RPS11 RNA-Seq in K562

General Information


RBP	RPS11
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS11-BGKcLV08-K562
ENCODE_series_ID	ENCSR942WGL
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR050ATA
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	RPS11-BGKcLV08-63
Rep2	RPS11-BGKcLV08-64
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	58.8
Rep2_qPCR	40.6
Rep1_WB	41.8
Rep2_WB	45.2
Antibody Cat#	A303-936A
Antibody Lot#	A303-936A
Antibody DCC ID	ENCAB560LKV
Status	Released
Project	ENCODE4
ID	210

Experiment Information (Status: Released)

	BGKcLV08-63	BGKcLV08-64
idx	288	289
TRCN#_or_BGC#	BGC#0000140	BGC#0000140
shRNA_or_gRNA_sequence	CTGGTAATGTGTCCATTCGA	CTGGTAATGTGTCCATTCGA
PAM	GGG	GGG
Name	RPS11-83F	RPS11-83F
Sample_ID	BGKcLV08-63	BGKcLV08-64
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	RPS11	RPS11
qPCR_result	58.8	40.6
Ave_qPCR	49.7
RT-qPCR_primer-F	gcaagtacaaccgcttcgag
RT-qPCR_primer-R	tgtgacgatgtcaccgatct
protein_conc	3193	3529
WB_result	41.8	45.2
Ave_WB	43.5
WB_DONE_date	3/23/18
MW	18 kDa
IP	1
antibody_Cat#	A303-936A	A303-936A
Antibody DCC ID	ENCAB560LKV
submitted_to_DCC_date	9/6/18
Rep1_TPM	1036.7	0
Rep2_TPM	1107.4	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4388	4389

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS11	Product_ID: A303-936A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS11-human

Experiment Status

	BGKcLV08-63	BGKcLV08-64
Sample_ID	BGKcLV08-63	BGKcLV08-64
Sample Name
Sample Name	RPS11-BGKcLV08-63	RPS11-BGKcLV08-64
RBP	RPS11	RPS11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6191	6192

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-63	BGKcLV08-64
Sample #	27	28
Sample Name	RPS11-BGKcLV08-63	RPS11-BGKcLV08-64
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	279	277
Peak_Molarity	56.60	60.40
libSampleQC_DNA_Well	DNA_Library_set41/set2/C4.png	DNA_Library_set41/set2/D4.png
RIN	9.5	9.3
libSample_RNA_Well	RNA_Library_set41/set1/C4.png	RNA_Library_set41/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-63	BGKcLV08-64
RBP	RPS11	RPS11
Batch_ID	BGKcLV08	BGKcLV08
WB_result	41.800	45.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	877	878

Sequencing Information

	BGKcLV08-63	BGKcLV08-64
Sample_ID	BGKcLV08-63	BGKcLV08-64
Sample Name	RPS11-BGKcLV08-63	RPS11-BGKcLV08-64
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	233,442,678	190,051,530
total_aligned_reads	230,911,470	180,967,670
unique_aligned_reads	207,573,486	162,365,308
percent_uniqueAligned	0.88918	0.85432
correlation_replicates	0.994784	0.994784
spikein_reads	343,848	292,586
percent_spikeins	0.00147	0.00154
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	283	284

Data Submission Information

	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-64	BGKcLV08-64	BGKcLV08-64	BGKcLV08-64
ENCODE_alias	brenton-graveley:RPS11-BGKcLV08	brenton-graveley:RPS11-BGKcLV08-63	brenton-graveley:L-RPS11-BGKcLV08-63	brenton-graveley:RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS11-BGKcLV08-K562	brenton-graveley:RPS11-BGKcLV08-64	brenton-graveley:L-RPS11-BGKcLV08-64	brenton-graveley:RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR050ATA	ENCBS138GDT	ENCLB509YTX	ENCFF565FCA	ENCFF735STT	ENCSR942WGL	ENCBS897WWG	ENCLB018GVM	ENCFF144FYE	ENCFF629BHH
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	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-63	BGKcLV08-64	BGKcLV08-64	BGKcLV08-64	BGKcLV08-64
Sample Name	RPS11-BGKcLV08-63	RPS11-BGKcLV08-63	RPS11-BGKcLV08-63	RPS11-BGKcLV08-63	RPS11-BGKcLV08-63	RPS11-BGKcLV08-63	RPS11-BGKcLV08-64	RPS11-BGKcLV08-64	RPS11-BGKcLV08-64	RPS11-BGKcLV08-64
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		RPS11-BGKcLV08-63.pdf	L-RPS11-BGKcLV08-63.pdf				RPS11-BGKcLV08-64.pdf	L-RPS11-BGKcLV08-64.pdf
ID	1140	1200	1270	1340	1404	7311	1201	1271	1341	1405

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	283				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	547
RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	283				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	617
RPS11-BGKcLV08-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26785
RPS11-BGKcLV08-63_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	26855
RPS11-BGKcLV08-63_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	26925
RPS11-BGKcLV08-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	26995
RPS11-BGKcLV08-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	27065
RPS11-BGKcLV08-63_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	283	GRCh38	V40	RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS11-BGKcLV08-63_CTTGGTAT+CCAAGTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27135
RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	284				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	548
RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	284				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	618
RPS11-BGKcLV08-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26786
RPS11-BGKcLV08-64_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	26856
RPS11-BGKcLV08-64_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	26926
RPS11-BGKcLV08-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	26996
RPS11-BGKcLV08-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	27066
RPS11-BGKcLV08-64_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	284	GRCh38	V40	RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS11-BGKcLV08-64_TCCAACGC+TTGGACTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27136