SMNDC1 RNA-Seq in HepG2

General Information


RBP	SMNDC1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SMNDC1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR383KJZ
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR995ZGJ
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	SMNDC1_BGHLV14-49
Rep2	SMNDC1_BGHLV14-50
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	41.4
Rep2_qPCR	48.9
Rep1_WB	51.6
Rep2_WB	42.9
Antibody Cat#	RN078PW
Antibody Lot#	RN078PW
Antibody DCC ID	ENCAB616ASE
Status	Released
Project	ENCODE3
ID	405

Experiment Information (Status: Released)

	BGHLV14-49	BGHLV14-50
idx	145	146
TRCN#_or_BGC#	TRCN0000001138	TRCN0000001138
shRNA_or_gRNA_sequence	CTGGTAAAGTTGGAGTAGGAA	CTGGTAAAGTTGGAGTAGGAA
PAM
Name	SMNDC1	SMNDC1
Sample_ID	BGHLV14-49	BGHLV14-50
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	SMNDC1	SMNDC1
qPCR_result	41.4	48.9
Ave_qPCR	45.2
RT-qPCR_primer-F	ctccactgttgaacctcaagc
RT-qPCR_primer-R	gctgggcaatcatttcttttt
protein_conc	2803	2974
WB_result	51.6	42.9
Ave_WB	47.2
WB_DONE_date	7/30/2014
MW	27kDa
IP	1	1
antibody_Cat#	RN078PW	RN078PW
Antibody DCC ID	ENCAB616ASE	ENCAB616ASE
submitted_to_DCC_date	5/6/2015
Rep1_TPM	16.8	0
Rep2_TPM	13.7	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2208	2209

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

	BGHLV14-49	BGHLV14-50
Sample_ID	BGHLV14-49	BGHLV14-50
Sample Name	SMNDC1_BGHLV14-49	SMNDC1_BGHLV14-50
Sample Name	SMNDC1_BGHLV14-49	SMNDC1_BGHLV14-50
RBP	SMNDC1	SMNDC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	534	535

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-49	BGHLV14-50
Sample #
Sample Name	SMNDC1-BGHLV14-49	SMNDC1-BGHLV14-50
Sample_Name_Alias	SMNDC1_BGHLV14-49	SMNDC1_BGHLV14-50
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set2/E1.png	DNA_Library_LV13-14/set2/F1.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E9.png	RNA_Library_LV13-14-16/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-49	BGHLV14-50
RBP	SMNDC1	SMNDC1
Batch_ID	BGHLV14	BGHLV14
WB_result	51.600	42.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2218	2219

Sequencing Information

	BGHLV14-49	BGHLV14-50
Sample_ID	BGHLV14-49	BGHLV14-50
Sample Name	SMNDC1_BGHLV14-49	SMNDC1_BGHLV14-50
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	49,070,000	51,600,000
total_aligned_reads	45,671,664	47,004,760
unique_aligned_reads	43,018,560	44,301,274
percent_uniqueAligned	0.87668	0.85855
correlation_replicates	0.997900	0.997900
spikein_reads	304,118	327,024
percent_spikeins	0.00620	0.00634
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	860	861

Data Submission Information

	BGHLV14-49	BGHLV14-49
ENCODE_alias	brenton-graveley:SMNDC1_BGHLV14	brenton-graveley:SMNDC1-BGHLV14-HepG2
ENCODE_accession	ENCSR995ZGJ	ENCSR383KJZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-49	BGHLV14-49
Sample Name	SMNDC1_BGHLV14-49	SMNDC1_BGHLV14-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2816	6954

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_BGHLV14-49_TTAGGC_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	860	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13826
SMNDC1_BGHLV14-49_TTAGGC_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	860	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13888
SMNDC1_BGHLV14-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49_TTAGGC_L006_R1_001.fastq.gz,SMNDC1_BGHLV14-49_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	13950
SMNDC1_BGHLV14-49_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	14012
SMNDC1_BGHLV14-49_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	14074
SMNDC1_BGHLV14-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	14136
SMNDC1_BGHLV14-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49/Aligned.sortedByCoord.out.bam		ENCORE2	14198
SMNDC1_BGHLV14-49_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	860					GRCh38	V40	SMNDC1_BGHLV14-49_TTAGGC_L006_R1_001.fastq.gz,SMNDC1_BGHLV14-49_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	14260
SMNDC1_BGHLV14-50_TGACCA_L006_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	861	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13827
SMNDC1_BGHLV14-50_TGACCA_L006_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	861	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13889
SMNDC1_BGHLV14-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50_TGACCA_L006_R1_001.fastq.gz,SMNDC1_BGHLV14-50_TGACCA_L006_R2_001.fastq.gz		ENCORE2	13951
SMNDC1_BGHLV14-50_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	14013
SMNDC1_BGHLV14-50_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	14075
SMNDC1_BGHLV14-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	14137
SMNDC1_BGHLV14-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50/Aligned.sortedByCoord.out.bam		ENCORE2	14199
SMNDC1_BGHLV14-50_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	861					GRCh38	V40	SMNDC1_BGHLV14-50_TGACCA_L006_R1_001.fastq.gz,SMNDC1_BGHLV14-50_TGACCA_L006_R2_001.fastq.gz		ENCORE2	14261