SAFB2 RNA-Seq in HepG2

General Information


RBP	SAFB2
Cell_Line	HepG2
Method	shRNA
Exp_Name	SAFB2-BGHLV20-HepG2
ENCODE_series_ID	ENCSR616DAC
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR110ZYD
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	SAFB2-57-BGHLV20-53_17734
Rep2	SAFB2-57-BGHLV20-54_17735
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	67.5
Rep2_qPCR	70.4
Rep1_WB	71.0
Rep2_WB	73.8
Antibody Cat#	A301-112A
Antibody Lot#	A301-112A
Antibody DCC ID	ENCAB303CHK
Status	Released
Project	ENCODE3
ID	502

Experiment Information (Status: Released)

	BGHLV20-53	BGHLV20-54
idx	417	418
TRCN#_or_BGC#	TRCN0000075057	TRCN0000075057
shRNA_or_gRNA_sequence	GACATGAGTGTGCTAGACGAA	GACATGAGTGTGCTAGACGAA
PAM
Name	SAFB2_57	SAFB2_57
Sample_ID	BGHLV20-53	BGHLV20-54
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	SAFB2	SAFB2
qPCR_result	67.5	70.4
Ave_qPCR	68.9
RT-qPCR_primer-F	ggccttctcgattccttttg
RT-qPCR_primer-R	taaatccttccccatccaca
protein_conc	6620	7102
WB_result	71.0	73.8
Ave_WB	72.4
WB_DONE_date	1/19/2016
MW	107kDa	WES
IP	1	1
antibody_Cat#	A301-112A	A301-112A
Antibody DCC ID	ENCAB303CHK	ENCAB303CHK
submitted_to_DCC_date	3/8/2016
Rep1_TPM	43	0
Rep2_TPM	41.8	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2482	2483

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAFB2	Product_ID: A301-112A Lot_ID: 1 Source: Bethyl Labs Target Name: SAFB2-human

Experiment Status

	BGHLV20-53	BGHLV20-54
Sample_ID	BGHLV20-53	BGHLV20-54
Sample Name	SAFB2-57-BGHLV20-53_17734	SAFB2-57-BGHLV20-54_17735
Sample Name	SAFB2-57-BGHLV20-53_17734	SAFB2-57-BGHLV20-54_17735
RBP	SAFB2	SAFB2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	736	737

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-53	BGHLV20-54
Sample #
Sample Name	SAFB2-BGHLV20-53	SAFB2-BGHLV20-54
Sample_Name_Alias	SAFB2-57-BGHLV20-53_17734	SAFB2-57-BGHLV20-54_17735
Index Well Position	S05	S06
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/E4.png	DNA_Library_LV20-22-23/set1/F4.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G10.png	RNA_Library_LV20-22-24/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-53	BGHLV20-54
RBP	SAFB2	SAFB2
Batch_ID	BGHLV20	BGHLV20
WB_result	71.000	73.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2422	2423

Sequencing Information

	BGHLV20-53	BGHLV20-54
Sample_ID	BGHLV20-53	BGHLV20-54
Sample Name	SAFB2-57-BGHLV20-53_17734	SAFB2-57-BGHLV20-54_17735
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	42,090,000	43,640,000
total_aligned_reads	38,421,858	40,002,128
unique_aligned_reads	36,190,622	37,765,544
percent_uniqueAligned	0.85984	0.86539
correlation_replicates	0.997914	0.997914
spikein_reads	205,610	187,240
percent_spikeins	0.00489	0.00429
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1190	1191

Data Submission Information

	BGHLV20-53	BGHLV20-53
ENCODE_alias	brenton-graveley:SAFB2-57-BGHLV20	brenton-graveley:SAFB2-BGHLV20-HepG2
ENCODE_accession	ENCSR110ZYD	ENCSR616DAC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-53	BGHLV20-53
Sample Name	SAFB2-57-BGHLV20-53_17734	SAFB2-57-BGHLV20-53_17734
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2917	6928

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
SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1190	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	15618
SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1190	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	15660
SAFB2-57-BGHLV20-53_17734_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R1_001.fastq.gz,SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	15702
SAFB2-57-BGHLV20-53_17734_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	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734/Aligned.sortedByCoord.out.bam		ENCORE2	15744
SAFB2-57-BGHLV20-53_17734_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	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734/Aligned.sortedByCoord.out.bam		ENCORE2	15786
SAFB2-57-BGHLV20-53_17734_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	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734/Aligned.sortedByCoord.out.bam		ENCORE2	15828
SAFB2-57-BGHLV20-53_17734_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	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734/Aligned.sortedByCoord.out.bam		ENCORE2	15870
SAFB2-57-BGHLV20-53_17734_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1190					GRCh38	V40	SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R1_001.fastq.gz,SAFB2-57-BGHLV20-53_17734_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	15912
SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1191	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	15619
SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1191	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	15661
SAFB2-57-BGHLV20-54_17735_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R1_001.fastq.gz,SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	15703
SAFB2-57-BGHLV20-54_17735_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	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735/Aligned.sortedByCoord.out.bam		ENCORE2	15745
SAFB2-57-BGHLV20-54_17735_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	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735/Aligned.sortedByCoord.out.bam		ENCORE2	15787
SAFB2-57-BGHLV20-54_17735_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	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735/Aligned.sortedByCoord.out.bam		ENCORE2	15829
SAFB2-57-BGHLV20-54_17735_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	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735/Aligned.sortedByCoord.out.bam		ENCORE2	15871
SAFB2-57-BGHLV20-54_17735_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1191					GRCh38	V40	SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R1_001.fastq.gz,SAFB2-57-BGHLV20-54_17735_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	15913