PPP1CA RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV05-11	BG293LV05-12
idx	0	0
TRCN#_or_BGC#	TRCN0000002453	TRCN0000002453
shRNA_or_gRNA_sequence	CCGGACTACGACCTTCTGCGACTATCTCGAGATAGTCGCAGAAGGTCGTAGTTTTTT	CCGGACTACGACCTTCTGCGACTATCTCGAGATAGTCGCAGAAGGTCGTAGTTTTTT
PAM
Name	PPP1CA	PPP1CA
Sample_ID	BG293LV05-11	BG293LV05-12
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	PPP1CA	PPP1CA
qPCR_result	92	93.9
Ave_qPCR	92.95
RT-qPCR_primer-F	ccatgatgagtgtggacgag
RT-qPCR_primer-R	ccactgaactgcccgtactt
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	12031	12032

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-11	BG293LV05-12
Sample_ID	BG293LV05-11	BG293LV05-12
Sample Name
Sample Name	PPP1CA-BG293LV05-11	PPP1CA-BG293LV05-12
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	12840	12841

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-11	BG293LV05-12
Sample #	7	8
Sample Name	PPP1CA-BG293LV05-11	PPP1CA-BG293LV05-12
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	265	284
Peak_Molarity	12.00	43.00
libSampleQC_DNA_Well	DNA_Library_set69/set1/G1.png	DNA_Library_set69/set1/H1.png
RIN	9.6	9.9
libSample_RNA_Well	RNA_Library_set69/set1/G6.png	RNA_Library_set69/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-11	BG293LV05-12
RBP	PPP1CA	PPP1CA
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4188	4189

Sequencing Information

	BG293LV05-11	BG293LV05-12
Sample_ID	BG293LV05-11	BG293LV05-12
Sample Name	PPP1CA-BG293LV05-11	PPP1CA-BG293LV05-12
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	25,224,873	26,944,239
total_aligned_reads	20,543,711	22,969,016
unique_aligned_reads	18,751,365	21,139,299
percent_uniqueAligned	0.74337	0.78456
correlation_replicates	0.987349	0.987349
spikein_reads	7,814	9,624
percent_spikeins	0.00031	0.00036
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2907	2908

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-BG293LV05-11_S139_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2907	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28515
PPP1CA-BG293LV05-11_S139_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2907	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28559
PPP1CA-BG293LV05-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11_S139_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV05-11_S139_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28603
PPP1CA-BG293LV05-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11/Aligned.sortedByCoord.out.bam		ENCORE2	28647
PPP1CA-BG293LV05-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11/Aligned.sortedByCoord.out.bam		ENCORE2	28691
PPP1CA-BG293LV05-11_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11/Aligned.sortedByCoord.out.bam		ENCORE2	28735
PPP1CA-BG293LV05-11_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11/Aligned.sortedByCoord.out.bam		ENCORE2	28779
PPP1CA-BG293LV05-11_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2907					GRCh38	V40	PPP1CA-BG293LV05-11_S139_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV05-11_S139_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28823
PPP1CA-BG293LV05-12_S140_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2908	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28516
PPP1CA-BG293LV05-12_S140_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2908	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28560
PPP1CA-BG293LV05-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12_S140_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV05-12_S140_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28604
PPP1CA-BG293LV05-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12/Aligned.sortedByCoord.out.bam		ENCORE2	28648
PPP1CA-BG293LV05-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12/Aligned.sortedByCoord.out.bam		ENCORE2	28692
PPP1CA-BG293LV05-12_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12/Aligned.sortedByCoord.out.bam		ENCORE2	28736
PPP1CA-BG293LV05-12_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12/Aligned.sortedByCoord.out.bam		ENCORE2	28780
PPP1CA-BG293LV05-12_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2908					GRCh38	V40	PPP1CA-BG293LV05-12_S140_L002_R1_001.filtered.trimmed.paired.fastq.gz,PPP1CA-BG293LV05-12_S140_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28824