ZXDC RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-61	BGRSLV08-62
idx	0	0
TRCN#_or_BGC#	TRCN0000245357	TRCN0000245357
shRNA_or_gRNA_sequence	CCGGGCAGTCTGTACATTCACTCTACTCGAGTAGAGTGAATGTACAGACTGCTTTTTG	CCGGAGAAGTTCACTACGGTCTATACTCGAGTATAGACCGTAGTGAACTTCTTTTTTG
PAM
Name	ZXDC	ZXDC
Sample_ID	BGRSLV08-61	BGRSLV08-62
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZXDC	ZXDC
qPCR_result	83.4	80.1
Ave_qPCR	81.7
RT-qPCR_primer-F	acatggtcagacagcacagc
RT-qPCR_primer-R	tggcaggtgtgtcagagaag
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	8710	8711

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-61	BGRSLV08-62
Sample_ID	BGRSLV08-61	BGRSLV08-62
Sample Name
Sample Name	ZXDC-BGRSLV08-61	ZXDC-BGRSLV08-62
RBP	ZXDC	ZXDC
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	11794	11795

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-61	BGRSLV08-62
Sample #	59	60
Sample Name	ZXDC-BGRSLV08-61	ZXDC-BGRSLV08-62
Sample_Name_Alias
Index Well Position	C08	D08
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	286	290
Peak_Molarity	95.80	78.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C8.png	DNA_Library_set60-62/set4/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/C8.png	RNA_Library_set60-62/set2/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-61	BGRSLV08-62
RBP	ZXDC	ZXDC
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3742	3743

Sequencing Information

	BGRSLV08-61	BGRSLV08-62
Sample_ID	BGRSLV08-61	BGRSLV08-62
Sample Name	ZXDC-BGRSLV08-61	ZXDC-BGRSLV08-62
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	22,655,979	38,571,263
total_aligned_reads	19,698,649	31,805,699
unique_aligned_reads	18,502,552	29,891,998
percent_uniqueAligned	0.81667	0.77498
correlation_replicates	0.996397	0.996397
spikein_reads	21,916	24,812
percent_spikeins	0.00097	0.00064
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2613	2614

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
ZXDC-BGRSLV08-61_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2613	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7916
ZXDC-BGRSLV08-61_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2613	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7960
ZXDC-BGRSLV08-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZXDC-BGRSLV08-61_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10221
ZXDC-BGRSLV08-61_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	10265
ZXDC-BGRSLV08-61_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	10309
ZXDC-BGRSLV08-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	10353
ZXDC-BGRSLV08-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	10397
ZXDC-BGRSLV08-61_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2613					GRCh38	V40	ZXDC-BGRSLV08-61_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZXDC-BGRSLV08-61_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10441
ZXDC-BGRSLV08-62_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2614	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7917
ZXDC-BGRSLV08-62_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2614	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7961
ZXDC-BGRSLV08-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZXDC-BGRSLV08-62_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10222
ZXDC-BGRSLV08-62_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	10266
ZXDC-BGRSLV08-62_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	10310
ZXDC-BGRSLV08-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	10354
ZXDC-BGRSLV08-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	10398
ZXDC-BGRSLV08-62_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2614					GRCh38	V40	ZXDC-BGRSLV08-62_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZXDC-BGRSLV08-62_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10442