SMN1 RNA-Seq in HepG2

General Information


RBP	SMN1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SMN1-BGHLV20-HepG2
ENCODE_series_ID	ENCSR351TBB
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR090UMI
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	SMN1-BGHLV20-55_17736
Rep2	SMN1-BGHLV20-56_17737
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	70.3
Rep2_qPCR	68.3
Rep1_WB	64.2
Rep2_WB	66.4
Antibody Cat#	RN077PW
Antibody Lot#	RN077PW
Antibody DCC ID	ENCAB135MQH
Status	Released
Project	ENCODE3
ID	503

Experiment Information (Status: Released)

	BGHLV20-55	BGHLV20-55	BGHLV20-56	BGHLV20-56
idx	419	419	420	420
TRCN#_or_BGC#	TRCN0000118704	TRCN0000118704	TRCN0000118704	TRCN0000118704
shRNA_or_gRNA_sequence	CAGAGCGATGATTCTGACATT	CAGAGCGATGATTCTGACATT	CAGAGCGATGATTCTGACATT	CAGAGCGATGATTCTGACATT
PAM
Name	SMN1	SMN1	SMN1	SMN1
Sample_ID	BGHLV20-55	BGHLV20-55	BGHLV20-56	BGHLV20-56
transduction_Date	10/2/2014	10/2/2014	10/2/2014	10/2/2014
days
RBP_name	SMN1	SMN1	SMN1	SMN1
qPCR_result	70.3	70.3	68.3	68.3
Ave_qPCR	69.3	69.3
RT-qPCR_primer-F	aggaggattccgtgctgttc	aggaggattccgtgctgttc
RT-qPCR_primer-R	tcagtgctgtatcatcccaaa	tcagtgctgtatcatcccaaa
protein_conc	4552	4552	4228	4228
WB_result	64.2	63.6	66.4	77.9
Ave_WB	65.3	70.8
WB_DONE_date	4/17/2015	6/28/22
MW	32kd	32kd
IP	1IP		1IP
antibody_Cat#	RN077PW	A301-863A	RN077PW	lot # 1
Antibody DCC ID	ENCAB135MQH	ENCAB606FBU	ENCAB135MQH
submitted_to_DCC_date	5/6/2015
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action
Library_start_date	5/29/2015		5/29/2015
repeat_library
Note
ID	2484	2486	2485	2487

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMN1	Product_ID: RN077PW Lot_ID: 1 Source: MBLI Target Name: SMN1-human
SMN1	Product_ID: A301-863A Lot_ID: 1 Source: Bethyl Labs Target Name: SMN1-human

Experiment Status

	BGHLV20-55	BGHLV20-56
Sample_ID	BGHLV20-55	BGHLV20-56
Sample Name	SMN1-BGHLV20-55_17736	SMN1-BGHLV20-56_17737
Sample Name	SMN1-BGHLV20-55_17736	SMN1-BGHLV20-56_17737
RBP	SMN1	SMN1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	738	739

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-55	BGHLV20-56
Sample #
Sample Name	SMN1-BGHLV20-55	SMN1-BGHLV20-56
Sample_Name_Alias	SMN1-BGHLV20-55_17736	SMN1-BGHLV20-56_17737
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G4.png	DNA_Library_LV20-22-23/set1/H4.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/F3.png	RNA_Library_LV19-21-24/set2/G3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-55	BGHLV20-56
RBP	SMN1	SMN1
Batch_ID	BGHLV20	BGHLV20
WB_result	64.200	66.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2424	2425

Sequencing Information

	BGHLV20-55	BGHLV20-56
Sample_ID	BGHLV20-55	BGHLV20-56
Sample Name	SMN1-BGHLV20-55_17736	SMN1-BGHLV20-56_17737
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	45,810,000	54,550,000
total_aligned_reads	41,795,282	49,525,670
unique_aligned_reads	39,484,358	46,699,468
percent_uniqueAligned	0.86192	0.85609
correlation_replicates	0.999256	0.999256
spikein_reads	201,800	235,716
percent_spikeins	0.00441	0.00432
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1192	1193

Data Submission Information

	BGHLV20-55	BGHLV20-55
ENCODE_alias	brenton-graveley:SMN1-BGHLV20	brenton-graveley:SMN1-BGHLV20-HepG2
ENCODE_accession	ENCSR090UMI	ENCSR351TBB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-55	BGHLV20-55
Sample Name	SMN1-BGHLV20-55_17736	SMN1-BGHLV20-55_17736
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2918	6952

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
SMN1-BGHLV20-55_17736_CAGATC_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1192	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15620
SMN1-BGHLV20-55_17736_CAGATC_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1192	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15662
SMN1-BGHLV20-55_17736_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736_CAGATC_L005_R1_001.fastq.gz,SMN1-BGHLV20-55_17736_CAGATC_L005_R2_001.fastq.gz		ENCORE2	15704
SMN1-BGHLV20-55_17736_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736/Aligned.sortedByCoord.out.bam		ENCORE2	15746
SMN1-BGHLV20-55_17736_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736/Aligned.sortedByCoord.out.bam		ENCORE2	15788
SMN1-BGHLV20-55_17736_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736/Aligned.sortedByCoord.out.bam		ENCORE2	15830
SMN1-BGHLV20-55_17736_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736/Aligned.sortedByCoord.out.bam		ENCORE2	15872
SMN1-BGHLV20-55_17736_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1192					GRCh38	V40	SMN1-BGHLV20-55_17736_CAGATC_L005_R1_001.fastq.gz,SMN1-BGHLV20-55_17736_CAGATC_L005_R2_001.fastq.gz		ENCORE2	15914
SMN1-BGHLV20-56_17737_ACTTGA_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1193	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15621
SMN1-BGHLV20-56_17737_ACTTGA_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1193	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15663
SMN1-BGHLV20-56_17737_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737_ACTTGA_L005_R1_001.fastq.gz,SMN1-BGHLV20-56_17737_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	15705
SMN1-BGHLV20-56_17737_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737/Aligned.sortedByCoord.out.bam		ENCORE2	15747
SMN1-BGHLV20-56_17737_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737/Aligned.sortedByCoord.out.bam		ENCORE2	15789
SMN1-BGHLV20-56_17737_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737/Aligned.sortedByCoord.out.bam		ENCORE2	15831
SMN1-BGHLV20-56_17737_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737/Aligned.sortedByCoord.out.bam		ENCORE2	15873
SMN1-BGHLV20-56_17737_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1193					GRCh38	V40	SMN1-BGHLV20-56_17737_ACTTGA_L005_R1_001.fastq.gz,SMN1-BGHLV20-56_17737_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	15915