SDAD1 RNA-Seq in HepG2

General Information


RBP	SDAD1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SDAD1-BGHcLV07-HepG2
ENCODE_series_ID	ENCSR919NYR
Batch_ID	BGHcLV07
Pool ID	Pool-170911
Local_Set_Name	set39_H
ENCODE_KD_Exp_ID	ENCSR715QWM
ENCODE_CN_Exp_ID	ENCSR521WAI
Rep1	SDAD1-BGHcLV07-31
Rep2	SDAD1-BGHcLV07-32
CN1	NT-BGHcLV07-1
CN2	NT-BGHcLV07-2
Rep1_qPCR	0.0
Rep2_qPCR	0.7
Rep1_WB	74.8
Rep2_WB	84.2
Antibody Cat#	A304-692A
Antibody Lot#
Antibody DCC ID	ENCAB322LZP
Status	Released
Project	ENCODE3
ID	767

Experiment Information (Status: Released)

	BGHcLV07-31	BGHcLV07-32
idx	143	144
TRCN#_or_BGC#	BGC#0000067	BGC#0000067
shRNA_or_gRNA_sequence	AGACCCGCCGGCCTACATCG	AGACCCGCCGGCCTACATCG
PAM
Name	SDAD1_96F_2	SDAD1_96F_2
Sample_ID	BGHcLV07-31	BGHcLV07-32
transduction_Date	6/13/17	6/13/17
days	D6	D6
RBP_name	SDAD1	SDAD1
qPCR_result	0.0	0.7
Ave_qPCR	0.4
RT-qPCR_primer-F	acctgccgcagttacagaat
RT-qPCR_primer-R	tgctgggtttatttggttgc
protein_conc	3401	4053
WB_result	74.8	84.2
Ave_WB	79.5
WB_DONE_date	7/25/17
MW	80kd
IP
antibody_Cat#	A304-692A
Antibody DCC ID	ENCAB322LZP	ENCAB322LZP
submitted_to_DCC_date	9/27/17
Rep1_TPM	19	0
Rep2_TPM	36	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	6286	6287

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SDAD1	Product_ID: A304-692A Lot_ID: 1 Source: Bethyl Labs Target Name: SDAD1-human

Experiment Status

	BGHcLV07-31	BGHcLV07-32
Sample_ID	BGHcLV07-31	BGHcLV07-32
Sample Name	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-32
Sample Name	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-32
RBP	SDAD1	SDAD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1389	1390

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-31	BGHcLV07-32
Sample #
Sample Name	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-32
Sample_Name_Alias	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-32
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/G4.png	DNA_Library_set39/set1/E8.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set39/set2/A2.png	RNA_Library_set39/set2/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV07-31	BGHcLV07-32
RBP	SDAD1	SDAD1
Batch_ID	BGHcLV07	BGHcLV07
WB_result	74.800	84.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3084	3085

Sequencing Information

	BGHcLV07-31	BGHcLV07-32
Sample_ID	BGHcLV07-31	BGHcLV07-32
Sample Name	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-32
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_H	set39_H
total_reads	42,969,692	87,940,470
total_aligned_reads	37,515,440	75,899,612
unique_aligned_reads	35,419,702	71,517,394
percent_uniqueAligned	0.82429	0.81325
correlation_replicates	0.995885	0.995885
spikein_reads	9,140	28,310
percent_spikeins	0.00021	0.00032
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1735	1736

Data Submission Information

	BGHcLV07-31	BGHcLV07-31
ENCODE_alias	brenton-graveley:SDAD1-BGHcLV07	brenton-graveley:SDAD1-BGHcLV07-HepG2
ENCODE_accession	ENCSR715QWM	ENCSR919NYR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV07-31	BGHcLV07-31
Sample Name	SDAD1-BGHcLV07-31	SDAD1-BGHcLV07-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3234	6934

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
SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1735	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22288
SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1735	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22312
SDAD1-BGHcLV07-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R1.fastq.gz,SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22336
SDAD1-BGHcLV07-31_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31/Aligned.sortedByCoord.out.bam		ENCORE2	22360
SDAD1-BGHcLV07-31_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31/Aligned.sortedByCoord.out.bam		ENCORE2	22384
SDAD1-BGHcLV07-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31/Aligned.sortedByCoord.out.bam		ENCORE2	22408
SDAD1-BGHcLV07-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31/Aligned.sortedByCoord.out.bam		ENCORE2	22432
SDAD1-BGHcLV07-31_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1735					GRCh38	V40	SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R1.fastq.gz,SDAD1-BGHcLV07-31_ATGTCA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22456
SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1736	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22289
SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1736	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22313
SDAD1-BGHcLV07-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R1.fastq.gz,SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22337
SDAD1-BGHcLV07-32_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32/Aligned.sortedByCoord.out.bam		ENCORE2	22361
SDAD1-BGHcLV07-32_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32/Aligned.sortedByCoord.out.bam		ENCORE2	22385
SDAD1-BGHcLV07-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32/Aligned.sortedByCoord.out.bam		ENCORE2	22409
SDAD1-BGHcLV07-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32/Aligned.sortedByCoord.out.bam		ENCORE2	22433
SDAD1-BGHcLV07-32_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1736					GRCh38	V40	SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R1.fastq.gz,SDAD1-BGHcLV07-32_CCGTCC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22457