RBM17 RNA-Seq in K562

General Information


RBP	RBM17
Cell_Line	K562
Method	shRNA
Exp_Name	RBM17-BGKLV29-K562
ENCODE_series_ID	ENCSR723ZTN
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR898OPN
ENCODE_CN_Exp_ID	ENCSR118EFE
Rep1	RBM17_BGKLV29-53B
Rep2	RBM17_BGKLV29-54B
CN1	NTB_BGKLV29-1
CN2	NTB_BGKLV29-2
Rep1_qPCR	71.2
Rep2_qPCR	76.2
Rep1_WB	80.1
Rep2_WB	80.3
Antibody Cat#	A302-498A
Antibody Lot#	A302-498A
Antibody DCC ID	ENCAB959TNR
Status	Released
Project	ENCODE3
ID	675

Experiment Information (Status: Released)

	BGKLV29-53	BGKLV29-54
idx	588	589
TRCN#_or_BGC#	TRCN0000010600	TRCN0000010600
shRNA_or_gRNA_sequence	CCGGTGATCCTTAAATGAACT	CCGGTGATCCTTAAATGAACT
PAM
Name	RBM17_00	RBM17_00
Sample_ID	BGKLV29-53	BGKLV29-54
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	RBM17	RBM17
qPCR_result	71.2	76.2
Ave_qPCR	73.7
RT-qPCR_primer-F	TGGAAGTTGAAACCAAGGAAG
RT-qPCR_primer-R	ATCCGTACTGCTTCATCATC
protein_conc	2726	3146
WB_result	80.1	80.3
Ave_WB	80.2
WB_DONE_date	9/22/2015
MW	45kDa
IP	1	1
antibody_Cat#	A302-498A	A302-498A
Antibody DCC ID	ENCAB959TNR	ENCAB959TNR
submitted_to_DCC_date	12/7/2015
Rep1_TPM	35.5810854	0
Rep2_TPM	24.8093666	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	667	668

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM17	Product_ID: A302-498A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM17-human

Experiment Status

	BGKLV29-53	BGKLV29-54
Sample_ID	BGKLV29-53	BGKLV29-54
Sample Name	RBM17_BGKLV29-53B	RBM17_BGKLV29-54B
Sample Name	RBM17_BGKLV29-53B	RBM17_BGKLV29-54B
RBP	RBM17	RBM17
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1034	1035

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-53	BGKLV29-54
Sample #
Sample Name	RBM17-BGKLV29-53B	RBM17-BGKLV29-54B
Sample_Name_Alias	RBM17_BGKLV29-53B	RBM17_BGKLV29-54B
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-03	2015-11-03
Lib_ID	Lib-151103	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set2/D2.png	DNA_Library_LV28-29-30/set2/E2.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H9.png	RNA_Library_LV29-30-31-32/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-53	BGKLV29-54
RBP	RBM17	RBM17
Batch_ID	BGKLV29	BGKLV29
WB_result	80.100	80.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2732	2733

Sequencing Information

	BGKLV29-53	BGKLV29-54
Sample_ID	BGKLV29-53	BGKLV29-54
Sample Name	RBM17_BGKLV29-53B	RBM17_BGKLV29-54B
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	107,998,998	116,270,760
total_aligned_reads	98,639,228	106,911,392
unique_aligned_reads	89,926,648	97,379,004
percent_uniqueAligned	0.83266	0.83752
correlation_replicates	0.996733	0.996733
spikein_reads	481,254	593,986
percent_spikeins	0.00446	0.00511
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1395	1396

Data Submission Information

	BGKLV29-53	BGKLV29-53
ENCODE_alias	brenton-graveley:RBM17_BGKLV29-B	brenton-graveley:RBM17-BGKLV29-K562
ENCODE_accession	ENCSR898OPN	ENCSR723ZTN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-53	BGKLV29-53
Sample Name	RBM17_BGKLV29-53B	RBM17_BGKLV29-53B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3066	6895

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
RBM17_BGKLV29-53B_CAGATC_L008_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1395	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20436
RBM17_BGKLV29-53B_CAGATC_L008_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1395	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20466
RBM17_BGKLV29-53B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B_CAGATC_L008_001.R1.fastq.gz,RBM17_BGKLV29-53B_CAGATC_L008_001.R2.fastq.gz		ENCORE2	20496
RBM17_BGKLV29-53B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B/Aligned.sortedByCoord.out.bam		ENCORE2	20526
RBM17_BGKLV29-53B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B/Aligned.sortedByCoord.out.bam		ENCORE2	20556
RBM17_BGKLV29-53B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B/Aligned.sortedByCoord.out.bam		ENCORE2	20586
RBM17_BGKLV29-53B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B/Aligned.sortedByCoord.out.bam		ENCORE2	20616
RBM17_BGKLV29-53B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1395					GRCh38	V40	RBM17_BGKLV29-53B_CAGATC_L008_001.R1.fastq.gz,RBM17_BGKLV29-53B_CAGATC_L008_001.R2.fastq.gz		ENCORE2	20646
RBM17_BGKLV29-54B_ACTTGA_L008_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1396	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20437
RBM17_BGKLV29-54B_ACTTGA_L008_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1396	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20467
RBM17_BGKLV29-54B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B_ACTTGA_L008_001.R1.fastq.gz,RBM17_BGKLV29-54B_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	20497
RBM17_BGKLV29-54B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B/Aligned.sortedByCoord.out.bam		ENCORE2	20527
RBM17_BGKLV29-54B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B/Aligned.sortedByCoord.out.bam		ENCORE2	20557
RBM17_BGKLV29-54B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B/Aligned.sortedByCoord.out.bam		ENCORE2	20587
RBM17_BGKLV29-54B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B/Aligned.sortedByCoord.out.bam		ENCORE2	20617
RBM17_BGKLV29-54B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1396					GRCh38	V40	RBM17_BGKLV29-54B_ACTTGA_L008_001.R1.fastq.gz,RBM17_BGKLV29-54B_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	20647