SSB RNA-Seq in HepG2

General Information


RBP	SSB
Cell_Line	HepG2
Method	shRNA
Exp_Name	SSB-BGHLV37-HepG2
ENCODE_series_ID	ENCSR623QDI
Batch_ID	BGHLV37
Pool ID	Pool-161129
Local_Set_Name	set37
ENCODE_KD_Exp_ID	ENCSR278CHI
ENCODE_CN_Exp_ID	ENCSR997HCQ
Rep1	SSB_BGHLV37-61
Rep2	SSB_BGHLV37-62
CN1	NT_BGHLV37-1
CN2	NT_BGHLV37-2
Rep1_qPCR	67.4
Rep2_qPCR	71.9
Rep1_WB	55.5
Rep2_WB	59.4
Antibody Cat#	RN074PW
Antibody Lot#	RN074PW
Antibody DCC ID	ENCAB214FIO
Status	Released
Project	ENCODE3
ID	754

Experiment Information (Status: Released)

	BGHLV37-61	BGHLV37-62
idx	973	974
TRCN#_or_BGC#	TRCN0000062197	TRCN0000062197
shRNA_or_gRNA_sequence	GCTGAAATGAAATCTCTAGAA	GCTGAAATGAAATCTCTAGAA
PAM
Name	SSB	SSB
Sample_ID	BGHLV37-61	BGHLV37-62
transduction_Date	9/1/16	9/1/16
days
RBP_name	SSB	SSB
qPCR_result	67.4	71.9
Ave_qPCR	69.7
RT-qPCR_primer-F	gccacgggacaagtttctaa
RT-qPCR_primer-R	gttctgccttggatttgctc
protein_conc	2357	2759
WB_result	55.5	59.4
Ave_WB	57.5
WB_DONE_date	9/15/16
MW
IP	1	1
antibody_Cat#	RN074PW	RN074PW
Antibody DCC ID	ENCAB214FIO	ENCAB214FIO
submitted_to_DCC_date	10/26/16
Rep1_TPM	174.5	0
Rep2_TPM	147.1	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	3066	3067

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSB	Product_ID: RN074PW Lot_ID: 1 Source: MBLI Target Name: SSB-human

Experiment Status

	BGHLV37-61	BGHLV37-62
Sample_ID	BGHLV37-61	BGHLV37-62
Sample Name	SSB_BGHLV37-61	SSB_BGHLV37-62
Sample Name	SSB_BGHLV37-61	SSB_BGHLV37-62
RBP	SSB	SSB
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1303	1304

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-61	BGHLV37-62
Sample #
Sample Name	SSB-BGHLV37-61	SSB-BGHLV37-62
Sample_Name_Alias	SSB_BGHLV37-61	SSB_BGHLV37-62
Index Well Position	S05	S06
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/E4.png	DNA_Library_LV37-38/set1/F4.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV37_38/set1/E2.png	RNA_Library_LV37_38/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV37-61	BGHLV37-62
RBP	SSB	SSB
Batch_ID	BGHLV37	BGHLV37
WB_result	55.500	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2990	2991

Sequencing Information

	BGHLV37-61	BGHLV37-62
Sample_ID	BGHLV37-61	BGHLV37-62
Sample Name	SSB_BGHLV37-61	SSB_BGHLV37-62
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set37	set37
total_reads	77,551,368	70,284,198
total_aligned_reads	71,082,280	65,071,488
unique_aligned_reads	67,002,594	61,427,528
percent_uniqueAligned	0.86398	0.87399
correlation_replicates	0.996651	0.996651
spikein_reads	201,920	254,910
percent_spikeins	0.00260	0.00363
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1639	1640

Data Submission Information

	BGHLV37-61	BGHLV37-61
ENCODE_alias	brenton-graveley:SSB_BGHLV37	brenton-graveley:SSB-BGHLV37-HepG2
ENCODE_accession	ENCSR278CHI	ENCSR623QDI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-61	BGHLV37-61
Sample Name	SSB_BGHLV37-61	SSB_BGHLV37-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3191	6980

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
SSB_BGHLV37-61_ACAGTG_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1639	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22046
SSB_BGHLV37-61_ACAGTG_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1639	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22062
SSB_BGHLV37-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1639					GRCh38	V40	SSB_BGHLV37-61_ACAGTG_L006_001.R1.fastq.gz,SSB_BGHLV37-61_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	22078
SSB_BGHLV37-61_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	1639					GRCh38	V40	SSB_BGHLV37-61/Aligned.sortedByCoord.out.bam		ENCORE2	22094
SSB_BGHLV37-61_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	1639					GRCh38	V40	SSB_BGHLV37-61/Aligned.sortedByCoord.out.bam		ENCORE2	22110
SSB_BGHLV37-61_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	1639					GRCh38	V40	SSB_BGHLV37-61/Aligned.sortedByCoord.out.bam		ENCORE2	22126
SSB_BGHLV37-61_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	1639					GRCh38	V40	SSB_BGHLV37-61/Aligned.sortedByCoord.out.bam		ENCORE2	22142
SSB_BGHLV37-61_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1639					GRCh38	V40	SSB_BGHLV37-61_ACAGTG_L006_001.R1.fastq.gz,SSB_BGHLV37-61_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	22158
SSB_BGHLV37-62_GCCAAT_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1640	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22047
SSB_BGHLV37-62_GCCAAT_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1640	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22063
SSB_BGHLV37-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1640					GRCh38	V40	SSB_BGHLV37-62_GCCAAT_L006_001.R1.fastq.gz,SSB_BGHLV37-62_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	22079
SSB_BGHLV37-62_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	1640					GRCh38	V40	SSB_BGHLV37-62/Aligned.sortedByCoord.out.bam		ENCORE2	22095
SSB_BGHLV37-62_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	1640					GRCh38	V40	SSB_BGHLV37-62/Aligned.sortedByCoord.out.bam		ENCORE2	22111
SSB_BGHLV37-62_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	1640					GRCh38	V40	SSB_BGHLV37-62/Aligned.sortedByCoord.out.bam		ENCORE2	22127
SSB_BGHLV37-62_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	1640					GRCh38	V40	SSB_BGHLV37-62/Aligned.sortedByCoord.out.bam		ENCORE2	22143
SSB_BGHLV37-62_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1640					GRCh38	V40	SSB_BGHLV37-62_GCCAAT_L006_001.R1.fastq.gz,SSB_BGHLV37-62_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	22159