RPL11 RNA-Seq in K562

General Information


RBP	RPL11
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL11-BGKcLV15-K562
ENCODE_series_ID	ENCSR420MHI
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR816LHY
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	RPL11-BGKcLV15-51
Rep2	RPL11-BGKcLV15-52
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	72.1
Rep2_qPCR	79.1
Rep1_WB	90.7
Rep2_WB	93.2
Antibody Cat#	37-3000
Antibody Lot#	TB259358
Antibody DCC ID	ENCAB959BBQ
Status	Released
Project	ENCODE4
ID	134

Experiment Information (Status: Released)

	BGKcLV15-51	BGKcLV15-52
idx	589	590
TRCN#_or_BGC#	BGC#0000364	BGC#0000364
shRNA_or_gRNA_sequence	GCGGATGCGAAGTTCCCGCA	GCGGATGCGAAGTTCCCGCA
PAM	tgg	tgg
Name	RPL11-94	RPL11-94
Sample_ID	BGKcLV15-51	BGKcLV15-52
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	RPL11	RPL11
qPCR_result	72.1	79.1
Ave_qPCR	75.6
RT-qPCR_primer-F	AGCCAAGGTGTTGGAGCAG
RT-qPCR_primer-R	TGTGCAGTGGACAGCAATCT
protein_conc	5392	5340
WB_result	90.7	93.2
Ave_WB	91.9
WB_DONE_date	4/9/19
MW	20KD
IP	Mouse / Ig
antibody_Cat#	37-3000
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	3260.4	0
Rep2_TPM	3367.6	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4701	4702

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL11	Product_ID: 37-3000 Lot_ID: TB259358 Source: Thermo Fisher Target Name: RPL11-human

Experiment Status

	BGKcLV15-51	BGKcLV15-52
Sample_ID	BGKcLV15-51	BGKcLV15-52
Sample Name
Sample Name	RPL11-BGKcLV15-51	RPL11-BGKcLV15-52
RBP	RPL11	RPL11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5357	5358

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-51	BGKcLV15-52
Sample #	27	28
Sample Name	RPL11-BGKcLV15-51	RPL11-BGKcLV15-52
Sample_Name_Alias
Index Well Position	C04	D04
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-C2	2-D2
Tecan	33.25	37.43
Tecan_date	2019-12-10	2019-12-10
Size_bp	264	269
Peak_Molarity	18.10	19.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C4.png	DNA_Library_set43-44/set1/D4.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/C4.png	RNA_Library_set43-44/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-51	BGKcLV15-52
RBP	RPL11	RPL11
Batch_ID	BGKcLV15	BGKcLV15
WB_result	90.700	93.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	603	604

Sequencing Information

	BGKcLV15-51	BGKcLV15-52
Sample_ID	BGKcLV15-51	BGKcLV15-52
Sample Name	RPL11-BGKcLV15-51	RPL11-BGKcLV15-52
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	99,760,392	105,951,484
total_aligned_reads	89,328,208	101,503,352
unique_aligned_reads	81,302,650	92,350,320
percent_uniqueAligned	0.81498	0.87163
correlation_replicates	0.999325	0.999325
spikein_reads	54,048	57,952
percent_spikeins	0.00054	0.00055
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	109	110

Data Submission Information

	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-52	BGKcLV15-52	BGKcLV15-52	BGKcLV15-52
ENCODE_alias	brenton-graveley:RPL11-BGKcLV15	brenton-graveley:RPL11-BGKcLV15-51	brenton-graveley:L-RPL11-BGKcLV15-51	brenton-graveley:RPL11-BGKcLV15-51_S27_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGKcLV15-51_S27_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGKcLV15-K562	brenton-graveley:RPL11-BGKcLV15-52	brenton-graveley:L-RPL11-BGKcLV15-52	brenton-graveley:RPL11-BGKcLV15-52_S28_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGKcLV15-52_S28_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR816LHY	ENCBS600KIV	ENCLB124FWX	ENCFF722BTJ	ENCFF778YMB	ENCSR420MHI	ENCBS432KQK	ENCLB535XLP	ENCFF312BEZ	ENCFF243JYZ
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	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-51	BGKcLV15-52	BGKcLV15-52	BGKcLV15-52	BGKcLV15-52
Sample Name	RPL11-BGKcLV15-51	RPL11-BGKcLV15-51	RPL11-BGKcLV15-51	RPL11-BGKcLV15-51	RPL11-BGKcLV15-51	RPL11-BGKcLV15-51	RPL11-BGKcLV15-52	RPL11-BGKcLV15-52	RPL11-BGKcLV15-52	RPL11-BGKcLV15-52
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		RPL11-BGKcLV15-51.pdf	L-RPL11-BGKcLV15-51.pdf				RPL11-BGKcLV15-52.pdf	L-RPL11-BGKcLV15-52.pdf
ID	30	142	306	504	556	7304	143	307	505	557

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
RPL11-BGKcLV15-51_S27_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	109	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	105
RPL11-BGKcLV15-51_S27_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	109	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	157
RPL11-BGKcLV15-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	109					GRCh38	V40	RPL11-BGKcLV15-51_S27_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGKcLV15-51_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24396
RPL11-BGKcLV15-51_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	109					GRCh38	V40	RPL11-BGKcLV15-51/Aligned.sortedByCoord.out.bam		ENCORE2	24448
RPL11-BGKcLV15-51_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	109					GRCh38	V40	RPL11-BGKcLV15-51/Aligned.sortedByCoord.out.bam		ENCORE2	24500
RPL11-BGKcLV15-51_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	109					GRCh38	V40	RPL11-BGKcLV15-51/Aligned.sortedByCoord.out.bam		ENCORE2	24552
RPL11-BGKcLV15-51_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	109					GRCh38	V40	RPL11-BGKcLV15-51/Aligned.sortedByCoord.out.bam		ENCORE2	24604
RPL11-BGKcLV15-51_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	109					GRCh38	V40	RPL11-BGKcLV15-51_S27_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGKcLV15-51_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24656
RPL11-BGKcLV15-52_S28_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	110	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	106
RPL11-BGKcLV15-52_S28_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	110	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	158
RPL11-BGKcLV15-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	110					GRCh38	V40	RPL11-BGKcLV15-52_S28_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGKcLV15-52_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24397
RPL11-BGKcLV15-52_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	110					GRCh38	V40	RPL11-BGKcLV15-52/Aligned.sortedByCoord.out.bam		ENCORE2	24449
RPL11-BGKcLV15-52_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	110					GRCh38	V40	RPL11-BGKcLV15-52/Aligned.sortedByCoord.out.bam		ENCORE2	24501
RPL11-BGKcLV15-52_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	110					GRCh38	V40	RPL11-BGKcLV15-52/Aligned.sortedByCoord.out.bam		ENCORE2	24553
RPL11-BGKcLV15-52_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	110					GRCh38	V40	RPL11-BGKcLV15-52/Aligned.sortedByCoord.out.bam		ENCORE2	24605
RPL11-BGKcLV15-52_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	110					GRCh38	V40	RPL11-BGKcLV15-52_S28_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGKcLV15-52_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24657