PTGES3 RNA-Seq in K562

General Information


RBP	PTGES3
Cell_Line	K562
Method	CRISPR
Exp_Name	PTGES3-BGKcLV15-K562
ENCODE_series_ID	ENCSR917FAG
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR728VRY
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	PTGES3-BGKcLV15-49
Rep2	PTGES3-BGKcLV15-50
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	88.4
Rep2_qPCR	89.9
Rep1_WB	62.3
Rep2_WB	66.6
Antibody Cat#	MA3-414
Antibody Lot#	SH2575558
Antibody DCC ID	ENCAB371NVC
Status	Released
Project	ENCODE4
ID	133

Experiment Information (Status: Released)

	BGKcLV15-49	BGKcLV15-50
idx	587	588
TRCN#_or_BGC#	BGC#0000385	BGC#0000385
shRNA_or_gRNA_sequence	ATTTTATACAGTTGTCTCGG	ATTTTATACAGTTGTCTCGG
PAM	agg	agg
Name	PTGES3_89	PTGES3_89
Sample_ID	BGKcLV15-49	BGKcLV15-50
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	PTGES3	PTGES3
qPCR_result	88.4	89.9
Ave_qPCR	89.2
RT-qPCR_primer-F	AAAGGAGAATCTGGCCAGTCA
RT-qPCR_primer-R	ATCATCTTCCCAGTCTTTCCAAT
protein_conc	5322	5691
WB_result	62.3	66.6
Ave_WB	64.5
WB_DONE_date	4/9/19
MW	23KD
IP	Mouse / Ig
antibody_Cat#	MA3-414
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	376.7	0
Rep2_TPM	339.6	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4699	4700

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

	BGKcLV15-49	BGKcLV15-50
Sample_ID	BGKcLV15-49	BGKcLV15-50
Sample Name
Sample Name	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-50
RBP	PTGES3	PTGES3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5355	5356

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-49	BGKcLV15-50
Sample #	25	26
Sample Name	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-50
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-A2	2-B2
Tecan	17.91	32.17
Tecan_date	2019-12-10	2019-12-10
Size_bp	265	270
Peak_Molarity	18.00	18.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A4.png	DNA_Library_set43-44/set1/B4.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A4.png	RNA_Library_set43-44/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-49	BGKcLV15-50
RBP	PTGES3	PTGES3
Batch_ID	BGKcLV15	BGKcLV15
WB_result	62.300	66.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	601	602

Sequencing Information

	BGKcLV15-49	BGKcLV15-50
Sample_ID	BGKcLV15-49	BGKcLV15-50
Sample Name	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-50
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	98,411,188	108,388,696
total_aligned_reads	85,577,148	105,554,616
unique_aligned_reads	78,051,612	96,411,480
percent_uniqueAligned	0.79312	0.88950
correlation_replicates	0.996784	0.996784
spikein_reads	84,754	76,772
percent_spikeins	0.00086	0.00071
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	107	108

Data Submission Information

	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-50	BGKcLV15-50	BGKcLV15-50	BGKcLV15-50
ENCODE_alias	brenton-graveley:PTGES3-BGKcLV15	brenton-graveley:PTGES3-BGKcLV15-49	brenton-graveley:L-PTGES3-BGKcLV15-49	brenton-graveley:PTGES3-BGKcLV15-49_S25_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGKcLV15-49_S25_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGKcLV15-K562	brenton-graveley:PTGES3-BGKcLV15-50	brenton-graveley:L-PTGES3-BGKcLV15-50	brenton-graveley:PTGES3-BGKcLV15-50_S26_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PTGES3-BGKcLV15-50_S26_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR728VRY	ENCBS289LMY	ENCLB153UOO	ENCFF643TNV	ENCFF352FDV	ENCSR917FAG	ENCBS350NXO	ENCLB722VXR	ENCFF467GHE	ENCFF912HRO
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	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-49	BGKcLV15-50	BGKcLV15-50	BGKcLV15-50	BGKcLV15-50
Sample Name	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-49	PTGES3-BGKcLV15-50	PTGES3-BGKcLV15-50	PTGES3-BGKcLV15-50	PTGES3-BGKcLV15-50
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		PTGES3-BGKcLV15-49.pdf	L-PTGES3-BGKcLV15-49.pdf				PTGES3-BGKcLV15-50.pdf	L-PTGES3-BGKcLV15-50.pdf
ID	29	140	304	502	554	7295	141	305	503	555

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-BGKcLV15-49_S25_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	107	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	103
PTGES3-BGKcLV15-49_S25_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	107	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	155
PTGES3-BGKcLV15-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49_S25_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGKcLV15-49_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24394
PTGES3-BGKcLV15-49_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49/Aligned.sortedByCoord.out.bam		ENCORE2	24446
PTGES3-BGKcLV15-49_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49/Aligned.sortedByCoord.out.bam		ENCORE2	24498
PTGES3-BGKcLV15-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49/Aligned.sortedByCoord.out.bam		ENCORE2	24550
PTGES3-BGKcLV15-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49/Aligned.sortedByCoord.out.bam		ENCORE2	24602
PTGES3-BGKcLV15-49_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	107					GRCh38	V40	PTGES3-BGKcLV15-49_S25_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGKcLV15-49_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24654
PTGES3-BGKcLV15-50_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	108	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	104
PTGES3-BGKcLV15-50_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	108	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	156
PTGES3-BGKcLV15-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50_S26_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGKcLV15-50_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24395
PTGES3-BGKcLV15-50_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50/Aligned.sortedByCoord.out.bam		ENCORE2	24447
PTGES3-BGKcLV15-50_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50/Aligned.sortedByCoord.out.bam		ENCORE2	24499
PTGES3-BGKcLV15-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50/Aligned.sortedByCoord.out.bam		ENCORE2	24551
PTGES3-BGKcLV15-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50/Aligned.sortedByCoord.out.bam		ENCORE2	24603
PTGES3-BGKcLV15-50_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	108					GRCh38	V40	PTGES3-BGKcLV15-50_S26_R1_001.filtered.trimmed.paired.fastq.gz,PTGES3-BGKcLV15-50_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24655