SUCLG1 RNA-Seq in HepG2

General Information


RBP	SUCLG1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SUCLG1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR439GMT
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR810JYX
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	SUCLG1-BGHLV23-47
Rep2	SUCLG1-BGHLV23-48
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	78.6
Rep2_qPCR	83.0
Rep1_WB	76.6
Rep2_WB	68.2
Antibody Cat#	GTX109215
Antibody Lot#	GTX109215
Antibody DCC ID	ENCAB020DGN
Status	Released
Project	ENCODE3
ID	552

Experiment Information (Status: Released)

	BGHLV23-47	BGHLV23-48
idx	539	540
TRCN#_or_BGC#	TRCN0000048510	TRCN0000048510
shRNA_or_gRNA_sequence	CGGCAACATCTCTATGTTGAT	CGGCAACATCTCTATGTTGAT
PAM
Name	SUCLG1	SUCLG1
Sample_ID	BGHLV23-47	BGHLV23-48
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	SUCLG1	SUCLG1
qPCR_result	78.6	83.0
Ave_qPCR	80.8
RT-qPCR_primer-F	ttcggcattgttcctacaca
RT-qPCR_primer-R	ctgtgaaaggtgccctgttt
protein_conc	4977	4384
WB_result	76.6	68.2
Ave_WB	72.4
WB_DONE_date	5/13/2015
MW	36kDa
IP	1	1
antibody_Cat#	GTX109215	GTX109215
Antibody DCC ID	ENCAB020DGN	ENCAB020DGN
submitted_to_DCC_date	8/6/2015
Rep1_TPM	38.8	0
Rep2_TPM	24.6	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2620	2621

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUCLG1	Product_ID: GTX109215 Lot_ID: 40023 Source: GeneTex Target Name: SUCLG1-human

Experiment Status

	BGHLV23-47	BGHLV23-48
Sample_ID	BGHLV23-47	BGHLV23-48
Sample Name	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-48
Sample Name	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-48
RBP	SUCLG1	SUCLG1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	842	843

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-47	BGHLV23-48
Sample #
Sample Name	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-48
Sample_Name_Alias	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-48
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/G2.png	DNA_Library_LV20-22-23/set4/H2.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C8.png	RNA_Library_LV22-23-25/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-47	BGHLV23-48
RBP	SUCLG1	SUCLG1
Batch_ID	BGHLV23	BGHLV23
WB_result	76.600	68.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2530	2531

Sequencing Information

	BGHLV23-47	BGHLV23-48
Sample_ID	BGHLV23-47	BGHLV23-48
Sample Name	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-48
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	56,940,000	67,170,000
total_aligned_reads	52,117,316	61,340,160
unique_aligned_reads	49,011,898	57,714,742
percent_uniqueAligned	0.86076	0.85923
correlation_replicates	0.998573	0.998573
spikein_reads	288,570	315,338
percent_spikeins	0.00507	0.00469
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1152	1153

Data Submission Information

	BGHLV23-47	BGHLV23-47
ENCODE_alias	brenton-graveley:SUCLG1-BGHLV23	brenton-graveley:SUCLG1-BGHLV23-HepG2
ENCODE_accession	ENCSR810JYX	ENCSR439GMT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-47	BGHLV23-47
Sample Name	SUCLG1-BGHLV23-47	SUCLG1-BGHLV23-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2953	6990

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
SUCLG1-BGHLV23-47_ACTGAT_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1152	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16682
SUCLG1-BGHLV23-47_ACTGAT_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1152	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16720
SUCLG1-BGHLV23-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47_ACTGAT_L008_R1_001.fastq.gz,SUCLG1-BGHLV23-47_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	16758
SUCLG1-BGHLV23-47_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47/Aligned.sortedByCoord.out.bam		ENCORE2	16796
SUCLG1-BGHLV23-47_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47/Aligned.sortedByCoord.out.bam		ENCORE2	16834
SUCLG1-BGHLV23-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47/Aligned.sortedByCoord.out.bam		ENCORE2	16872
SUCLG1-BGHLV23-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47/Aligned.sortedByCoord.out.bam		ENCORE2	16910
SUCLG1-BGHLV23-47_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1152					GRCh38	V40	SUCLG1-BGHLV23-47_ACTGAT_L008_R1_001.fastq.gz,SUCLG1-BGHLV23-47_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	16948
SUCLG1-BGHLV23-48_ATTCCT_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1153	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16683
SUCLG1-BGHLV23-48_ATTCCT_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1153	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16721
SUCLG1-BGHLV23-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48_ATTCCT_L008_R1_001.fastq.gz,SUCLG1-BGHLV23-48_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	16759
SUCLG1-BGHLV23-48_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48/Aligned.sortedByCoord.out.bam		ENCORE2	16797
SUCLG1-BGHLV23-48_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48/Aligned.sortedByCoord.out.bam		ENCORE2	16835
SUCLG1-BGHLV23-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48/Aligned.sortedByCoord.out.bam		ENCORE2	16873
SUCLG1-BGHLV23-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48/Aligned.sortedByCoord.out.bam		ENCORE2	16911
SUCLG1-BGHLV23-48_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1153					GRCh38	V40	SUCLG1-BGHLV23-48_ATTCCT_L008_R1_001.fastq.gz,SUCLG1-BGHLV23-48_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	16949