ZC3HAV1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV03-31	BG293LV03-32
idx	0	0
TRCN#_or_BGC#	TRCN0000004516	TRCN0000004516
shRNA_or_gRNA_sequence	CCGGCCGTGCCTATGTGGAATCTATCTCGAGATAGATTCCACATAGGCACGGTTTTT	CCGGCCGTGCCTATGTGGAATCTATCTCGAGATAGATTCCACATAGGCACGGTTTTT
PAM
Name	ZC3HAV1	ZC3HAV1
Sample_ID	BG293LV03-31	BG293LV03-32
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	ZC3HAV1	ZC3HAV1
qPCR_result	91.2	90.4
Ave_qPCR	90.8
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	11929	11930

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-31	BG293LV03-32
Sample_ID	BG293LV03-31	BG293LV03-32
Sample Name
Sample Name	ZC3HAV1-BG293LV03-31	ZC3HAV1-BG293LV03-32
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	11750	11751

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-31	BG293LV03-32
Sample #	15	16
Sample Name	ZC3HAV1-BG293LV03-31	ZC3HAV1-BG293LV03-32
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	292	294
Peak_Molarity	62.80	59.60
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G2.png	DNA_Library_set60-62/set4/H2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/G2.png	RNA_Library_set60-62/set2/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-31	BG293LV03-32
RBP	ZC3HAV1	ZC3HAV1
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3698	3699

Sequencing Information

	BG293LV03-31	BG293LV03-32
Sample_ID	BG293LV03-31	BG293LV03-32
Sample Name	ZC3HAV1-BG293LV03-31	ZC3HAV1-BG293LV03-32
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	20,518,353	42,032,477
total_aligned_reads	13,499,964	32,881,149
unique_aligned_reads	12,658,022	30,791,481
percent_uniqueAligned	0.61691	0.73256
correlation_replicates	0.985012	0.985012
spikein_reads	19,908	55,534
percent_spikeins	0.00097	0.00132
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2569	2570

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
ZC3HAV1-BG293LV03-31_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2569	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7856
ZC3HAV1-BG293LV03-31_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2569	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7872
ZC3HAV1-BG293LV03-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV03-31_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10097
ZC3HAV1-BG293LV03-31_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31/Aligned.sortedByCoord.out.bam		ENCORE2	10113
ZC3HAV1-BG293LV03-31_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31/Aligned.sortedByCoord.out.bam		ENCORE2	10129
ZC3HAV1-BG293LV03-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31/Aligned.sortedByCoord.out.bam		ENCORE2	10145
ZC3HAV1-BG293LV03-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31/Aligned.sortedByCoord.out.bam		ENCORE2	10161
ZC3HAV1-BG293LV03-31_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2569					GRCh38	V40	ZC3HAV1-BG293LV03-31_S15_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV03-31_S15_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10177
ZC3HAV1-BG293LV03-32_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2570	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7857
ZC3HAV1-BG293LV03-32_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2570	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7873
ZC3HAV1-BG293LV03-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV03-32_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10098
ZC3HAV1-BG293LV03-32_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32/Aligned.sortedByCoord.out.bam		ENCORE2	10114
ZC3HAV1-BG293LV03-32_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32/Aligned.sortedByCoord.out.bam		ENCORE2	10130
ZC3HAV1-BG293LV03-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32/Aligned.sortedByCoord.out.bam		ENCORE2	10146
ZC3HAV1-BG293LV03-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32/Aligned.sortedByCoord.out.bam		ENCORE2	10162
ZC3HAV1-BG293LV03-32_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2570					GRCh38	V40	ZC3HAV1-BG293LV03-32_S16_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HAV1-BG293LV03-32_S16_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10178