ZC3HAV1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-35	BG293LV06-36
idx	0	0
TRCN#_or_BGC#	TRCN0000004516	TRCN0000004516
shRNA_or_gRNA_sequence	CCGGCCGTGCCTATGTGGAATCTATCTCGAGATAGATTCCACATAGGCACGGTTTTT	CCGGCCGTGCCTATGTGGAATCTATCTCGAGATAGATTCCACATAGGCACGGTTTTT
PAM
Name	ZC3HAV1	ZC3HAV1
Sample_ID	BG293LV06-35	BG293LV06-36
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	ZC3HAV1	ZC3HAV1
qPCR_result	92.0	87.4
Ave_qPCR	89.7
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	12170	12171

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-35	BG293LV06-36
Sample_ID	BG293LV06-35	BG293LV06-36
Sample Name
Sample Name	ZC3HAV1-BG293LV06-35	ZC3HAV1-BG293LV06-36
RBP	ZC3HAV1	ZC3HAV1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13472	13473

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-35	BG293LV06-36
Sample #	39	40
Sample Name	ZC3HAV1-BG293LV06-35	ZC3HAV1-BG293LV06-36
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	270	281
Peak_Molarity	100.00	75.70
libSampleQC_DNA_Well	DNA_Library_set71/set1/G5.png	DNA_Library_set71/set1/H5.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/G5.png	RNA_Library_set71/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-35	BG293LV06-36
RBP	ZC3HAV1	ZC3HAV1
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4464	4465

Sequencing Information

	BG293LV06-35	BG293LV06-36
Sample_ID	BG293LV06-35	BG293LV06-36
Sample Name	ZC3HAV1-BG293LV06-35	ZC3HAV1-BG293LV06-36
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	37,457,522	39,610,518
total_aligned_reads	34,012,244	36,553,703
unique_aligned_reads	31,645,439	33,998,981
percent_uniqueAligned	0.84484	0.85833
correlation_replicates	0.970395	0.970395
spikein_reads	93,298	147,770
percent_spikeins	0.00249	0.00373
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3033	3034

Data Submission Information DCC submission information was not avaliable

File Information

Search:

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
ZC3HAV1-BG293LV06-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3033					GRCh38	V40	ZC3HAV1-BG293LV06-35_S39_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV06-35_S39_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29506
ZC3HAV1-BG293LV06-35_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3033					GRCh38	V40	ZC3HAV1-BG293LV06-35_S39_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV06-35_S39_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29762
ZC3HAV1-BG293LV06-35_S39_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3033	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29377
ZC3HAV1-BG293LV06-35_S39_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3033	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29441
ZC3HAV1-BG293LV06-35_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3033					GRCh38	V40	ZC3HAV1-BG293LV06-35_Aligned.sortedByCoord.out.bam		ENCORE2	29698
ZC3HAV1-BG293LV06-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3033					GRCh38	V40	ZC3HAV1-BG293LV06-35_Aligned.sortedByCoord.out.bam		ENCORE2	29634
ZC3HAV1-BG293LV06-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3033					GRCh38	V40	ZC3HAV1-BG293LV06-35_Aligned.sortedByCoord.out.bam		ENCORE2	29570
ZC3HAV1-BG293LV06-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3034					GRCh38	V40	ZC3HAV1-BG293LV06-36_S40_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV06-36_S40_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29507
ZC3HAV1-BG293LV06-36_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3034					GRCh38	V40	ZC3HAV1-BG293LV06-36_S40_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV06-36_S40_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29763
ZC3HAV1-BG293LV06-36_S40_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3034	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29378
ZC3HAV1-BG293LV06-36_S40_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3034	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29442
ZC3HAV1-BG293LV06-36_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3034					GRCh38	V40	ZC3HAV1-BG293LV06-36_Aligned.sortedByCoord.out.bam		ENCORE2	29699
ZC3HAV1-BG293LV06-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3034					GRCh38	V40	ZC3HAV1-BG293LV06-36_Aligned.sortedByCoord.out.bam		ENCORE2	29635
ZC3HAV1-BG293LV06-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3034					GRCh38	V40	ZC3HAV1-BG293LV06-36_Aligned.sortedByCoord.out.bam		ENCORE2	29571

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