PTGES3 RNA-Seq in HepG2

General Information


RBP	PTGES3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PTGES3-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR037EPO
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR528LDT
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	PTGES3-BGHcLV16-45
Rep2	PTGES3-BGHcLV16-46
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	42.9
Rep2_qPCR	59.5
Rep1_WB	62.8
Rep2_WB	70.6
Antibody Cat#	MA3-414
Antibody Lot#	SH2575558
Antibody DCC ID	ENCAB371NVC
Status	Released
Project	ENCODE4
ID	155

Experiment Information (Status: Released)

	BGHcLV16-45	BGHcLV16-46
idx	475	476
TRCN#_or_BGC#	BGC#0000385	BGC#0000385
shRNA_or_gRNA_sequence	ATTTTATACAGTTGTCTCGG	ATTTTATACAGTTGTCTCGG
PAM	agg	agg
Name	PTGES3_89	PTGES3_89
Sample_ID	BGHcLV16-45	BGHcLV16-46
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	PTGES3	PTGES3
qPCR_result	42.9	59.5
Ave_qPCR	51.2
RT-qPCR_primer-F	AAAGGAGAATCTGGCCAGTCA
RT-qPCR_primer-R	ATCATCTTCCCAGTCTTTCCAAT
protein_conc	2253	2261
WB_result	62.8	70.6
Ave_WB	66.7
WB_DONE_date	4/24/19
MW	23KD
IP	Mouse / Ig
antibody_Cat#	MA3-414
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	146	0
Rep2_TPM	265	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6624	6625

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PTGES3	Product_ID: MA3-414 Lot_ID: SH2575558 Source: Thermo Fisher Target Name: PTGES3-human

Experiment Status

	BGHcLV16-45	BGHcLV16-46
Sample_ID	BGHcLV16-45	BGHcLV16-46
Sample Name
Sample Name	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-46
RBP	PTGES3	PTGES3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5429	5430

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-45	BGHcLV16-46
Sample #	63	64
Sample Name	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-46
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-E1	2-F1
Tecan	37.97	33.15
Tecan_date	2019-12-10	2019-12-10
Size_bp	275	282
Peak_Molarity	34.80	34.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E3.png	DNA_Library_set43-44/set2/F3.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set43-44/set1/E8.png	RNA_Library_set43-44/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-45	BGHcLV16-46
RBP	PTGES3	PTGES3
Batch_ID	BGHcLV16	BGHcLV16
WB_result	62.800	70.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	639	640

Sequencing Information

	BGHcLV16-45	BGHcLV16-46
Sample_ID	BGHcLV16-45	BGHcLV16-46
Sample Name	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-46
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	122,985,574	130,921,860
total_aligned_reads	113,091,944	119,869,464
unique_aligned_reads	105,890,258	112,237,044
percent_uniqueAligned	0.86100	0.85728
correlation_replicates	0.998025	0.998025
spikein_reads	134,730	158,810
percent_spikeins	0.00110	0.00121
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	141	142

Data Submission Information

	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-46	BGHcLV16-46	BGHcLV16-46	BGHcLV16-46
ENCODE_alias	brenton-graveley:PTGES3-BGHcLV16	brenton-graveley:PTGES3-BGHcLV16-45	brenton-graveley:L-PTGES3-BGHcLV16-45	brenton-graveley:PTGES3-BGHcLV16-45_S59_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGHcLV16-45_S59_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGHcLV16-HepG2	brenton-graveley:PTGES3-BGHcLV16-46	brenton-graveley:L-PTGES3-BGHcLV16-46	brenton-graveley:PTGES3-BGHcLV16-46_S60_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGHcLV16-46_S60_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR528LDT	ENCBS686VBD	ENCLB781HVX	ENCFF223HNZ	ENCFF410AVA	ENCSR037EPO	ENCBS515RKO	ENCLB366WJG	ENCFF503ZFN	ENCFF959NTL
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	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-45	BGHcLV16-46	BGHcLV16-46	BGHcLV16-46	BGHcLV16-46
Sample Name	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-45	PTGES3-BGHcLV16-46	PTGES3-BGHcLV16-46	PTGES3-BGHcLV16-46	PTGES3-BGHcLV16-46
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
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		PTGES3-BGHcLV16-45.pdf	L-PTGES3-BGHcLV16-45.pdf				PTGES3-BGHcLV16-46.pdf	L-PTGES3-BGHcLV16-46.pdf
ID	11	104	268	434	466	7294	105	269	435	467

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
PTGES3-BGHcLV16-45_S59_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	141	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	21
PTGES3-BGHcLV16-45_S59_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	141	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	53
PTGES3-BGHcLV16-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45_S59_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGHcLV16-45_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24184
PTGES3-BGHcLV16-45_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45/Aligned.sortedByCoord.out.bam		ENCORE2	24216
PTGES3-BGHcLV16-45_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45/Aligned.sortedByCoord.out.bam		ENCORE2	24248
PTGES3-BGHcLV16-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45/Aligned.sortedByCoord.out.bam		ENCORE2	24280
PTGES3-BGHcLV16-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45/Aligned.sortedByCoord.out.bam		ENCORE2	24312
PTGES3-BGHcLV16-45_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	141					GRCh38	V40	PTGES3-BGHcLV16-45_S59_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGHcLV16-45_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24344
PTGES3-BGHcLV16-46_S60_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	142	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	22
PTGES3-BGHcLV16-46_S60_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	142	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	54
PTGES3-BGHcLV16-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46_S60_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGHcLV16-46_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24185
PTGES3-BGHcLV16-46_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46/Aligned.sortedByCoord.out.bam		ENCORE2	24217
PTGES3-BGHcLV16-46_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46/Aligned.sortedByCoord.out.bam		ENCORE2	24249
PTGES3-BGHcLV16-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46/Aligned.sortedByCoord.out.bam		ENCORE2	24281
PTGES3-BGHcLV16-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46/Aligned.sortedByCoord.out.bam		ENCORE2	24313
PTGES3-BGHcLV16-46_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	142					GRCh38	V40	PTGES3-BGHcLV16-46_S60_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGHcLV16-46_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24345