PPP1R8 RNA-Seq in HepG2

General Information


RBP	PPP1R8
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PPP1R8-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR538YZF
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR592AQT
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	PPP1R8-BGHcLV12-63
Rep2	PPP1R8-BGHcLV12-64
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	44.4
Rep2_qPCR	48.6
Rep1_WB	74.3
Rep2_WB	67.6
Antibody Cat#	RN068PW
Antibody Lot#
Antibody DCC ID	ENCAB563YNZ
Status	Released
Project	ENCODE4
ID	185

Experiment Information (Status: Released)

	BGHcLV12-63	BGHcLV12-63	BGHcLV12-64	BGHcLV12-64
idx	323	323	324	324
TRCN#_or_BGC#	BGC#0000206	BGC#0000206	BGC#0000206	BGC#0000206
shRNA_or_gRNA_sequence	GGGTAGAAATCCGCTTGTTG	GGGTAGAAATCCGCTTGTTG	GGGTAGAAATCCGCTTGTTG	GGGTAGAAATCCGCTTGTTG
PAM	TGG	TGG	TGG	TGG
Name	PPP1R8-84F	PPP1R8-84F	PPP1R8-84F	PPP1R8-84F
Sample_ID	BGHcLV12-63	BGHcLV12-63	BGHcLV12-64	BGHcLV12-64
transduction_Date	8/17/18	8/17/18	8/17/18	8/17/18
days	D6	D6	D6	D6
RBP_name	PPP1R8	PPP1R8	PPP1R8	PPP1R8
qPCR_result	44.4	44.4	48.6	48.6
Ave_qPCR	46.5	46.5
RT-qPCR_primer-F	ggatgtggatccctcagttg	ggatgtggatccctcagttg
RT-qPCR_primer-R	ctccacacgcttcttcttga	ctccacacgcttcttcttga
protein_conc	5825	5825	6063	6063
WB_result	74.3	77.5	67.6	82.2
Ave_WB	70.9	79.8
WB_DONE_date	2/19/19	6/13/19		Question
MW	38kda	38kda
IP
antibody_Cat#	RN068PW	RN068PW
Antibody DCC ID	ENCAB563YNZ
submitted_to_DCC_date	2/22/19
Rep1_TPM	71	71	0	0
Rep2_TPM	55	55	0	0
Action	Ready	Question	Ready	Question
Library_start_date	03/13/19		03/13/19
repeat_library
Note
ID	6466	6468	6467	6469

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

	BGHcLV12-63	BGHcLV12-64
Sample_ID	BGHcLV12-63	BGHcLV12-64
Sample Name	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-64
Sample Name	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-64
RBP	PPP1R8	PPP1R8
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2811	2812

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-63	BGHcLV12-64
Sample #	41	42
Sample Name	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-64
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-A2	3-B2
Tecan	39.17	35.97
Tecan_date	2019-03-13	2019-03-13
Size_bp	324	305
Peak_Molarity	60.30	138.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/A6.png	DNA_Library_set42/set1/B6.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_set42/set1/A6.png	RNA_Library_set42/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-63	BGHcLV12-64
RBP	PPP1R8	PPP1R8
Batch_ID	BGHcLV12	BGHcLV12
WB_result	74.300	67.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	41	42

Sequencing Information

	BGHcLV12-63	BGHcLV12-64
Sample_ID	BGHcLV12-63	BGHcLV12-64
Sample Name	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-64
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	47,141,076	107,176,946
total_aligned_reads	45,437,058	102,986,374
unique_aligned_reads	42,744,766	96,795,740
percent_uniqueAligned	0.90674	0.90314
correlation_replicates	0.967833	0.967833
spikein_reads	43,406	68,892
percent_spikeins	0.00092	0.00064
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	57	58

Data Submission Information

	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-64	BGHcLV12-64	BGHcLV12-64	BGHcLV12-64
ENCODE_alias	brenton-graveley:PPP1R8-BGHcLV12	brenton-graveley:PPP1R8-BGHcLV12-63	brenton-graveley:L-PPP1R8-BGHcLV12-63	brenton-graveley:PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R8-BGHcLV12-HepG2	brenton-graveley:PPP1R8-BGHcLV12-64	brenton-graveley:L-PPP1R8-BGHcLV12-64	brenton-graveley:PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR592AQT	ENCBS888XEO	ENCLB635ROV	ENCFF463WZI	ENCFF210IRQ	ENCSR538YZF	ENCBS866IEI	ENCLB145NRG	ENCFF793JWZ	ENCFF278KVJ
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	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-63	BGHcLV12-64	BGHcLV12-64	BGHcLV12-64	BGHcLV12-64
Sample Name	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-63	PPP1R8-BGHcLV12-64	PPP1R8-BGHcLV12-64	PPP1R8-BGHcLV12-64	PPP1R8-BGHcLV12-64
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		PPP1R8-BGHcLV12-63.pdf	L-PPP1R8-BGHcLV12-63.pdf				PPP1R8-BGHcLV12-64.pdf	L-PPP1R8-BGHcLV12-64.pdf
ID	752	799	881	1007	1089	7286	800	882	1008	1090

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-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	57	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	389
PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	57	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	471
PPP1R8-BGHcLV12-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23728
PPP1R8-BGHcLV12-63_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63/Aligned.sortedByCoord.out.bam		ENCORE2	23810
PPP1R8-BGHcLV12-63_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63/Aligned.sortedByCoord.out.bam		ENCORE2	23892
PPP1R8-BGHcLV12-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63/Aligned.sortedByCoord.out.bam		ENCORE2	23974
PPP1R8-BGHcLV12-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63/Aligned.sortedByCoord.out.bam		ENCORE2	24056
PPP1R8-BGHcLV12-63_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	57					GRCh38	V40	PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R8-BGHcLV12-63_ATATGGAT+CTGTATTA_HK3H2DSXX_S41_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24138
PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	58	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	390
PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	58	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	472
PPP1R8-BGHcLV12-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23729
PPP1R8-BGHcLV12-64_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64/Aligned.sortedByCoord.out.bam		ENCORE2	23811
PPP1R8-BGHcLV12-64_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64/Aligned.sortedByCoord.out.bam		ENCORE2	23893
PPP1R8-BGHcLV12-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64/Aligned.sortedByCoord.out.bam		ENCORE2	23975
PPP1R8-BGHcLV12-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64/Aligned.sortedByCoord.out.bam		ENCORE2	24057
PPP1R8-BGHcLV12-64_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	58					GRCh38	V40	PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R1_001.filtered.trimmed.paired.fastq.gz,PPP1R8-BGHcLV12-64_GCGCAAGC+TCACGCCG_HK3H2DSXX_S42_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24139