ZNF335 RNA-Seq in HepG2

General Information


RBP	ZNF335
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ZNF335-BGHcLV50-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV50
Pool ID	Pool-251003
Local_Set_Name	set80
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ZNF335-BGHcLV50-113
Rep2	ZNF335-BGHcLV50-114
CN1	NT-BGHcLV50-1
CN2	NT-BGHcLV50-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	63.2
Rep2_WB	59.7803
Antibody Cat#	PA5-67158
Antibody Lot#	lot# UC2731469A
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1694

Experiment Information (Status: Submitting)

	BGHcLV50-113	BGHcLV50-114
idx	1936	1937
TRCN#_or_BGC#	BGC#0001444	BGC#0001444
shRNA_or_gRNA_sequence	GTGGGGCAAAGCTCGGACCG	GTGGGGCAAAGCTCGGACCG
PAM	CGG	CGG
Name	ZNF335_90	ZNF335_90
Sample_ID	BGHcLV50-113	BGHcLV50-114
transduction_Date	7/29/25	7/29/25
days	D6	D6
RBP_name	ZNF335	ZNF335
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	AGCTGAAGCAGCAGCACAGT
RT-qPCR_primer-R	GGAGCCTCAGATGACTGGAA
protein_conc	3059	2894
WB_result	63.2	59.7803
Ave_WB
WB_DONE_date	8/28/25
MW	145KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-67158	lot# UC2731469A
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	10125	10126

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-113	BGHcLV50-114
Sample_ID	BGHcLV50-113	BGHcLV50-114
Sample Name
Sample Name	ZNF335-BGHcLV50-113	ZNF335-BGHcLV50-114
RBP	ZNF335	ZNF335
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14470	14471

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-113	BGHcLV50-114
Sample #	23	24
Sample Name	ZNF335-BGHcLV50-113	ZNF335-BGHcLV50-114
Sample_Name_Alias
Index Well Position	G12	H12
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	281	282
Peak_Molarity	69.50	54.60
libSampleQC_DNA_Well	DNA_Library_set80/set1/G12.png	DNA_Library_set80/set1/H12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set80/set1/G9.png	RNA_Library_set80/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-113	BGHcLV50-114
RBP	ZNF335	ZNF335
Batch_ID	BGHcLV50	BGHcLV50
WB_result	63.200	59.780
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4838	4839

Sequencing Information

	BGHcLV50-113	BGHcLV50-114
Sample_ID	BGHcLV50-113	BGHcLV50-114
Sample Name	ZNF335-BGHcLV50-113	ZNF335-BGHcLV50-114
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	18,417,695	19,038,343
total_aligned_reads	16,381,328	15,925,572
unique_aligned_reads	15,483,572	15,036,537
percent_uniqueAligned	0.84069	0.78980
correlation_replicates	0.992255	0.992255
spikein_reads	86,066	60,534
percent_spikeins	0.00467	0.00318
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3493	3494

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
ZNF335-BGHcLV50-113_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3493	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	32996
ZNF335-BGHcLV50-113_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3493	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	33020
ZNF335-BGHcLV50-113_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3493					GRCh38	V40	ZNF335-BGHcLV50-113_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGHcLV50-113_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33044
ZNF335-BGHcLV50-113_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	3493					GRCh38	V40	ZNF335-BGHcLV50-113_Aligned.sortedByCoord.out.bam		ENCORE2	33068
ZNF335-BGHcLV50-113_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	3493					GRCh38	V40	ZNF335-BGHcLV50-113_Aligned.sortedByCoord.out.bam		ENCORE2	33092
ZNF335-BGHcLV50-113_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	3493					GRCh38	V40	ZNF335-BGHcLV50-113_Aligned.sortedByCoord.out.bam		ENCORE2	33116
ZNF335-BGHcLV50-113_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	3493					GRCh38	V40	ZNF335-BGHcLV50-113_Aligned.sortedByCoord.out.bam		ENCORE2	33140
ZNF335-BGHcLV50-113_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3493					GRCh38	V40	ZNF335-BGHcLV50-113_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGHcLV50-113_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33164
ZNF335-BGHcLV50-114_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3494	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	32997
ZNF335-BGHcLV50-114_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3494	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	33021
ZNF335-BGHcLV50-114_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3494					GRCh38	V40	ZNF335-BGHcLV50-114_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGHcLV50-114_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33045
ZNF335-BGHcLV50-114_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	3494					GRCh38	V40	ZNF335-BGHcLV50-114_Aligned.sortedByCoord.out.bam		ENCORE2	33069
ZNF335-BGHcLV50-114_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	3494					GRCh38	V40	ZNF335-BGHcLV50-114_Aligned.sortedByCoord.out.bam		ENCORE2	33093
ZNF335-BGHcLV50-114_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	3494					GRCh38	V40	ZNF335-BGHcLV50-114_Aligned.sortedByCoord.out.bam		ENCORE2	33117
ZNF335-BGHcLV50-114_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	3494					GRCh38	V40	ZNF335-BGHcLV50-114_Aligned.sortedByCoord.out.bam		ENCORE2	33141
ZNF335-BGHcLV50-114_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3494					GRCh38	V40	ZNF335-BGHcLV50-114_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGHcLV50-114_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33165