RPS19 RNA-Seq in K562

General Information


RBP	RPS19
Cell_Line	K562
Method	shRNA
Exp_Name	RPS19-BGKLV19-K562
ENCODE_series_ID	ENCSR602APO
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR098NHI
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	RPS19_BGKLV19_45B
Rep2	RPS19_BGKLV19_46B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	94.8
Rep2_qPCR	94.1
Rep1_WB	no AB
Rep2_WB	no AB
Antibody Cat#	RN071PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB123ROG
Status	Released
Project	ENCODE3
ID	479

Experiment Information (Status: Released)

	BGKLV19-45	BGKLV19-46
idx	252	253
TRCN#_or_BGC#	TRCN0000074913	TRCN0000074913
shRNA_or_gRNA_sequence	CTACGATGAGAACTGGTTCTA	CTACGATGAGAACTGGTTCTA
PAM
Name	RPS19_13	RPS19_13
Sample_ID	BGKLV19-45	BGKLV19-46
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	RPS19	RPS19
qPCR_result	94.8	94.1
Ave_qPCR	94.4
RT-qPCR_primer-F	agacgtgaaccagcaggagt
RT-qPCR_primer-R	cttgacggtatccacccatt
protein_conc	1721	1735
WB_result	no AB	no AB
Ave_WB
WB_DONE_date
MW
IP	1	1
antibody_Cat#	RN071PW	RN071PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	279	280

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-45	BGKLV19-46
Sample_ID	BGKLV19-45	BGKLV19-46
Sample Name	RPS19_BGKLV19_45B	RPS19_BGKLV19_46B
Sample Name	RPS19_BGKLV19_45B	RPS19_BGKLV19_46B
RBP	RPS19	RPS19
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	692	693

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-45	BGKLV19-46
Sample #
Sample Name	RPS19-BGKLV19-45B	RPS19-BGKLV19-46B
Sample_Name_Alias	RPS19_BGKLV19_45B	RPS19_BGKLV19_46B
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E10.png	DNA_Library_LV18-19/set1/F10.png
RIN	8.7	8.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A5.png	RNA_Library_LV19-21-24/set2/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-45	BGKLV19-46
RBP	RPS19	RPS19
Batch_ID	BGKLV19	BGKLV19
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2376	2377

Sequencing Information

	BGKLV19-45	BGKLV19-46
Sample_ID	BGKLV19-45	BGKLV19-46
Sample Name	RPS19_BGKLV19_45B	RPS19_BGKLV19_46B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	36,350,000	47,050,000
total_aligned_reads	32,092,680	43,488,752
unique_aligned_reads	29,555,082	40,003,862
percent_uniqueAligned	0.81307	0.85024
correlation_replicates	0.994809	0.994809
spikein_reads	575,616	250,250
percent_spikeins	0.01584	0.00532
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1018	1019

Data Submission Information

	BGKLV19-45	BGKLV19-45
ENCODE_alias	brenton-graveley:RPS19_BGKLV19	brenton-graveley:RPS19-BGKLV19-K562
ENCODE_accession	ENCSR098NHI	ENCSR602APO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-45	BGKLV19-45
Sample Name	RPS19_BGKLV19_45B	RPS19_BGKLV19_45B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2894	6917

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
RPS19_BGKLV19_45B_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1018	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15134
RPS19_BGKLV19_45B_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1018	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15192
RPS19_BGKLV19_45B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B_ACAGTG_L005_R1_001.fastq.gz,RPS19_BGKLV19_45B_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	15250
RPS19_BGKLV19_45B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B/Aligned.sortedByCoord.out.bam		ENCORE2	15321
RPS19_BGKLV19_45B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B/Aligned.sortedByCoord.out.bam		ENCORE2	15379
RPS19_BGKLV19_45B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B/Aligned.sortedByCoord.out.bam		ENCORE2	15437
RPS19_BGKLV19_45B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B/Aligned.sortedByCoord.out.bam		ENCORE2	15495
RPS19_BGKLV19_45B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1018					GRCh38	V40	RPS19_BGKLV19_45B_ACAGTG_L005_R1_001.fastq.gz,RPS19_BGKLV19_45B_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	16392
RPS19_BGKLV19_46B_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1019	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15135
RPS19_BGKLV19_46B_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1019	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15193
RPS19_BGKLV19_46B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B_GCCAAT_L005_R1_001.fastq.gz,RPS19_BGKLV19_46B_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	15251
RPS19_BGKLV19_46B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B/Aligned.sortedByCoord.out.bam		ENCORE2	15322
RPS19_BGKLV19_46B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B/Aligned.sortedByCoord.out.bam		ENCORE2	15380
RPS19_BGKLV19_46B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B/Aligned.sortedByCoord.out.bam		ENCORE2	15438
RPS19_BGKLV19_46B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B/Aligned.sortedByCoord.out.bam		ENCORE2	15496
RPS19_BGKLV19_46B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1019					GRCh38	V40	RPS19_BGKLV19_46B_GCCAAT_L005_R1_001.fastq.gz,RPS19_BGKLV19_46B_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	16393