RBM39 RNA-Seq in K562

General Information


RBP	RBM39
Cell_Line	K562
Method	shRNA
Exp_Name	RBM39-BGKLV28-K562
ENCODE_series_ID	ENCSR785KDC
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR678WOA
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	RBM39_BGKLV28-43
Rep2	RBM39_BGKLV28-44
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	65.9
Rep2_qPCR	59.8
Rep1_WB	51.8
Rep2_WB	46.5
Antibody Cat#	A300-291A
Antibody Lot#	A300-291A
Antibody DCC ID	ENCAB975CWB
Status	Released
Project	ENCODE3
ID	654

Experiment Information (Status: Released)

	BGKLV28-43	BGKLV28-44
idx	512	513
TRCN#_or_BGC#	TRCN0000021770	TRCN0000021770
shRNA_or_gRNA_sequence	GCTGGACCTATGAGGCTTTAT	GCTGGACCTATGAGGCTTTAT
PAM
Name	RBM39_70	RBM39_70
Sample_ID	BGKLV28-43	BGKLV28-44
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	RBM39	RBM39
qPCR_result	65.9	59.8
Ave_qPCR	62.8
RT-qPCR_primer-F	TTTAGGCGTGCCAATCATA
RT-qPCR_primer-R	TCATAGGTCCAGCACTTCCC
protein_conc	2906	2608
WB_result	51.8	46.5
Ave_WB	49.1
WB_DONE_date	6/26/2015
MW	59kd
IP	1	1
antibody_Cat#	A300-291A	A300-291A
Antibody DCC ID	ENCAB975CWB	ENCAB975CWB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	60.7035708	0
Rep2_TPM	52.1944205	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	587	588

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM39	Product_ID: A300-291A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM39-human

Experiment Status

	BGKLV28-43	BGKLV28-44
Sample_ID	BGKLV28-43	BGKLV28-44
Sample Name	RBM39_BGKLV28-43	RBM39_BGKLV28-44
Sample Name	RBM39_BGKLV28-43	RBM39_BGKLV28-44
RBP	RBM39	RBM39
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	994	995

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-43	BGKLV28-44
Sample #
Sample Name	RBM39-BGKLV28-43	RBM39-BGKLV28-44
Sample_Name_Alias	RBM39_BGKLV28-43	RBM39_BGKLV28-44
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G2.png	DNA_Library_LV28-29-30/set1/H2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C8.png	RNA_Library_LV26-27-28-29/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-43	BGKLV28-44
RBP	RBM39	RBM39
Batch_ID	BGKLV28	BGKLV28
WB_result	51.800	46.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2686	2687

Sequencing Information

	BGKLV28-43	BGKLV28-44
Sample_ID	BGKLV28-43	BGKLV28-44
Sample Name	RBM39_BGKLV28-43	RBM39_BGKLV28-44
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	102,369,412	97,940,282
total_aligned_reads	89,606,964	82,085,558
unique_aligned_reads	81,469,220	74,785,322
percent_uniqueAligned	0.79584	0.76358
correlation_replicates	0.994273	0.994273
spikein_reads	278,580	253,960
percent_spikeins	0.00272	0.00259
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1328	1329

Data Submission Information

	BGKLV28-43	BGKLV28-43
ENCODE_alias	brenton-graveley:RBM39_BGKLV28	brenton-graveley:RBM39-BGKLV28-K562
ENCODE_accession	ENCSR678WOA	ENCSR785KDC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-43	BGKLV28-43
Sample Name	RBM39_BGKLV28-43	RBM39_BGKLV28-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3046	6904

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
RBM39_BGKLV28-43_ATGTCA_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1328	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20172
RBM39_BGKLV28-43_ATGTCA_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1328	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20204
RBM39_BGKLV28-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43_ATGTCA_L002_001.R1.fastq.gz,RBM39_BGKLV28-43_ATGTCA_L002_001.R2.fastq.gz		ENCORE2	20236
RBM39_BGKLV28-43_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	20268
RBM39_BGKLV28-43_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	20300
RBM39_BGKLV28-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	20332
RBM39_BGKLV28-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	20364
RBM39_BGKLV28-43_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1328					GRCh38	V40	RBM39_BGKLV28-43_ATGTCA_L002_001.R1.fastq.gz,RBM39_BGKLV28-43_ATGTCA_L002_001.R2.fastq.gz		ENCORE2	20396
RBM39_BGKLV28-44_CCGTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1329	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20173
RBM39_BGKLV28-44_CCGTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1329	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20205
RBM39_BGKLV28-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44_CCGTCC_L002_001.R1.fastq.gz,RBM39_BGKLV28-44_CCGTCC_L002_001.R2.fastq.gz		ENCORE2	20237
RBM39_BGKLV28-44_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	20269
RBM39_BGKLV28-44_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	20301
RBM39_BGKLV28-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	20333
RBM39_BGKLV28-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	20365
RBM39_BGKLV28-44_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1329					GRCh38	V40	RBM39_BGKLV28-44_CCGTCC_L002_001.R1.fastq.gz,RBM39_BGKLV28-44_CCGTCC_L002_001.R2.fastq.gz		ENCORE2	20397