SMNDC1 RNA-Seq in K562

General Information


RBP	SMNDC1
Cell_Line	K562
Method	shRNA
Exp_Name	SMNDC1-BGKLV13-K562
ENCODE_series_ID	ENCSR791XKC
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR408SDL
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	SMNDC1_BGKLV13_15
Rep2	SMNDC1_BGKLV13_16
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	47.8
Rep2_qPCR	46.5
Rep1_WB	52.8
Rep2_WB	50.9
Antibody Cat#	RN078PW
Antibody Lot#	RN078PW
Antibody DCC ID	ENCAB616ASE
Status	Released
Project	ENCODE3
ID	365

Experiment Information (Status: Released)

	BGKLV13-15	BGKLV13-16
idx	148	149
TRCN#_or_BGC#	TRCN0000001138	TRCN0000001138
shRNA_or_gRNA_sequence	CTGGTAAAGTTGGAGTAGGAA	CTGGTAAAGTTGGAGTAGGAA
PAM
Name	SMNDC1	SMNDC1
Sample_ID	BGKLV13-15	BGKLV13-16
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	SMNDC1	SMNDC1
qPCR_result	47.8	46.5
Ave_qPCR	47.1
RT-qPCR_primer-F	ctccactgttgaacctcaagc
RT-qPCR_primer-R	gctgggcaatcatttcttttt
protein_conc	2134	2273
WB_result	52.8	50.9
Ave_WB	51.8
WB_DONE_date	7/30/2014
MW	27kDa
IP	1	1
antibody_Cat#	RN078PW	RN078PW
Antibody DCC ID	ENCAB616ASE	ENCAB616ASE
submitted_to_DCC_date	5/4/2015
Rep1_TPM	18.7906831	0
Rep2_TPM	13.6112994	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	163	164

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMNDC1	Product_ID: RN078PW Lot_ID: 1 Source: MBLI Target Name: SMNDC1-human

Experiment Status

	BGKLV13-15	BGKLV13-16
Sample_ID	BGKLV13-15	BGKLV13-16
Sample Name	SMNDC1_BGKLV13_15	SMNDC1_BGKLV13_16
Sample Name	SMNDC1_BGKLV13_15	SMNDC1_BGKLV13_16
RBP	SMNDC1	SMNDC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	474	475

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-15	BGKLV13-16
Sample #
Sample Name	SMNDC1-BGKLV13-15	SMNDC1-BGKLV13-16
Sample_Name_Alias	SMNDC1_BGKLV13_15	SMNDC1_BGKLV13_16
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F2.png	DNA_Library_LV13-14/set1/G2.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/A11.png	RNA_Library_LV12/set1/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-15	BGKLV13-16
RBP	SMNDC1	SMNDC1
Batch_ID	BGKLV13	BGKLV13
WB_result	52.800	50.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2132	2133

Sequencing Information

	BGKLV13-15	BGKLV13-16
Sample_ID	BGKLV13-15	BGKLV13-16
Sample Name	SMNDC1_BGKLV13_15	SMNDC1_BGKLV13_16
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	50,980,000	53,680,000
total_aligned_reads	45,907,966	50,220,774
unique_aligned_reads	42,311,140	46,189,678
percent_uniqueAligned	0.82996	0.86046
correlation_replicates	0.998745	0.998745
spikein_reads	222,452	174,410
percent_spikeins	0.00436	0.00325
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	774	775

Data Submission Information

	BGKLV13-15	BGKLV13-15
ENCODE_alias	brenton-graveley:SMNDC1_BGKLV13	brenton-graveley:SMNDC1-BGKLV13-K562
ENCODE_accession	ENCSR408SDL	ENCSR791XKC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-15	BGKLV13-15
Sample Name	SMNDC1_BGKLV13_15	SMNDC1_BGKLV13_15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2786	6955

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
SMNDC1_BGKLV13_15_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	774	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13402
SMNDC1_BGKLV13_15_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	774	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13454
SMNDC1_BGKLV13_15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15_AGTCAA_L002_R1_001.fastq.gz,SMNDC1_BGKLV13_15_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	13506
SMNDC1_BGKLV13_15_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15/Aligned.sortedByCoord.out.bam		ENCORE2	13558
SMNDC1_BGKLV13_15_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15/Aligned.sortedByCoord.out.bam		ENCORE2	13610
SMNDC1_BGKLV13_15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15/Aligned.sortedByCoord.out.bam		ENCORE2	13662
SMNDC1_BGKLV13_15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15/Aligned.sortedByCoord.out.bam		ENCORE2	13714
SMNDC1_BGKLV13_15_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	774					GRCh38	V40	SMNDC1_BGKLV13_15_AGTCAA_L002_R1_001.fastq.gz,SMNDC1_BGKLV13_15_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	13766
SMNDC1_BGKLV13_16_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	775	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13403
SMNDC1_BGKLV13_16_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	775	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13455
SMNDC1_BGKLV13_16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16_AGTTCC_L002_R1_001.fastq.gz,SMNDC1_BGKLV13_16_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	13507
SMNDC1_BGKLV13_16_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16/Aligned.sortedByCoord.out.bam		ENCORE2	13559
SMNDC1_BGKLV13_16_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16/Aligned.sortedByCoord.out.bam		ENCORE2	13611
SMNDC1_BGKLV13_16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16/Aligned.sortedByCoord.out.bam		ENCORE2	13663
SMNDC1_BGKLV13_16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16/Aligned.sortedByCoord.out.bam		ENCORE2	13715
SMNDC1_BGKLV13_16_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	775					GRCh38	V40	SMNDC1_BGKLV13_16_AGTTCC_L002_R1_001.fastq.gz,SMNDC1_BGKLV13_16_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	13767