PPP1R8 RNA-Seq in K562

General Information


RBP	PPP1R8
Cell_Line	K562
Method	shRNA
Exp_Name	PPP1R8-BGKLV28-K562
ENCODE_series_ID	ENCSR383HIT
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR844QNT
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	PPP1R8_BGKLV28-41
Rep2	PPP1R8_BGKLV28-42
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	58.2
Rep2_qPCR	61.0
Rep1_WB	43.2
Rep2_WB	57.4
Antibody Cat#	RN068PW
Antibody Lot#	RN068PW
Antibody DCC ID	ENCAB563YNZ
Status	Released
Project	ENCODE3
ID	653

Experiment Information (Status: Released)

	BGKLV28-41	BGKLV28-42
idx	510	511
TRCN#_or_BGC#	TRCN0000002472	TRCN0000002472
shRNA_or_gRNA_sequence	TGAAGCTGTAAATGAACCCAA	TGAAGCTGTAAATGAACCCAA
PAM
Name	PPP1R8_72	PPP1R8_72
Sample_ID	BGKLV28-41	BGKLV28-42
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	PPP1R8	PPP1R8
qPCR_result	58.2	61.0
Ave_qPCR	59.6
RT-qPCR_primer-F	ggatgtggatccctcagttg
RT-qPCR_primer-R	ctccacacgcttcttcttga
protein_conc	2986	3238
WB_result	43.2	57.4
Ave_WB	50.3
WB_DONE_date	7/27/2015
MW	38kDa
IP	1	1
antibody_Cat#	RN068PW	RN068PW
Antibody DCC ID	ENCAB563YNZ	ENCAB563YNZ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	585	586

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PPP1R8	Product_ID: RN068PW Lot_ID: 1 Source: MBLI Target Name: PPP1R8-human

Experiment Status

	BGKLV28-41	BGKLV28-42
Sample_ID	BGKLV28-41	BGKLV28-42
Sample Name	PPP1R8_BGKLV28-41	PPP1R8_BGKLV28-42
Sample Name	PPP1R8_BGKLV28-41	PPP1R8_BGKLV28-42
RBP	PPP1R8	PPP1R8
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	992	993

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-41	BGKLV28-42
Sample #
Sample Name	PPP1R8-BGKLV28-41	PPP1R8-BGKLV28-42
Sample_Name_Alias	PPP1R8_BGKLV28-41	PPP1R8_BGKLV28-42
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E2.png	DNA_Library_LV28-29-30/set1/F2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A8.png	RNA_Library_LV26-27-28-29/set1/B8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-41	BGKLV28-42
RBP	PPP1R8	PPP1R8
Batch_ID	BGKLV28	BGKLV28
WB_result	43.200	57.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2684	2685

Sequencing Information

	BGKLV28-41	BGKLV28-42
Sample_ID	BGKLV28-41	BGKLV28-42
Sample Name	PPP1R8_BGKLV28-41	PPP1R8_BGKLV28-42
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	92,482,602	72,716,794
total_aligned_reads	80,577,308	62,547,672
unique_aligned_reads	73,523,862	57,141,228
percent_uniqueAligned	0.79500	0.78581
correlation_replicates	0.995618	0.995618
spikein_reads	306,978	205,226
percent_spikeins	0.00332	0.00282
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1326	1327

Data Submission Information

	BGKLV28-41	BGKLV28-41
ENCODE_alias	brenton-graveley:PPP1R8_BGKLV28	brenton-graveley:PPP1R8-BGKLV28-K562
ENCODE_accession	ENCSR844QNT	ENCSR383HIT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-41	BGKLV28-41
Sample Name	PPP1R8_BGKLV28-41	PPP1R8_BGKLV28-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3045	6866

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
PPP1R8_BGKLV28-41_AGTCAA_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1326	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20170
PPP1R8_BGKLV28-41_AGTCAA_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1326	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20202
PPP1R8_BGKLV28-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41_AGTCAA_L002_001.R1.fastq.gz,PPP1R8_BGKLV28-41_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	20234
PPP1R8_BGKLV28-41_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41/Aligned.sortedByCoord.out.bam		ENCORE2	20266
PPP1R8_BGKLV28-41_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41/Aligned.sortedByCoord.out.bam		ENCORE2	20298
PPP1R8_BGKLV28-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41/Aligned.sortedByCoord.out.bam		ENCORE2	20330
PPP1R8_BGKLV28-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41/Aligned.sortedByCoord.out.bam		ENCORE2	20362
PPP1R8_BGKLV28-41_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1326					GRCh38	V40	PPP1R8_BGKLV28-41_AGTCAA_L002_001.R1.fastq.gz,PPP1R8_BGKLV28-41_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	20394
PPP1R8_BGKLV28-42_AGTTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1327	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20171
PPP1R8_BGKLV28-42_AGTTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1327	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20203
PPP1R8_BGKLV28-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42_AGTTCC_L002_001.R1.fastq.gz,PPP1R8_BGKLV28-42_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	20235
PPP1R8_BGKLV28-42_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42/Aligned.sortedByCoord.out.bam		ENCORE2	20267
PPP1R8_BGKLV28-42_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42/Aligned.sortedByCoord.out.bam		ENCORE2	20299
PPP1R8_BGKLV28-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42/Aligned.sortedByCoord.out.bam		ENCORE2	20331
PPP1R8_BGKLV28-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42/Aligned.sortedByCoord.out.bam		ENCORE2	20363
PPP1R8_BGKLV28-42_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1327					GRCh38	V40	PPP1R8_BGKLV28-42_AGTTCC_L002_001.R1.fastq.gz,PPP1R8_BGKLV28-42_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	20395