0.71978	0.75852
correlation_replicates	0.986809	0.986809
spikein_reads	36,416	44,932
percent_spikeins	0.00216	0.00263
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3555	3556

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
RC3H1-BGKcLV51-85_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3555	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33686
RC3H1-BGKcLV51-85_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3555	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33744
RC3H1-BGKcLV51-85_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_R1.filtered.trimmed.paired.fastq.gz,RC3H1-BGKcLV51-85_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33804
RC3H1-BGKcLV51-85_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_Aligned.sortedByCoord.out.bam		ENCORE2	33862
RC3H1-BGKcLV51-85_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_Aligned.sortedByCoord.out.bam		ENCORE2	33920
RC3H1-BGKcLV51-85_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_Aligned.sortedByCoord.out.bam		ENCORE2	33978
RC3H1-BGKcLV51-85_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_Aligned.sortedByCoord.out.bam		ENCORE2	34036
RC3H1-BGKcLV51-85_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3555					GRCh38	V40	RC3H1-BGKcLV51-85_R1.filtered.trimmed.paired.fastq.gz,RC3H1-BGKcLV51-85_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34094
RC3H1-BGKcLV51-86_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3556	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33687
RC3H1-BGKcLV51-86_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3556	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33745
RC3H1-BGKcLV51-86_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_R1.filtered.trimmed.paired.fastq.gz,RC3H1-BGKcLV51-86_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33805
RC3H1-BGKcLV51-86_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_Aligned.sortedByCoord.out.bam		ENCORE2	33863
RC3H1-BGKcLV51-86_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_Aligned.sortedByCoord.out.bam		ENCORE2	33921
RC3H1-BGKcLV51-86_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_Aligned.sortedByCoord.out.bam		ENCORE2	33979
RC3H1-BGKcLV51-86_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_Aligned.sortedByCoord.out.bam		ENCORE2	34037
RC3H1-BGKcLV51-86_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3556					GRCh38	V40	RC3H1-BGKcLV51-86_R1.filtered.trimmed.paired.fastq.gz,RC3H1-BGKcLV51-86_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34095