RPS6 RNA-Seq in K562

General Information


RBP	RPS6
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS6-BGKcLV13-K562
ENCODE_series_ID	ENCSR413XGY
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR539PFV
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	RPS6-BGKcLV13-67
Rep2	RPS6-BGKcLV13-68
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	78.7
Rep2_qPCR	71.7
Rep1_WB	82.0
Rep2_WB	70.1
Antibody Cat#	A300-556A
Antibody Lot#	Lot# 2
Antibody DCC ID	ENCAB305KJD
Status	Released
Project	ENCODE4
ID	189

Experiment Information (Status: Released)

	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68
idx	522	522	524	526	523	523	525	527
TRCN#_or_BGC#	BGC#0000337	BGC#0000337	BGC#0000337	BGC#0000337	BGC#0000337	BGC#0000337	BGC#0000337	BGC#0000337
shRNA_or_gRNA_sequence	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT	ACTACAGTGCCTCGCCGCCT
PAM	ggg	ggg	ggg	ggg	ggg	ggg	ggg	ggg
Name	RPS6_94	RPS6_94	RPS6_94	RPS6_94	RPS6_94	RPS6_94	RPS6_94	RPS6_94
Sample_ID	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68
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
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	RPS6	RPS6	RPS6	RPS6	RPS6	RPS6	RPS6	RPS6
qPCR_result	78.7	78.7	78.7	78.7	71.7	71.7	71.7	71.7
Ave_qPCR	75.2	75.2	75.2	75.2
RT-qPCR_primer-F	tctgagcgttctcaacttgg	tctgagcgttctcaacttgg	tctgagcgttctcaacttgg	tctgagcgttctcaacttgg
RT-qPCR_primer-R	tgcggattctgctagctctt	tgcggattctgctagctctt	tgcggattctgctagctctt	tgcggattctgctagctctt
protein_conc	4932	4932	4932	4932	5271	5271	5271	5271
WB_result	82.0	52.0	75.4	88.2	70.1	50.0367	76.7	90.2
Ave_WB	76.0	51.0	76.1	89.2
WB_DONE_date	1/4/19	7/6/22	1/11/19	6/12/19
MW	27KD	27KD	27KD	27KD
IP	Rabbit		Rabbit		Polyclonal		Monoclonal
antibody_Cat#	A300-556A	A300-557A	701374	701845	Lot# 2	Lot# 2	Lot# TH2627537A	Lot# RF236380
Antibody DCC ID	ENCAB305KJD	ENCAB970UUI	ENCAB286NJH	NO ID				RPS6-pSer240,Ser244
submitted_to_DCC_date	3/11/19		3/11/19
Rep1_TPM	1245.7	0	1245.7	1245.7	0	0	0	0
Rep2_TPM	1407.4	0	1407.4	1407.4	0	0	0	0
Action	Ready				Ready
Library_start_date	03/18/19				03/18/19
repeat_library
Note
ID	4630	4632	4634	4636	4631	4633	4635	4637

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS6	Product_ID: 701374 Lot_ID: TH2627537A Source: Thermo Fisher Target Name: RPS6-human
RPS6	Product_ID: A300-556A Lot_ID: 2 Source: Bethyl Labs Target Name: RPS6-human
RPS6	Product_ID: 701845 Lot_ID: RF236380 Source: Thermo Fisher Target Name: RPS6phosphoS240phosphoS244-human Phosphate: pSer240pSer244
RPS6	Product_ID: A300-557A Lot_ID: 2 Source: Bethyl Labs Target Name: RPS6-human

Experiment Status

	BGKcLV13-67	BGKcLV13-68
Sample_ID	BGKcLV13-67	BGKcLV13-68
Sample Name	RPS6-BGKcLV13-67	RPS6-BGKcLV13-68
Sample Name	RPS6-BGKcLV13-67	RPS6-BGKcLV13-68
RBP	RPS6	RPS6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2915	2916

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-67	BGKcLV13-68
Sample #	69	70
Sample Name	RPS6-BGKcLV13-67	RPS6-BGKcLV13-68
Sample_Name_Alias
Index Well Position	E09	F09
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-E1	2-F1
Tecan	51.81	66.91
Tecan_date	2019-03-18	2019-03-18
Size_bp	281	285
Peak_Molarity	41.60	44.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/E9.png	DNA_Library_set42/set1/F9.png
RIN	9.6	8.6
libSample_RNA_Well	RNA_Library_set42/set1/E9.png	RNA_Library_set42/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-67	BGKcLV13-68
RBP	RPS6	RPS6
Batch_ID	BGKcLV13	BGKcLV13
WB_result	82.000	70.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	69	70

Sequencing Information

	BGKcLV13-67	BGKcLV13-68
Sample_ID	BGKcLV13-67	BGKcLV13-68
Sample Name	RPS6-BGKcLV13-67	RPS6-BGKcLV13-68
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	61,805,764	55,422,970
total_aligned_reads	60,755,164	53,307,818
unique_aligned_reads	55,654,052	48,788,184
percent_uniqueAligned	0.90047	0.88029
correlation_replicates	0.998225	0.998225
spikein_reads	31,450	27,646
percent_spikeins	0.00051	0.00050
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	65	66

Data Submission Information

	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68
ENCODE_alias	brenton-graveley:RPS6-BGKcLV13	brenton-graveley:RPS6-BGKcLV13-67	brenton-graveley:L-RPS6-BGKcLV13-67	brenton-graveley:RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS6-BGKcLV13-K562	brenton-graveley:RPS6-BGKcLV13-68	brenton-graveley:L-RPS6-BGKcLV13-68	brenton-graveley:RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR539PFV	ENCBS804XVO	ENCLB056BLZ	ENCFF229JUP	ENCFF310TKS	ENCSR413XGY	ENCBS044FWN	ENCLB203IGX	ENCFF945UCS	ENCFF809RXW
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	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-67	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68	BGKcLV13-68
Sample Name	RPS6-BGKcLV13-67	RPS6-BGKcLV13-67	RPS6-BGKcLV13-67	RPS6-BGKcLV13-67	RPS6-BGKcLV13-67	RPS6-BGKcLV13-67	RPS6-BGKcLV13-68	RPS6-BGKcLV13-68	RPS6-BGKcLV13-68	RPS6-BGKcLV13-68
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		RPS6-BGKcLV13-67.pdf	L-RPS6-BGKcLV13-67.pdf				RPS6-BGKcLV13-68.pdf	L-RPS6-BGKcLV13-68.pdf
ID	786	867	949	1015	1097	7314	868	950	1016	1098

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
RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	65	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	397
RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	65	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	479
RPS6-BGKcLV13-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	65					GRCh38	V40	RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23736
RPS6-BGKcLV13-67_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	65					GRCh38	V40	RPS6-BGKcLV13-67/Aligned.sortedByCoord.out.bam		ENCORE2	23818
RPS6-BGKcLV13-67_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	65					GRCh38	V40	RPS6-BGKcLV13-67/Aligned.sortedByCoord.out.bam		ENCORE2	23900
RPS6-BGKcLV13-67_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	65					GRCh38	V40	RPS6-BGKcLV13-67/Aligned.sortedByCoord.out.bam		ENCORE2	23982
RPS6-BGKcLV13-67_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	65					GRCh38	V40	RPS6-BGKcLV13-67/Aligned.sortedByCoord.out.bam		ENCORE2	24064
RPS6-BGKcLV13-67_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	65					GRCh38	V40	RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPS6-BGKcLV13-67_GCCACAGG+CATGCCAT_HK3H2DSXX_S69_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24146
RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	66	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	398
RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	66	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	480
RPS6-BGKcLV13-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	66					GRCh38	V40	RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23737
RPS6-BGKcLV13-68_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	66					GRCh38	V40	RPS6-BGKcLV13-68/Aligned.sortedByCoord.out.bam		ENCORE2	23819
RPS6-BGKcLV13-68_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	66					GRCh38	V40	RPS6-BGKcLV13-68/Aligned.sortedByCoord.out.bam		ENCORE2	23901
RPS6-BGKcLV13-68_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	66					GRCh38	V40	RPS6-BGKcLV13-68/Aligned.sortedByCoord.out.bam		ENCORE2	23983
RPS6-BGKcLV13-68_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	66					GRCh38	V40	RPS6-BGKcLV13-68/Aligned.sortedByCoord.out.bam		ENCORE2	24065
RPS6-BGKcLV13-68_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	66					GRCh38	V40	RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPS6-BGKcLV13-68_ATTGTGAA+TGCATTGC_HK3H2DSXX_S70_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24147