SMAD4 RNA-Seq in HepG2

General Information


RBP	SMAD4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SMAD4-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR178RVM
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR700FWD
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	SMAD4-BGHcLV18-45
Rep2	SMAD4-BGHcLV18-46
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	39.4
Rep2_qPCR	31.7
Rep1_WB	91.5
Rep2_WB	90.3
Antibody Cat#	701682
Antibody Lot#	lot# 2023880
Antibody DCC ID	ENCAB628ZTV
Status	Released
Project	ENCODE4
ID	118

Experiment Information (Status: Released)

	BGHcLV18-45	BGHcLV18-46
idx	538	539
TRCN#_or_BGC#	BGC#0000426	BGC#0000426
shRNA_or_gRNA_sequence	GTCGATGCACGATTACTTGG	GTCGATGCACGATTACTTGG
PAM	TGG	TGG
Name	SMAD4_97	SMAD4_97
Sample_ID	BGHcLV18-45	BGHcLV18-46
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	SMAD4	SMAD4
qPCR_result	39.4	31.7
Ave_qPCR	35.6
RT-qPCR_primer-F	CTGGCCCAGGATCAGTAGGT
RT-qPCR_primer-R	CATCAACACCAATTCCAGCA
protein_conc	3924	4195
WB_result	91.5	90.3
Ave_WB	90.9
WB_DONE_date	8/21/19
MW	60KD
IP	Rabbit / I	Monoclonal
antibody_Cat#	701682	lot# 2023880
Antibody DCC ID	ENCAB628ZTV
submitted_to_DCC_date
Rep1_TPM	44	0
Rep2_TPM	53	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6693	6694

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD4	Product_ID: 701682 Lot_ID: 2023880 Source: Thermo Fisher Target Name: SMAD4-human

Experiment Status

	BGHcLV18-45	BGHcLV18-46
Sample_ID	BGHcLV18-45	BGHcLV18-46
Sample Name
Sample Name	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-46
RBP	SMAD4	SMAD4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5653	5654

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-45	BGHcLV18-46
Sample #	159	160
Sample Name	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-46
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-C2	5-D2
Tecan	35.49	35.13
Tecan_date	2019-12-16	2019-12-16
Size_bp	269	273
Peak_Molarity	29.50	32.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E9.png	DNA_Library_set43-44/set2/F9.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/A11.png	RNA_Library_set43-44/set4/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-45	BGHcLV18-46
RBP	SMAD4	SMAD4
Batch_ID	BGHcLV18	BGHcLV18
WB_result	91.500	90.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	735	736

Sequencing Information

	BGHcLV18-45	BGHcLV18-46
Sample_ID	BGHcLV18-45	BGHcLV18-46
Sample Name	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-46
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	150,129,472	173,989,588
total_aligned_reads	147,187,420	169,898,506
unique_aligned_reads	137,697,556	159,091,138
percent_uniqueAligned	0.91719	0.91437
correlation_replicates	0.999505	0.999505
spikein_reads	221,454	262,242
percent_spikeins	0.00148	0.00151
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	241	242

Data Submission Information

	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-46	BGHcLV18-46	BGHcLV18-46	BGHcLV18-46
ENCODE_alias	brenton-graveley:SMAD4-BGHcLV18	brenton-graveley:SMAD4-BGHcLV18-45	brenton-graveley:L-SMAD4-BGHcLV18-45	brenton-graveley:SMAD4-BGHcLV18-45_S71_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGHcLV18-45_S71_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGHcLV18-HepG2	brenton-graveley:SMAD4-BGHcLV18-46	brenton-graveley:L-SMAD4-BGHcLV18-46	brenton-graveley:SMAD4-BGHcLV18-46_S72_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGHcLV18-46_S72_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR700FWD	ENCBS825NAN	ENCLB811UZM	ENCFF825JUA	ENCFF576JKC	ENCSR178RVM	ENCBS949DYY	ENCLB210KIY	ENCFF442SXF	ENCFF591YVS
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	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-45	BGHcLV18-46	BGHcLV18-46	BGHcLV18-46	BGHcLV18-46
Sample Name	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-45	SMAD4-BGHcLV18-46	SMAD4-BGHcLV18-46	SMAD4-BGHcLV18-46	SMAD4-BGHcLV18-46
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		SMAD4-BGHcLV18-45.pdf	L-SMAD4-BGHcLV18-45.pdf				SMAD4-BGHcLV18-46.pdf	L-SMAD4-BGHcLV18-46.pdf
ID	65	210	376	626	678	7327	211	377	627	679

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
SMAD4-BGHcLV18-45_S71_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	241	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	213
SMAD4-BGHcLV18-45_S71_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	241	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	265
SMAD4-BGHcLV18-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45_S71_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGHcLV18-45_S71_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24933
SMAD4-BGHcLV18-45_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45/Aligned.sortedByCoord.out.bam		ENCORE2	24985
SMAD4-BGHcLV18-45_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45/Aligned.sortedByCoord.out.bam		ENCORE2	25037
SMAD4-BGHcLV18-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45/Aligned.sortedByCoord.out.bam		ENCORE2	25089
SMAD4-BGHcLV18-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45/Aligned.sortedByCoord.out.bam		ENCORE2	25141
SMAD4-BGHcLV18-45_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	241					GRCh38	V40	SMAD4-BGHcLV18-45_S71_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGHcLV18-45_S71_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25193
SMAD4-BGHcLV18-46_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	242	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	214
SMAD4-BGHcLV18-46_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	242	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	266
SMAD4-BGHcLV18-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46_S72_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGHcLV18-46_S72_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24934
SMAD4-BGHcLV18-46_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46/Aligned.sortedByCoord.out.bam		ENCORE2	24986
SMAD4-BGHcLV18-46_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46/Aligned.sortedByCoord.out.bam		ENCORE2	25038
SMAD4-BGHcLV18-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46/Aligned.sortedByCoord.out.bam		ENCORE2	25090
SMAD4-BGHcLV18-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46/Aligned.sortedByCoord.out.bam		ENCORE2	25142
SMAD4-BGHcLV18-46_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	242					GRCh38	V40	SMAD4-BGHcLV18-46_S72_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGHcLV18-46_S72_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25194