SMAD2 RNA-Seq in HepG2

General Information


RBP	SMAD2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SMAD2-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR429MST
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR036ANR
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	SMAD2-BGHcLV16-51
Rep2	SMAD2-BGHcLV16-52
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	12.9
Rep2_qPCR	0.0
Rep1_WB	99.6
Rep2_WB	99.8
Antibody Cat#	700048
Antibody Lot#	LOT# TH2627538
Antibody DCC ID	ENCAB373WLA
Status	Released
Project	ENCODE4
ID	157

Experiment Information (Status: Released)

	BGHcLV16-51	BGHcLV16-51	BGHcLV16-52	BGHcLV16-52
idx	481	0	482	0
TRCN#_or_BGC#	BGC#0000368	BGC#0000368	BGC#0000368	BGC#0000368
shRNA_or_gRNA_sequence	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG
PAM	GGG	GGG	GGG	GGG
Name	SMAD2-94	SMAD2-94	SMAD2-94	SMAD2-94
Sample_ID	BGHcLV16-51	BGHcLV16-51	BGHcLV16-52	BGHcLV16-52
transduction_Date	4/16/19	4/16/19	4/16/19	4/16/19
days	D6	D6	D6	D6
RBP_name	SMAD2	SMAD2	SMAD2	SMAD2
qPCR_result	12.9		0.0
Ave_qPCR	6.4
RT-qPCR_primer-F	TAACTTCCCAGCAGGAATTGAG
RT-qPCR_primer-R	TTCAACTGTTGGTCACTTGTTTCT
protein_conc	3858	3858	5396	5396
WB_result	99.6	NO CLEAR BAND ON THE POSION	99.8
Ave_WB	99.7
WB_DONE_date	4/25/19	5/6/19	WES	WES
MW	60KD	58kd
IP	Rabbit / I	Rabbit / I		Monoclonal
antibody_Cat#	700048	700050	LOT# TH2627538	SMAD2 pThr8
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	36	36	0	0
Rep2_TPM	43	43	0	0
Action	Ready		Ready
Library_start_date	12/03/19		12/03/19
repeat_library
Note
ID	6630	6632	6631	6633

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD2	Product_ID: 700048 Lot_ID: TH2627538 Source: Thermo Fisher Target Name: SMAD2-human

Experiment Status

	BGHcLV16-51	BGHcLV16-52
Sample_ID	BGHcLV16-51	BGHcLV16-52
Sample Name
Sample Name	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-52
RBP	SMAD2	SMAD2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5433	5434

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-51	BGHcLV16-52
Sample #	67	68
Sample Name	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-52
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-A2	2-B2
Tecan	25.60	34.52
Tecan_date	2019-12-10	2019-12-10
Size_bp	277	280
Peak_Molarity	41.10	50.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A4.png	DNA_Library_set43-44/set3/B11.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A9.png	RNA_Library_set43-44/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-16
Sample_ID	BGHcLV16-51	BGHcLV16-52
RBP	SMAD2	SMAD2
Batch_ID	BGHcLV16	BGHcLV16
WB_result	99.600	99.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	643	644

Sequencing Information

	BGHcLV16-51	BGHcLV16-52
Sample_ID	BGHcLV16-51	BGHcLV16-52
Sample Name	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-52
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	103,310,116	223,343,498
total_aligned_reads	95,477,840	203,442,292
unique_aligned_reads	89,582,450	190,832,226
percent_uniqueAligned	0.86712	0.85443
correlation_replicates	0.993347	0.993347
spikein_reads	180,972	316,662
percent_spikeins	0.00175	0.00142
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	145	146

Data Submission Information

	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-52	BGHcLV16-52	BGHcLV16-52	BGHcLV16-52
ENCODE_alias	brenton-graveley:SMAD2-BGHcLV16	brenton-graveley:SMAD2-BGHcLV16-51	brenton-graveley:L-SMAD2-BGHcLV16-51	brenton-graveley:SMAD2-BGHcLV16-51_S63_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGHcLV16-51_S63_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGHcLV16-HepG2	brenton-graveley:SMAD2-BGHcLV16-52	brenton-graveley:L-SMAD2-BGHcLV16-52	brenton-graveley:SMAD2-BGHcLV16-52_S64_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGHcLV16-52_S64_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR036ANR	ENCBS554PNG	ENCLB521BHC	ENCFF951XMO	ENCFF620DRO	ENCSR429MST	ENCBS142KLP	ENCLB233RED	ENCFF518ZFP	ENCFF222WVJ
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	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-51	BGHcLV16-52	BGHcLV16-52	BGHcLV16-52	BGHcLV16-52
Sample Name	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-51	SMAD2-BGHcLV16-52	SMAD2-BGHcLV16-52	SMAD2-BGHcLV16-52	SMAD2-BGHcLV16-52
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		SMAD2-BGHcLV16-51.pdf	L-SMAD2-BGHcLV16-51.pdf				SMAD2-BGHcLV16-52.pdf	L-SMAD2-BGHcLV16-52.pdf
ID	13	108	272	438	470	7325	109	273	439	471

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
SMAD2-BGHcLV16-51_S63_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	145	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	25
SMAD2-BGHcLV16-51_S63_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	145	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	57
SMAD2-BGHcLV16-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51_S63_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGHcLV16-51_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24188
SMAD2-BGHcLV16-51_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51/Aligned.sortedByCoord.out.bam		ENCORE2	24220
SMAD2-BGHcLV16-51_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51/Aligned.sortedByCoord.out.bam		ENCORE2	24252
SMAD2-BGHcLV16-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51/Aligned.sortedByCoord.out.bam		ENCORE2	24284
SMAD2-BGHcLV16-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51/Aligned.sortedByCoord.out.bam		ENCORE2	24316
SMAD2-BGHcLV16-51_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	145					GRCh38	V40	SMAD2-BGHcLV16-51_S63_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGHcLV16-51_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24348
SMAD2-BGHcLV16-52_S64_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	146	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	26
SMAD2-BGHcLV16-52_S64_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	146	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	58
SMAD2-BGHcLV16-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52_S64_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGHcLV16-52_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24189
SMAD2-BGHcLV16-52_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52/Aligned.sortedByCoord.out.bam		ENCORE2	24221
SMAD2-BGHcLV16-52_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52/Aligned.sortedByCoord.out.bam		ENCORE2	24253
SMAD2-BGHcLV16-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52/Aligned.sortedByCoord.out.bam		ENCORE2	24285
SMAD2-BGHcLV16-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52/Aligned.sortedByCoord.out.bam		ENCORE2	24317
SMAD2-BGHcLV16-52_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	146					GRCh38	V40	SMAD2-BGHcLV16-52_S64_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGHcLV16-52_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24349