PPP1R10 RNA-Seq in K562

General Information


RBP	PPP1R10
Cell_Line	K562
Method	CRISPR
Exp_Name	PPP1R10-BGKcLV17-K562
ENCODE_series_ID	ENCSR820HUT
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR439CUH
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	PPP1R10-BGKcLV17-37
Rep2	PPP1R10-BGKcLV17-38
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	66.9
Rep2_WB	70.4
Antibody Cat#	RN067PW
Antibody Lot#	lot #001
Antibody DCC ID	ENCAB400PQW
Status	Released
Project	ENCODE4
ID	91

Experiment Information (Status: Released)

	BGKcLV17-37	BGKcLV17-38
idx	644	645
TRCN#_or_BGC#	BGC#0000418	BGC#0000418
shRNA_or_gRNA_sequence	AGAGCTGGAGACACCATCCT	AGAGCTGGAGACACCATCCT
PAM	TGG	TGG
Name	PPP1R10_2	PPP1R10_2
Sample_ID	BGKcLV17-37	BGKcLV17-38
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	PPP1R10	PPP1R10
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GCTGCAAGTGGTTCAAGTGG
RT-qPCR_primer-R	TAGGGCTGAGGATCATGGAG
protein_conc	4704	4070
WB_result	66.9	70.4
Ave_WB	68.6
WB_DONE_date	7/23/19
MW	99KD
IP	Rabbit / I
antibody_Cat#	RN067PW	lot #001
Antibody DCC ID	ENCAB400PQW
submitted_to_DCC_date
Rep1_TPM	3.6	0
Rep2_TPM	4.7	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4762	4763

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PPP1R10	Product_ID: RN067PW Lot_ID: 1 Source: MBLI Target Name: PPP1R10-human

Experiment Status

	BGKcLV17-37	BGKcLV17-38
Sample_ID	BGKcLV17-37	BGKcLV17-38
Sample Name
Sample Name	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-38
RBP	PPP1R10	PPP1R10
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5515	5516

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-37	BGKcLV17-38
Sample #	105	106
Sample Name	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-38
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-E1	2-F1
Tecan	25.05	18.21
Tecan_date	2019-12-16	2019-12-16
Size_bp	274	283
Peak_Molarity	22.80	22.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E9.png	DNA_Library_set43-44/set1/F9.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/E4.png	RNA_Library_set43-44/set4/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-37	BGKcLV17-38
RBP	PPP1R10	PPP1R10
Batch_ID	BGKcLV17	BGKcLV17
WB_result	66.900	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	681	682

Sequencing Information

	BGKcLV17-37	BGKcLV17-38
Sample_ID	BGKcLV17-37	BGKcLV17-38
Sample Name	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-38
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	428,105,432	380,795,066
total_aligned_reads	397,551,208	278,257,174
unique_aligned_reads	359,038,874	250,909,096
percent_uniqueAligned	0.83867	0.65891
correlation_replicates	0.995991	0.995991
spikein_reads	123,070	106,594
percent_spikeins	0.00029	0.00028
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	187	188

Data Submission Information

	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-38	BGKcLV17-38	BGKcLV17-38	BGKcLV17-38
ENCODE_alias	brenton-graveley:PPP1R10-BGKcLV17	brenton-graveley:PPP1R10-BGKcLV17-37	brenton-graveley:L-PPP1R10-BGKcLV17-37	brenton-graveley:PPP1R10-BGKcLV17-37_S15_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGKcLV17-37_S15_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGKcLV17-K562	brenton-graveley:PPP1R10-BGKcLV17-38	brenton-graveley:L-PPP1R10-BGKcLV17-38	brenton-graveley:PPP1R10-BGKcLV17-38_S16_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGKcLV17-38_S16_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR439CUH	ENCBS599LWW	ENCLB661BPM	ENCFF170AUJ	ENCFF614FIP	ENCSR820HUT	ENCBS050HZB	ENCLB239NUK	ENCFF272RMQ	ENCFF533ZMK
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-37	BGKcLV17-38	BGKcLV17-38	BGKcLV17-38	BGKcLV17-38
Sample Name	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-37	PPP1R10-BGKcLV17-38	PPP1R10-BGKcLV17-38	PPP1R10-BGKcLV17-38	PPP1R10-BGKcLV17-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		PPP1R10-BGKcLV17-37.pdf	L-PPP1R10-BGKcLV17-37.pdf				PPP1R10-BGKcLV17-38.pdf	L-PPP1R10-BGKcLV17-38.pdf
ID	77	234	400	702	732	7285	235	401	703	733

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
PPP1R10-BGKcLV17-37_S15_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	187	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	289
PPP1R10-BGKcLV17-37_S15_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	187	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	319
PPP1R10-BGKcLV17-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37_S15_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGKcLV17-37_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24685
PPP1R10-BGKcLV17-37_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37/Aligned.sortedByCoord.out.bam		ENCORE2	24715
PPP1R10-BGKcLV17-37_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37/Aligned.sortedByCoord.out.bam		ENCORE2	24745
PPP1R10-BGKcLV17-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37/Aligned.sortedByCoord.out.bam		ENCORE2	24775
PPP1R10-BGKcLV17-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37/Aligned.sortedByCoord.out.bam		ENCORE2	24805
PPP1R10-BGKcLV17-37_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	187					GRCh38	V40	PPP1R10-BGKcLV17-37_S15_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGKcLV17-37_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24835
PPP1R10-BGKcLV17-38_S16_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	188	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	290
PPP1R10-BGKcLV17-38_S16_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	188	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	320
PPP1R10-BGKcLV17-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38_S16_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGKcLV17-38_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24686
PPP1R10-BGKcLV17-38_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38/Aligned.sortedByCoord.out.bam		ENCORE2	24716
PPP1R10-BGKcLV17-38_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38/Aligned.sortedByCoord.out.bam		ENCORE2	24746
PPP1R10-BGKcLV17-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38/Aligned.sortedByCoord.out.bam		ENCORE2	24776
PPP1R10-BGKcLV17-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38/Aligned.sortedByCoord.out.bam		ENCORE2	24806
PPP1R10-BGKcLV17-38_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	188					GRCh38	V40	PPP1R10-BGKcLV17-38_S16_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGKcLV17-38_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24836