AUH RNA-Seq in HepG2

General Information


RBP	AUH
Cell_Line	HepG2
Method	shRNA
Exp_Name	AUH-BGHLV37-HepG2
ENCODE_series_ID	ENCSR828YUV
Batch_ID	BGHLV37
Pool ID	Pool-161129
Local_Set_Name	set37
ENCODE_KD_Exp_ID	ENCSR409CSO
ENCODE_CN_Exp_ID	ENCSR997HCQ
Rep1	AUH_BGHLV37-13
Rep2	AUH_BGHLV37-14
CN1	NT_BGHLV37-1
CN2	NT_BGHLV37-2
Rep1_qPCR	48.6
Rep2_qPCR	53.8
Rep1_WB	57.4
Rep2_WB	45.9
Antibody Cat#	RN037P
Antibody Lot#	RN037P
Antibody DCC ID	ENCAB000BFE
Status	Released
Project	ENCODE3
ID	750

Experiment Information (Status: Released)

	BGHLV37-13	BGHLV37-14
idx	925	926
TRCN#_or_BGC#	TRCN0000052449	TRCN0000052449
shRNA_or_gRNA_sequence	GCTTGGAATAAACAGAGCTTA	GCTTGGAATAAACAGAGCTTA
PAM
Name	AUH	AUH
Sample_ID	BGHLV37-13	BGHLV37-14
transduction_Date	9/1/16	9/1/16
days
RBP_name	AUH	AUH
qPCR_result	48.6	53.8
Ave_qPCR	51.2
RT-qPCR_primer-F	aggtggtggtcttgaactgg
RT-qPCR_primer-R	caccaggaataatcgccaat
protein_conc	3894	3632
WB_result	57.4	45.9
Ave_WB	51.6
WB_DONE_date	9/16/16	wes
MW	36kDa
IP	1IP	1IP
antibody_Cat#	RN037P	RN037P
Antibody DCC ID	ENCAB000BFE	ENCAB000BFE
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	3018	3019

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AUH	Product_ID: RN037P Lot_ID: 1 Source: MBLI Target Name: AUH-human

Experiment Status

	BGHLV37-13	BGHLV37-14
Sample_ID	BGHLV37-13	BGHLV37-14
Sample Name	AUH_BGHLV37-13	AUH_BGHLV37-14
Sample Name	AUH_BGHLV37-13	AUH_BGHLV37-14
RBP	AUH	AUH
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1293	1294

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-13	BGHLV37-14
Sample #
Sample Name	AUH-BGHLV37-13	AUH-BGHLV37-14
Sample_Name_Alias	AUH_BGHLV37-13	AUH_BGHLV37-14
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/C3.png	DNA_Library_LV37-38/set1/D3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV37_38/set1/C1.png	RNA_Library_LV37_38/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV37-13	BGHLV37-14
RBP	AUH	AUH
Batch_ID	BGHLV37	BGHLV37
WB_result	57.400	45.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2978	2979

Sequencing Information

	BGHLV37-13	BGHLV37-14
Sample_ID	BGHLV37-13	BGHLV37-14
Sample Name	AUH_BGHLV37-13	AUH_BGHLV37-14
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set37	set37
total_reads	70,307,220	95,687,016
total_aligned_reads	62,206,690	85,454,380
unique_aligned_reads	58,680,552	80,488,190
percent_uniqueAligned	0.83463	0.84116
correlation_replicates	0.998540	0.998540
spikein_reads	295,750	285,814
percent_spikeins	0.00421	0.00299
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1627	1628

Data Submission Information

	BGHLV37-13	BGHLV37-13
ENCODE_alias	brenton-graveley:AUH_BGHLV37	brenton-graveley:AUH-BGHLV37-HepG2
ENCODE_accession	ENCSR409CSO	ENCSR828YUV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-13	BGHLV37-13
Sample Name	AUH_BGHLV37-13	AUH_BGHLV37-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3186	6598

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
AUH_BGHLV37-13_GTGGCC_L005_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1627	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22034
AUH_BGHLV37-13_GTGGCC_L005_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1627	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22050
AUH_BGHLV37-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13_GTGGCC_L005_001.R1.fastq.gz,AUH_BGHLV37-13_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	22066
AUH_BGHLV37-13_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	22082
AUH_BGHLV37-13_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	22098
AUH_BGHLV37-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	22114
AUH_BGHLV37-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13/Aligned.sortedByCoord.out.bam		ENCORE2	22130
AUH_BGHLV37-13_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1627					GRCh38	V40	AUH_BGHLV37-13_GTGGCC_L005_001.R1.fastq.gz,AUH_BGHLV37-13_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	22146
AUH_BGHLV37-14_GTTTCG_L005_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1628	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22035
AUH_BGHLV37-14_GTTTCG_L005_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1628	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22051
AUH_BGHLV37-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14_GTTTCG_L005_001.R1.fastq.gz,AUH_BGHLV37-14_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	22067
AUH_BGHLV37-14_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	22083
AUH_BGHLV37-14_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	22099
AUH_BGHLV37-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	22115
AUH_BGHLV37-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14/Aligned.sortedByCoord.out.bam		ENCORE2	22131
AUH_BGHLV37-14_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1628					GRCh38	V40	AUH_BGHLV37-14_GTTTCG_L005_001.R1.fastq.gz,AUH_BGHLV37-14_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	22147