ZFC3H1 RNA-Seq in K562

General Information


RBP	ZFC3H1
Cell_Line	K562
Method	CRISPR
Exp_Name	ZFC3H1-BGKcLV48-K562
ENCODE_series_ID
Batch_ID	BGKcLV48
Pool ID	Pool-250822
Local_Set_Name	set79
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ZFC3H1-BGKcLV48-83
Rep2	ZFC3H1-BGKcLV48-84
CN1	NT-BGKcLV48-1
CN2	NT-BGKcLV48-2
Rep1_qPCR	19.7
Rep2_qPCR	5.8
Rep1_WB	86.0
Rep2_WB	90.8
Antibody Cat#	A301-455A
Antibody Lot#	lot# 001
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1683

Experiment Information (Status: Sequenced)

	BGKcLV48-83	BGKcLV48-84
idx	0	0
TRCN#_or_BGC#	BGC#0001387	BGC#0001387
shRNA_or_gRNA_sequence	GAAGGCATCCGTACAGAAGG	GAAGGCATCCGTACAGAAGG
PAM	CGG	CGG
Name	ZFC3H1_83	ZFC3H1_83
Sample_ID	BGKcLV48-83	BGKcLV48-84
transduction_Date	4/15/25	4/15/25
days	D6	D6
RBP_name	ZFC3H1	ZFC3H1
qPCR_result	19.7	5.8
Ave_qPCR	12.8
RT-qPCR_primer-F	ggaagaaatgctgcttcgag
RT-qPCR_primer-R	ggaggtgaaggtgggtcact
protein_conc	2208	2332
WB_result	86.0	90.8
Ave_WB
WB_DONE_date	5/28/25
MW	226kd
IP	1	old
antibody_Cat#	A301-455A	lot# 001
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	6231	6232

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZFC3H1	Product_ID: A301-455A Lot_ID: 001 Source: Bethyl Labs Target Name: ZFC3H1-human

Experiment Status

	BGKcLV48-83	BGKcLV48-84
Sample_ID	BGKcLV48-83	BGKcLV48-84
Sample Name
Sample Name	ZFC3H1-BGKcLV48-83	ZFC3H1-BGKcLV48-84
RBP	ZFC3H1	ZFC3H1
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-02	2025-10-02
Project	ENCORE2	ENCORE2
Note
ID	14258	14259

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV48-83	BGKcLV48-84
Sample #	21	22
Sample Name	ZFC3H1-BGKcLV48-83	ZFC3H1-BGKcLV48-84
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-18	2025-08-18
Lib_ID	Lib-250818	Lib-250818
Tecan_Location
Tecan
Tecan_date
Size_bp	265	256
Peak_Molarity	91.80	84.30
libSampleQC_DNA_Well	DNA_Library_set79/set1/E3.png	DNA_Library_set79/set1/F3.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set79/set1/E12.png	RNA_Library_set79/set1/F12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-08-19	2025-08-19
Sample_ID	BGKcLV48-83	BGKcLV48-84
RBP	ZFC3H1	ZFC3H1
Batch_ID	BGKcLV48	BGKcLV48
WB_result	86.000	90.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4766	4767

Sequencing Information

	BGKcLV48-83	BGKcLV48-84
Sample_ID	BGKcLV48-83	BGKcLV48-84
Sample Name	ZFC3H1-BGKcLV48-83	ZFC3H1-BGKcLV48-84
Pool ID	Pool-250822	Pool-250822
LocalServer_folder	set79	set79
total_reads	32,509,432	26,065,357
total_aligned_reads	28,516,294	22,407,294
unique_aligned_reads	26,434,685	20,728,140
percent_uniqueAligned	0.81314	0.79524
correlation_replicates	0.996722	0.996722
spikein_reads	86,066	60,534
percent_spikeins	0.00265	0.00232
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3469	3470

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
ZFC3H1-BGKcLV48-83_S185_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3469	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32840
ZFC3H1-BGKcLV48-83_S185_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3469	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32862
ZFC3H1-BGKcLV48-83_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3469					GRCh38	V40	ZFC3H1-BGKcLV48-83_S185_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZFC3H1-BGKcLV48-83_S185_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32884
ZFC3H1-BGKcLV48-83_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3469					GRCh38	V40	ZFC3H1-BGKcLV48-83_Aligned.sortedByCoord.out.bam		ENCORE2	32906
ZFC3H1-BGKcLV48-83_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3469					GRCh38	V40	ZFC3H1-BGKcLV48-83_Aligned.sortedByCoord.out.bam		ENCORE2	32928
ZFC3H1-BGKcLV48-83_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3469					GRCh38	V40	ZFC3H1-BGKcLV48-83_Aligned.sortedByCoord.out.bam		ENCORE2	32950
ZFC3H1-BGKcLV48-83_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3469					GRCh38	V40	ZFC3H1-BGKcLV48-83_Aligned.sortedByCoord.out.bam		ENCORE2	32972
ZFC3H1-BGKcLV48-84_S186_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3470	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32841
ZFC3H1-BGKcLV48-84_S186_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3470	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32863
ZFC3H1-BGKcLV48-84_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3470					GRCh38	V40	ZFC3H1-BGKcLV48-84_S186_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZFC3H1-BGKcLV48-84_S186_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32885
ZFC3H1-BGKcLV48-84_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3470					GRCh38	V40	ZFC3H1-BGKcLV48-84_Aligned.sortedByCoord.out.bam		ENCORE2	32907
ZFC3H1-BGKcLV48-84_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3470					GRCh38	V40	ZFC3H1-BGKcLV48-84_Aligned.sortedByCoord.out.bam		ENCORE2	32929
ZFC3H1-BGKcLV48-84_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3470					GRCh38	V40	ZFC3H1-BGKcLV48-84_Aligned.sortedByCoord.out.bam		ENCORE2	32951
ZFC3H1-BGKcLV48-84_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3470					GRCh38	V40	ZFC3H1-BGKcLV48-84_Aligned.sortedByCoord.out.bam		ENCORE2	32973