PPP1R10 RNA-Seq in HepG2

General Information


RBP	PPP1R10
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PPP1R10-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR936TZP
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR695RQF
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	PPP1R10-BGHcLV18-33
Rep2	PPP1R10-BGHcLV18-34
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	81.1
Rep2_WB	77.3
Antibody Cat#	RN067PW
Antibody Lot#	lot #001
Antibody DCC ID	ENCAB400PQW
Status	Released
Project	ENCODE4
ID	113

Experiment Information (Status: Released)

	BGHcLV18-33	BGHcLV18-34
idx	526	527
TRCN#_or_BGC#	BGC#0000418	BGC#0000418
shRNA_or_gRNA_sequence	AGAGCTGGAGACACCATCCT	AGAGCTGGAGACACCATCCT
PAM	TGG	TGG
Name	PPP1R10_2	PPP1R10_2
Sample_ID	BGHcLV18-33	BGHcLV18-34
transduction_Date	8/13/19	8/13/19
days	D6	D6
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	5068	5413
WB_result	81.1	77.3
Ave_WB	79.2
WB_DONE_date	8/26/19	wes
MW	99KD
IP	Rabbit / I
antibody_Cat#	RN067PW	lot #001
Antibody DCC ID	ENCAB400PQW
submitted_to_DCC_date
Rep1_TPM	17	0
Rep2_TPM	25	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6681	6682

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

	BGHcLV18-33	BGHcLV18-34
Sample_ID	BGHcLV18-33	BGHcLV18-34
Sample Name
Sample Name	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-34
RBP	PPP1R10	PPP1R10
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5643	5644

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-33	BGHcLV18-34
Sample #	149	150
Sample Name	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-34
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-A1	5-B1
Tecan	37.89	36.36
Tecan_date	2019-12-16	2019-12-16
Size_bp	272	280
Peak_Molarity	30.20	25.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C8.png	DNA_Library_set43-44/set2/D8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/G9.png	RNA_Library_set43-44/set4/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-33	BGHcLV18-34
RBP	PPP1R10	PPP1R10
Batch_ID	BGHcLV18	BGHcLV18
WB_result	81.100	77.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	725	726

Sequencing Information

	BGHcLV18-33	BGHcLV18-34
Sample_ID	BGHcLV18-33	BGHcLV18-34
Sample Name	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-34
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	175,655,642	160,385,352
total_aligned_reads	165,935,658	153,159,982
unique_aligned_reads	155,456,900	143,581,596
percent_uniqueAligned	0.88501	0.89523
correlation_replicates	0.998834	0.998834
spikein_reads	317,450	281,380
percent_spikeins	0.00181	0.00175
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	231	232

Data Submission Information

	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-34	BGHcLV18-34	BGHcLV18-34	BGHcLV18-34
ENCODE_alias	brenton-graveley:PPP1R10-BGHcLV18	brenton-graveley:PPP1R10-BGHcLV18-33	brenton-graveley:L-PPP1R10-BGHcLV18-33	brenton-graveley:PPP1R10-BGHcLV18-33_S61_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGHcLV18-33_S61_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGHcLV18-HepG2	brenton-graveley:PPP1R10-BGHcLV18-34	brenton-graveley:L-PPP1R10-BGHcLV18-34	brenton-graveley:PPP1R10-BGHcLV18-34_S62_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R10-BGHcLV18-34_S62_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR695RQF	ENCBS537VXF	ENCLB193JDP	ENCFF950ZOW	ENCFF273XUY	ENCSR936TZP	ENCBS611YBI	ENCLB224DHA	ENCFF486HNX	ENCFF514ODV
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	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-33	BGHcLV18-34	BGHcLV18-34	BGHcLV18-34	BGHcLV18-34
Sample Name	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-33	PPP1R10-BGHcLV18-34	PPP1R10-BGHcLV18-34	PPP1R10-BGHcLV18-34	PPP1R10-BGHcLV18-34
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		PPP1R10-BGHcLV18-33.pdf	L-PPP1R10-BGHcLV18-33.pdf				PPP1R10-BGHcLV18-34.pdf	L-PPP1R10-BGHcLV18-34.pdf
ID	60	200	366	616	668	7284	201	367	617	669

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-BGHcLV18-33_S61_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	231	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	203
PPP1R10-BGHcLV18-33_S61_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	231	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	255
PPP1R10-BGHcLV18-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33_S61_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGHcLV18-33_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24923
PPP1R10-BGHcLV18-33_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33/Aligned.sortedByCoord.out.bam		ENCORE2	24975
PPP1R10-BGHcLV18-33_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33/Aligned.sortedByCoord.out.bam		ENCORE2	25027
PPP1R10-BGHcLV18-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33/Aligned.sortedByCoord.out.bam		ENCORE2	25079
PPP1R10-BGHcLV18-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33/Aligned.sortedByCoord.out.bam		ENCORE2	25131
PPP1R10-BGHcLV18-33_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	231					GRCh38	V40	PPP1R10-BGHcLV18-33_S61_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGHcLV18-33_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25183
PPP1R10-BGHcLV18-34_S62_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	232	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	204
PPP1R10-BGHcLV18-34_S62_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	232	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	256
PPP1R10-BGHcLV18-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34_S62_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGHcLV18-34_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24924
PPP1R10-BGHcLV18-34_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34/Aligned.sortedByCoord.out.bam		ENCORE2	24976
PPP1R10-BGHcLV18-34_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34/Aligned.sortedByCoord.out.bam		ENCORE2	25028
PPP1R10-BGHcLV18-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34/Aligned.sortedByCoord.out.bam		ENCORE2	25080
PPP1R10-BGHcLV18-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34/Aligned.sortedByCoord.out.bam		ENCORE2	25132
PPP1R10-BGHcLV18-34_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	232					GRCh38	V40	PPP1R10-BGHcLV18-34_S62_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R10-BGHcLV18-34_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25184