PPP1CA RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-57	BG293LV06-58
idx	0	0
TRCN#_or_BGC#	TRCN0000002453	TRCN0000002453
shRNA_or_gRNA_sequence	CCGGACTACGACCTTCTGCGACTATCTCGAGATAGTCGCAGAAGGTCGTAGTTTTTT	CCGGACTACGACCTTCTGCGACTATCTCGAGATAGTCGCAGAAGGTCGTAGTTTTTT
PAM
Name	PPP1CA	PPP1CA
Sample_ID	BG293LV06-57	BG293LV06-58
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	PPP1CA	PPP1CA
qPCR_result	87.4	87.4
Ave_qPCR	87.4
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	12192	12193

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-57	BG293LV06-58
Sample_ID	BG293LV06-57	BG293LV06-58
Sample Name
Sample Name	PPP1CA-BG293LV06-57	PPP1CA-BG293LV06-58
RBP	PPP1CA	PPP1CA
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13494	13495

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-57	BG293LV06-58
Sample #	59	60
Sample Name	PPP1CA-BG293LV06-57	PPP1CA-BG293LV06-58
Sample_Name_Alias
Index Well Position	C08	D08
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	281	287
Peak_Molarity	110.00	91.40
libSampleQC_DNA_Well	DNA_Library_set71/set1/C8.png	DNA_Library_set71/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set71/set1/C8.png	RNA_Library_set71/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-57	BG293LV06-58
RBP	PPP1CA	PPP1CA
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	4484	4485

Sequencing Information

	BG293LV06-57	BG293LV06-58
Sample_ID	BG293LV06-57	BG293LV06-58
Sample Name	PPP1CA-BG293LV06-57	PPP1CA-BG293LV06-58
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	33,094,924	36,813,052
total_aligned_reads	30,199,341	33,464,484
unique_aligned_reads	28,299,335	31,344,077
percent_uniqueAligned	0.85510	0.85144
correlation_replicates	0.997047	0.997047
spikein_reads	81,720	79,758
percent_spikeins	0.00247	0.00217
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3053	3054

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
PPP1CA-BG293LV06-57_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3053	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	29353
PPP1CA-BG293LV06-57_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3053	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	29417
PPP1CA-BG293LV06-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3053					GRCh38	V40	PPP1CA-BG293LV06-57_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV06-57_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29482
PPP1CA-BG293LV06-57_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	3053					GRCh38	V40	PPP1CA-BG293LV06-57_Aligned.sortedByCoord.out.bam		ENCORE2	29546
PPP1CA-BG293LV06-57_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	3053					GRCh38	V40	PPP1CA-BG293LV06-57_Aligned.sortedByCoord.out.bam		ENCORE2	29610
PPP1CA-BG293LV06-57_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	3053					GRCh38	V40	PPP1CA-BG293LV06-57_Aligned.sortedByCoord.out.bam		ENCORE2	29674
PPP1CA-BG293LV06-57_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3053					GRCh38	V40	PPP1CA-BG293LV06-57_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV06-57_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29738
PPP1CA-BG293LV06-58_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3054	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	29354
PPP1CA-BG293LV06-58_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3054	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	29418
PPP1CA-BG293LV06-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3054					GRCh38	V40	PPP1CA-BG293LV06-58_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV06-58_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29483
PPP1CA-BG293LV06-58_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	3054					GRCh38	V40	PPP1CA-BG293LV06-58_Aligned.sortedByCoord.out.bam		ENCORE2	29547
PPP1CA-BG293LV06-58_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	3054					GRCh38	V40	PPP1CA-BG293LV06-58_Aligned.sortedByCoord.out.bam		ENCORE2	29611
PPP1CA-BG293LV06-58_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	3054					GRCh38	V40	PPP1CA-BG293LV06-58_Aligned.sortedByCoord.out.bam		ENCORE2	29675
PPP1CA-BG293LV06-58_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3054					GRCh38	V40	PPP1CA-BG293LV06-58_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV06-58_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29739