ZCRB1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-55	BGRSLV05-56
idx	0	0
TRCN#_or_BGC#	TRCN0000167342	TRCN0000167342
shRNA_or_gRNA_sequence	CCGGCAATGACTTGTACCGGATATTCTCGAGAATATCCGGTACAAGTCATTGTTTTTTG	CCGGCAATGACTTGTACCGGATATTCTCGAGAATATCCGGTACAAGTCATTGTTTTTTG
PAM
Name	ZCRB1	ZCRB1
Sample_ID	BGRSLV05-55	BGRSLV05-56
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	ZCRB1	ZCRB1
qPCR_result	89.7	90.5
Ave_qPCR	90.1
RT-qPCR_primer-F	gagaacgtgagcctccaaag
RT-qPCR_primer-R	ggatcctccccttcatcttc
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	8508	8509

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-55	BGRSLV05-56
Sample_ID	BGRSLV05-55	BGRSLV05-56
Sample Name
Sample Name	ZCRB1-BGRSLV05-55	ZCRB1-BGRSLV05-56
RBP	ZCRB1	ZCRB1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11626	11627

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-55	BGRSLV05-56
Sample #	59	60
Sample Name	ZCRB1-BGRSLV05-55	ZCRB1-BGRSLV05-56
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	287	276
Peak_Molarity	98.50	98.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G8.png	DNA_Library_set60-62/set1/H8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/C8.png	RNA_Library_set60-62/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-55	BGRSLV05-56
RBP	ZCRB1	ZCRB1
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3646	3647

Sequencing Information

	BGRSLV05-55	BGRSLV05-56
Sample_ID	BGRSLV05-55	BGRSLV05-56
Sample Name	ZCRB1-BGRSLV05-55	ZCRB1-BGRSLV05-56
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	27,910,969	23,974,191
total_aligned_reads	23,353,668	20,109,837
unique_aligned_reads	21,879,861	18,907,527
percent_uniqueAligned	0.78392	0.78866
correlation_replicates	0.997853	0.997853
spikein_reads	44,106	33,342
percent_spikeins	0.00158	0.00139
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2517	2518

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
ZCRB1-BGRSLV05-55_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2517	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8618
ZCRB1-BGRSLV05-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCRB1-BGRSLV05-55_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10483
ZCRB1-BGRSLV05-55_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55/Aligned.sortedByCoord.out.bam		ENCORE2	10535
ZCRB1-BGRSLV05-55_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55/Aligned.sortedByCoord.out.bam		ENCORE2	10587
ZCRB1-BGRSLV05-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55/Aligned.sortedByCoord.out.bam		ENCORE2	10639
ZCRB1-BGRSLV05-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55/Aligned.sortedByCoord.out.bam		ENCORE2	10691
ZCRB1-BGRSLV05-55_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2517					GRCh38	V40	ZCRB1-BGRSLV05-55_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCRB1-BGRSLV05-55_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10743
ZCRB1-BGRSLV05-55_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2517	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28885
ZCRB1-BGRSLV05-56_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2518	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8619
ZCRB1-BGRSLV05-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCRB1-BGRSLV05-56_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10484
ZCRB1-BGRSLV05-56_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56/Aligned.sortedByCoord.out.bam		ENCORE2	10536
ZCRB1-BGRSLV05-56_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56/Aligned.sortedByCoord.out.bam		ENCORE2	10588
ZCRB1-BGRSLV05-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56/Aligned.sortedByCoord.out.bam		ENCORE2	10640
ZCRB1-BGRSLV05-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56/Aligned.sortedByCoord.out.bam		ENCORE2	10692
ZCRB1-BGRSLV05-56_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2518					GRCh38	V40	ZCRB1-BGRSLV05-56_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCRB1-BGRSLV05-56_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10744
ZCRB1-BGRSLV05-56_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2518	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28886