POLR2A RNA-Seq in K562

General Information


RBP	POLR2A
Cell_Line	K562
Method	CRISPR
Exp_Name	POLR2A-BGKcLV13-K562
ENCODE_series_ID	ENCSR706XVM
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR963JFM
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	POLR2A-BGKcLV13-57
Rep2	POLR2A-BGKcLV13-58
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	89.6
Rep2_WB	91.6
Antibody Cat#	MA1-46093
Antibody Lot#	LOT# SC249656
Antibody DCC ID	ENCAB138WNB
Status	Released
Project	ENCODE4
ID	184

Experiment Information (Status: Released)

	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58
idx	502	504	506	508	510	512	503	505	507	509	511	513
TRCN#_or_BGC#	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332	BGC#0000332
shRNA_or_gRNA_sequence	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG	CGGGCATGCGCTGTCCCCCG
PAM	agg	agg	agg	agg	agg	agg	agg	agg	agg	agg	agg	agg
Name	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84	POLR2A_84
Sample_ID	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58
transduction_Date	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A	POLR2A
qPCR_result	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0	0.0	0.0	0.0	0.0
RT-qPCR_primer-F	gagtccagttcggagtcctg	gagtccagttcggagtcctg	gagtccagttcggagtcctg	gagtccagttcggagtcctg	gagtccagttcggagtcctg	gagtccagttcggagtcctg
RT-qPCR_primer-R	ccctcagtcgtctctgggta	ccctcagtcgtctctgggta	ccctcagtcgtctctgggta	ccctcagtcgtctctgggta	ccctcagtcgtctctgggta	ccctcagtcgtctctgggta
protein_conc	5760	5760	5760	5760	5760	5760	6015	6015	6015	6015	6015	6015
WB_result	89.6	71.0	84.0	73.0	63.0	80.0	91.6	66.0	83.0	66.0	58.0	81.0
Ave_WB	90.6	68.5	83.5	69.5	60.5	80.5
WB_DONE_date	4/25/19	2/26/19	2/25/19	3/21/19	2/26/19	2/26/19
MW	220 KD	240kd	240kd	240kd	240kd	240kd
IP	Mouse / Ig	Rat	Rat	Rat	Rat	Rat
antibody_Cat#	MA1-46093	61083-pSer2	61085-pSer5	61087-pSer7	61383-pTyr1	61361-pThr4	LOT# SC249656	Lot#22217002	Lot#10618002	Lot#15117003	Lot#31516002	Lot#22217002
Antibody DCC ID	ENCAB138WNB
submitted_to_DCC_date
Rep1_TPM	42.1	0	0	0	0	0	0	0	0	0	0	0
Rep2_TPM	37.6	0	0	0	0	0	0	0	0	0	0	0
Action	Ready						Ready
Library_start_date	03/18/19						03/18/19
repeat_library
Note
ID	4610	4612	4614	4616	4618	4620	4611	4613	4615	4617	4619	4621

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
POLR2A	Product_ID: MA1-46093 Lot_ID: SC249656 Source: Thermo Fisher Target Name: POLR2A-human
POLR2A	Product_ID: 61083 Lot_ID: 22217002 Source: Active Motif Target Name: POLR2AphosphoS2-human Phosphate: pSer2
POLR2A	Product_ID: 61085 Lot_ID: 10618002 Source: Active Motif Target Name: POLR2AphosphoS5-human Phosphate: pSer5
POLR2A	Product_ID: 61087 Lot_ID: 15117003 Source: Active Motif Target Name: POLR2AphosphoS7-human Phosphate: pSer7
POLR2A	Product_ID: 61361 Lot_ID: 22217002 Source: Active Motif Target Name: POLR2AphosphoT4-human Phosphate: pThr4
POLR2A	Product_ID: 61383 Lot_ID: 31516002 Source: Active Motif Target Name: POLR2AphosphoY1-human Phosphate: pTyr1

Experiment Status

	BGKcLV13-57	BGKcLV13-58
Sample_ID	BGKcLV13-57	BGKcLV13-58
Sample Name	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-58
Sample Name	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-58
RBP	POLR2A	POLR2A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2911	2912

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-57	BGKcLV13-58
Sample #	65	66
Sample Name	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-58
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-A1	2-B1
Tecan	56.75	50.85
Tecan_date	2019-03-18	2019-03-18
Size_bp	286	283
Peak_Molarity	30.00	45.30
libSampleQC_DNA_Well	DNA_Library_set42/set2/D1.png	DNA_Library_set42/set1/B9.png
RIN	9.3	9.7
libSample_RNA_Well	RNA_Library_set42/set1/A9.png	RNA_Library_set42/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-57	BGKcLV13-58
RBP	POLR2A	POLR2A
Batch_ID	BGKcLV13	BGKcLV13
WB_result	89.600	91.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	65	66

Sequencing Information

	BGKcLV13-57	BGKcLV13-58
Sample_ID	BGKcLV13-57	BGKcLV13-58
Sample Name	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-58
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	77,987,294	54,058,642
total_aligned_reads	76,102,124	52,482,064
unique_aligned_reads	69,141,038	47,500,658
percent_uniqueAligned	0.88657	0.87869
correlation_replicates	0.988029	0.988029
spikein_reads	49,150	47,030
percent_spikeins	0.00063	0.00087
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	55	56

Data Submission Information

	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58
ENCODE_alias	brenton-graveley:POLR2A-BGKcLV13	brenton-graveley:POLR2A-BGKcLV13-57	brenton-graveley:L-POLR2A-BGKcLV13-57	brenton-graveley:POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:POLR2A-BGKcLV13-K562	brenton-graveley:POLR2A-BGKcLV13-58	brenton-graveley:L-POLR2A-BGKcLV13-58	brenton-graveley:POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR963JFM	ENCBS723ITA	ENCLB078TDC	ENCFF750PSL	ENCFF818PEK	ENCSR706XVM	ENCBS500NBN	ENCLB504XBW	ENCFF773VCA	ENCFF966KQW
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	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-57	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58	BGKcLV13-58
Sample Name	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-57	POLR2A-BGKcLV13-58	POLR2A-BGKcLV13-58	POLR2A-BGKcLV13-58	POLR2A-BGKcLV13-58
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		POLR2A-BGKcLV13-57.pdf	L-POLR2A-BGKcLV13-57.pdf				POLR2A-BGKcLV13-58.pdf	L-POLR2A-BGKcLV13-58.pdf
ID	784	863	945	1005	1087	7283	864	946	1006	1088

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
POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	55	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	387
POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	55	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	469
POLR2A-BGKcLV13-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	55					GRCh38	V40	POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R1_001.filtered.trimmed.paired.fastq.gz,POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23726
POLR2A-BGKcLV13-57_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	55					GRCh38	V40	POLR2A-BGKcLV13-57/Aligned.sortedByCoord.out.bam		ENCORE2	23808
POLR2A-BGKcLV13-57_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	55					GRCh38	V40	POLR2A-BGKcLV13-57/Aligned.sortedByCoord.out.bam		ENCORE2	23890
POLR2A-BGKcLV13-57_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	55					GRCh38	V40	POLR2A-BGKcLV13-57/Aligned.sortedByCoord.out.bam		ENCORE2	23972
POLR2A-BGKcLV13-57_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	55					GRCh38	V40	POLR2A-BGKcLV13-57/Aligned.sortedByCoord.out.bam		ENCORE2	24054
POLR2A-BGKcLV13-57_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	55					GRCh38	V40	POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R1_001.filtered.trimmed.paired.fastq.gz,POLR2A-BGKcLV13-57_ACACTAAG+ATCCATAT_HK3H2DSXX_S65_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24136
POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	56	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	388
POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	56	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	470
POLR2A-BGKcLV13-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	56					GRCh38	V40	POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R1_001.filtered.trimmed.paired.fastq.gz,POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23727
POLR2A-BGKcLV13-58_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	56					GRCh38	V40	POLR2A-BGKcLV13-58/Aligned.sortedByCoord.out.bam		ENCORE2	23809
POLR2A-BGKcLV13-58_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	56					GRCh38	V40	POLR2A-BGKcLV13-58/Aligned.sortedByCoord.out.bam		ENCORE2	23891
POLR2A-BGKcLV13-58_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	56					GRCh38	V40	POLR2A-BGKcLV13-58/Aligned.sortedByCoord.out.bam		ENCORE2	23973
POLR2A-BGKcLV13-58_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	56					GRCh38	V40	POLR2A-BGKcLV13-58/Aligned.sortedByCoord.out.bam		ENCORE2	24055
POLR2A-BGKcLV13-58_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	56					GRCh38	V40	POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R1_001.filtered.trimmed.paired.fastq.gz,POLR2A-BGKcLV13-58_GTGTCGGA+GCTTGCGC_HK3H2DSXX_S66_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24137