SAFB RNA-Seq in HepG2

General Information


RBP	SAFB
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SAFB-BGHcLV09-HepG2
ENCODE_series_ID	ENCSR158KBU
Batch_ID	BGHcLV09
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR416YFB
ENCODE_CN_Exp_ID	ENCSR300EBW
Rep1	SAFB-BGHcLV09-17
Rep2	SAFB-BGHcLV09-18
CN1	NT-BGHcLV09-1
CN2	NT-BGHcLV09-2
Rep1_qPCR	64.0
Rep2_qPCR	74.3
Rep1_WB	75.1
Rep2_WB	85.1
Antibody Cat#	200580
Antibody Lot#
Antibody DCC ID	ENCAB180KRZ
Status	Released
Project	ENCODE4
ID	218

Experiment Information (Status: Released)

	BGHcLV09-17	BGHcLV09-18
idx	179	180
TRCN#_or_BGC#	BGC#0000064	BGC#0000064
shRNA_or_gRNA_sequence	CCCGCAGATCGATCACTCGC	CCCGCAGATCGATCACTCGC
PAM	AGG	AGG
Name	SAFB_97F_2	SAFB_97F_2
Sample_ID	BGHcLV09-17	BGHcLV09-18
transduction_Date	4/20/18	4/20/18
days	D6	D6
RBP_name	SAFB	SAFB
qPCR_result	64.0	74.3
Ave_qPCR	69.2
RT-qPCR_primer-F	agctgaggaaacggaatgtg
RT-qPCR_primer-R	tccctcggaggtaatttcaa
protein_conc	2909	2387
WB_result	75.1	85.1
Ave_WB	80.1
WB_DONE_date	6/4/18	WES
MW	130kd
IP
antibody_Cat#	200580
Antibody DCC ID	ENCAB180KRZ
submitted_to_DCC_date	9/6/18
Rep1_TPM	70	0
Rep2_TPM	60	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6322	6323

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAFB	Product_ID: #200580 Lot_ID: 20130304 Source: Zen Bioscience Target Name: SAFB-human

Experiment Status

	BGHcLV09-17	BGHcLV09-18
Sample_ID	BGHcLV09-17	BGHcLV09-18
Sample Name
Sample Name	SAFB-BGHcLV09-17	SAFB-BGHcLV09-18
RBP	SAFB	SAFB
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6263	6264

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV09-17	BGHcLV09-18
Sample #	45	46
Sample Name	SAFB-BGHcLV09-17	SAFB-BGHcLV09-18
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	264	267
Peak_Molarity	31.20	31.80
libSampleQC_DNA_Well	DNA_Library_set41/set5/A7.png	DNA_Library_set41/set5/B7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set41/set1/E6.png	RNA_Library_set41/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV09-17	BGHcLV09-18
RBP	SAFB	SAFB
Batch_ID	BGHcLV09	BGHcLV09
WB_result	75.100	85.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	895	896

Sequencing Information

	BGHcLV09-17	BGHcLV09-18
Sample_ID	BGHcLV09-17	BGHcLV09-18
Sample Name	SAFB-BGHcLV09-17	SAFB-BGHcLV09-18
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	116,076,916	102,953,556
total_aligned_reads	114,776,332	101,938,524
unique_aligned_reads	105,459,698	93,847,156
percent_uniqueAligned	0.90853	0.91155
correlation_replicates	0.995152	0.995152
spikein_reads	116,630	97,990
percent_spikeins	0.00100	0.00095
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	301	302

Data Submission Information

	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-18	BGHcLV09-18	BGHcLV09-18	BGHcLV09-18
ENCODE_alias	brenton-graveley:SAFB-BGHcLV09	brenton-graveley:SAFB-BGHcLV09-17	brenton-graveley:L-SAFB-BGHcLV09-17	brenton-graveley:SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAFB-BGHcLV09-HepG2	brenton-graveley:SAFB-BGHcLV09-18	brenton-graveley:L-SAFB-BGHcLV09-18	brenton-graveley:SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR416YFB	ENCBS640FZR	ENCLB327TAV	ENCFF168ZWJ	ENCFF177PKE	ENCSR158KBU	ENCBS080ZER	ENCLB764LBO	ENCFF373IOW	ENCFF937QMD
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-17	BGHcLV09-18	BGHcLV09-18	BGHcLV09-18	BGHcLV09-18
Sample Name	SAFB-BGHcLV09-17	SAFB-BGHcLV09-17	SAFB-BGHcLV09-17	SAFB-BGHcLV09-17	SAFB-BGHcLV09-17	SAFB-BGHcLV09-17	SAFB-BGHcLV09-18	SAFB-BGHcLV09-18	SAFB-BGHcLV09-18	SAFB-BGHcLV09-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		SAFB-BGHcLV09-17.pdf	L-SAFB-BGHcLV09-17.pdf				SAFB-BGHcLV09-18.pdf	L-SAFB-BGHcLV09-18.pdf
ID	1141	1202	1272	1342	1406	7317	1203	1273	1343	1407

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	301				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	549
SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	301				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	619
SAFB-BGHcLV09-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26787
SAFB-BGHcLV09-17_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17/Aligned.sortedByCoord.out.bam		ENCORE2	26857
SAFB-BGHcLV09-17_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17/Aligned.sortedByCoord.out.bam		ENCORE2	26927
SAFB-BGHcLV09-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17/Aligned.sortedByCoord.out.bam		ENCORE2	26997
SAFB-BGHcLV09-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17/Aligned.sortedByCoord.out.bam		ENCORE2	27067
SAFB-BGHcLV09-17_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	301	GRCh38	V40	SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAFB-BGHcLV09-17_ATATCTCG+ATCTTAGT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27137
SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	302				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	550
SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	302				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	620
SAFB-BGHcLV09-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26788
SAFB-BGHcLV09-18_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18/Aligned.sortedByCoord.out.bam		ENCORE2	26858
SAFB-BGHcLV09-18_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18/Aligned.sortedByCoord.out.bam		ENCORE2	26928
SAFB-BGHcLV09-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18/Aligned.sortedByCoord.out.bam		ENCORE2	26998
SAFB-BGHcLV09-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18/Aligned.sortedByCoord.out.bam		ENCORE2	27068
SAFB-BGHcLV09-18_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	302	GRCh38	V40	SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAFB-BGHcLV09-18_GCGCTCTA+GCTCCGAC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27138