RPS11 RNA-Seq in K562

General Information


RBP	RPS11
Cell_Line	K562
Method	shRNA
Exp_Name	RPS11-BGKLV34-K562
ENCODE_series_ID	ENCSR912GUX
Batch_ID	BGKLV34
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR193CCY
ENCODE_CN_Exp_ID	ENCSR774AEQ
Rep1	RPS11-BGKLV34-33B
Rep2	RPS11-BGKLV34-34B
CN1	NT-BGKLV34-1B
CN2	NT-BGKLV34-2B
Rep1_qPCR	91.7
Rep2_qPCR	92.5
Rep1_WB	43.5
Rep2_WB	40.9
Antibody Cat#	A303-936
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB560LKV
Status	Released
Project	ENCODE4
ID	270

Experiment Information (Status: Released)

	BGKLV34-33	BGKLV34-34
idx	696	697
TRCN#_or_BGC#	TRCN0000074982	TRCN0000074982
shRNA_or_gRNA_sequence	GATGCAGAGGACCATTGTCAT	GATGCAGAGGACCATTGTCAT
PAM
Name	RPS11	RPS11
Sample_ID	BGKLV34-33	BGKLV34-34
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	RPS11	RPS11
qPCR_result	91.7	92.5
Ave_qPCR	92.1
RT-qPCR_primer-F	gcaagtacaaccgcttcgag
RT-qPCR_primer-R	tgtgacgatgtcaccgatct
protein_conc	3091	2775
WB_result	43.5	40.9
Ave_WB	42.2
WB_DONE_date	2/19/2016
MW	18kd
IP
antibody_Cat#	A303-936	A303-936
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	1036.67	0
Rep2_TPM	1107.37499	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note	already tried CRISPR; CELL stoped grow after day6
ID	783	784

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV34-33	BGKLV34-34
Sample_ID	BGKLV34-33	BGKLV34-34
Sample Name
Sample Name	RPS11-BGKLV34-33B	RPS11-BGKLV34-34B
RBP	RPS11	RPS11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6457	6458

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-33	BGKLV34-34
Sample #	41	42
Sample Name	RPS11-BGKLV34-33B	RPS11-BGKLV34-34B
Sample_Name_Alias
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	289	294
Peak_Molarity	10.00	21.60
libSampleQC_DNA_Well	DNA_Library_set40/set1/A11.png	DNA_Library_set40/set1/B11.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_set40/set1/G5.png	RNA_Library_set40/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV34-33	BGKLV34-34
RBP	RPS11	RPS11
Batch_ID	BGKLV34	BGKLV34
WB_result	43.500	40.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	964	965

Sequencing Information

	BGKLV34-33	BGKLV34-34
Sample_ID	BGKLV34-33	BGKLV34-34
Sample Name	RPS11-BGKLV34-33B	RPS11-BGKLV34-34B
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	46,703,758	28,729,222
total_aligned_reads	35,097,196	22,330,914
unique_aligned_reads	32,008,558	20,423,236
percent_uniqueAligned	0.68535	0.71089
correlation_replicates	0.998673	0.998673
spikein_reads	14,188	7,008
percent_spikeins	0.00030	0.00024
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	367	368

Data Submission Information

	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-34	BGKLV34-34	BGKLV34-34	BGKLV34-34
ENCODE_alias	brenton-graveley:RPS11-BGKLV34-B	brenton-graveley:RPS11-BGKLV34-33B	brenton-graveley:L-RPS11-BGKLV34-33B	brenton-graveley:RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R2.fastq.gz	brenton-graveley:RPS11-BGKLV34-K562	brenton-graveley:RPS11-BGKLV34-34B	brenton-graveley:L-RPS11-BGKLV34-34B	brenton-graveley:RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R2.fastq.gz
ENCODE_accession	ENCSR193CCY	ENCBS518YFZ	ENCLB714UVV	ENCFF900XRF	ENCFF166GPD	ENCSR912GUX	ENCBS369TEV	ENCLB147HTJ	ENCFF407ZYA	ENCFF127XBT
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	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-33	BGKLV34-34	BGKLV34-34	BGKLV34-34	BGKLV34-34
Sample Name	RPS11-BGKLV34-33B	RPS11-BGKLV34-33B	RPS11-BGKLV34-33B	RPS11-BGKLV34-33B	RPS11-BGKLV34-33B	RPS11-BGKLV34-33B	RPS11-BGKLV34-34B	RPS11-BGKLV34-34B	RPS11-BGKLV34-34B	RPS11-BGKLV34-34B
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV40_library_protocol					LV40_library_protocol
protocol_URL			L-RPS11-BGKLV34-33B.pdf					L-RPS11-BGKLV34-34B.pdf
ID	1449	1496	1552	1669	1702	7312	1497	1553	1670	1703

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
RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	367	HiSeq2500	100	paired-ended	1				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE4	752
RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	367	HiSeq2500	100	paired-ended	2				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE4	795
RPS11-BGKLV34-33B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R1.fastq.gz,RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23492
RPS11-BGKLV34-33B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	23526
RPS11-BGKLV34-33B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	23560
RPS11-BGKLV34-33B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	23594
RPS11-BGKLV34-33B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	23628
RPS11-BGKLV34-33B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	367					GRCh38	V40	RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R1.fastq.gz,RPS11-BGKLV34-33B_ATCACG_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23662
RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	368	HiSeq2500	100	paired-ended	1				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE4	753
RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	368	HiSeq2500	100	paired-ended	2				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE4	796
RPS11-BGKLV34-34B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R1.fastq.gz,RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23493
RPS11-BGKLV34-34B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	23527
RPS11-BGKLV34-34B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	23561
RPS11-BGKLV34-34B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	23595
RPS11-BGKLV34-34B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	23629
RPS11-BGKLV34-34B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	368					GRCh38	V40	RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R1.fastq.gz,RPS11-BGKLV34-34B_CGATGT_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23663