SMAD5 RNA-Seq in HepG2

General Information


RBP	SMAD5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SMAD5-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR456RHD
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR383QYT
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	SMAD5-BGHcLV18-47
Rep2	SMAD5-BGHcLV18-48
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	75.5
Rep2_WB	85.5
Antibody Cat#	39-5700
Antibody Lot#	SA247535
Antibody DCC ID	ENCAB746HXR
Status	Released
Project	ENCODE4
ID	119

Experiment Information (Status: Released)

	BGHcLV18-47	BGHcLV18-48
idx	540	541
TRCN#_or_BGC#	BGC#0000409	BGC#0000409
shRNA_or_gRNA_sequence	TCATCATGAGCTAAAGCCGT	TCATCATGAGCTAAAGCCGT
PAM	TGG	TGG
Name	SMAD5_93	SMAD5_93
Sample_ID	BGHcLV18-47	BGHcLV18-48
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	SMAD5	SMAD5
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GAGTTTGCTCAGCTTCTGGC
RT-qPCR_primer-R	CTGCCGGTGATATTCTGCTC
protein_conc	4098	4232
WB_result	75.5	85.5
Ave_WB	80.5
WB_DONE_date	8/29/19	WES
MW	52KD
IP	Mouse / Ig
antibody_Cat#	39-5700
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	19	0
Rep2_TPM	24	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6695	6696

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD5	Product_ID: 39-5700 Lot_ID: SA247535 Source: Thermo Fisher Target Name: SMAD5-human

Experiment Status

	BGHcLV18-47	BGHcLV18-48
Sample_ID	BGHcLV18-47	BGHcLV18-48
Sample Name
Sample Name	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-48
RBP	SMAD5	SMAD5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5655	5656

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-47	BGHcLV18-48
Sample #	161	162
Sample Name	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-48
Sample_Name_Alias
Index Well Position	A09	B09
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-E2	5-F2
Tecan	40.69	37.36
Tecan_date	2019-12-16	2019-12-16
Size_bp	273	269
Peak_Molarity	33.80	34.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G9.png	DNA_Library_set43-44/set2/H9.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/C11.png	RNA_Library_set43-44/set4/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-47	BGHcLV18-48
RBP	SMAD5	SMAD5
Batch_ID	BGHcLV18	BGHcLV18
WB_result	75.500	85.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	737	738

Sequencing Information

	BGHcLV18-47	BGHcLV18-48
Sample_ID	BGHcLV18-47	BGHcLV18-48
Sample Name	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-48
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	161,255,290	146,050,476
total_aligned_reads	158,316,652	141,794,096
unique_aligned_reads	148,336,146	132,809,240
percent_uniqueAligned	0.91988	0.90934
correlation_replicates	0.998847	0.998847
spikein_reads	261,736	226,788
percent_spikeins	0.00162	0.00155
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	243	244

Data Submission Information

	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-48	BGHcLV18-48	BGHcLV18-48	BGHcLV18-48
ENCODE_alias	brenton-graveley:SMAD5-BGHcLV18	brenton-graveley:SMAD5-BGHcLV18-47	brenton-graveley:L-SMAD5-BGHcLV18-47	brenton-graveley:SMAD5-BGHcLV18-47_S73_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD5-BGHcLV18-47_S73_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD5-BGHcLV18-HepG2	brenton-graveley:SMAD5-BGHcLV18-48	brenton-graveley:L-SMAD5-BGHcLV18-48	brenton-graveley:SMAD5-BGHcLV18-48_S74_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD5-BGHcLV18-48_S74_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR383QYT	ENCBS010YSJ	ENCLB804LQI	ENCFF284NLV	ENCFF513WXY	ENCSR456RHD	ENCBS919ORJ	ENCLB274JXO	ENCFF319ANQ	ENCFF474AIV
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	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-47	BGHcLV18-48	BGHcLV18-48	BGHcLV18-48	BGHcLV18-48
Sample Name	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-47	SMAD5-BGHcLV18-48	SMAD5-BGHcLV18-48	SMAD5-BGHcLV18-48	SMAD5-BGHcLV18-48
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		SMAD5-BGHcLV18-47.pdf	L-SMAD5-BGHcLV18-47.pdf				SMAD5-BGHcLV18-48.pdf	L-SMAD5-BGHcLV18-48.pdf
ID	66	212	378	628	680	7329	213	379	629	681

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
SMAD5-BGHcLV18-47_S73_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	243	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	215
SMAD5-BGHcLV18-47_S73_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	243	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	267
SMAD5-BGHcLV18-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	243					GRCh38	V40	SMAD5-BGHcLV18-47_S73_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGHcLV18-47_S73_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24935
SMAD5-BGHcLV18-47_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	243					GRCh38	V40	SMAD5-BGHcLV18-47/Aligned.sortedByCoord.out.bam		ENCORE2	24987
SMAD5-BGHcLV18-47_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	243					GRCh38	V40	SMAD5-BGHcLV18-47/Aligned.sortedByCoord.out.bam		ENCORE2	25039
SMAD5-BGHcLV18-47_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	243					GRCh38	V40	SMAD5-BGHcLV18-47/Aligned.sortedByCoord.out.bam		ENCORE2	25091
SMAD5-BGHcLV18-47_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	243					GRCh38	V40	SMAD5-BGHcLV18-47/Aligned.sortedByCoord.out.bam		ENCORE2	25143
SMAD5-BGHcLV18-47_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	243					GRCh38	V40	SMAD5-BGHcLV18-47_S73_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGHcLV18-47_S73_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25195
SMAD5-BGHcLV18-48_S74_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	244	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	216
SMAD5-BGHcLV18-48_S74_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	244	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	268
SMAD5-BGHcLV18-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	244					GRCh38	V40	SMAD5-BGHcLV18-48_S74_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGHcLV18-48_S74_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24936
SMAD5-BGHcLV18-48_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	244					GRCh38	V40	SMAD5-BGHcLV18-48/Aligned.sortedByCoord.out.bam		ENCORE2	24988
SMAD5-BGHcLV18-48_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	244					GRCh38	V40	SMAD5-BGHcLV18-48/Aligned.sortedByCoord.out.bam		ENCORE2	25040
SMAD5-BGHcLV18-48_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	244					GRCh38	V40	SMAD5-BGHcLV18-48/Aligned.sortedByCoord.out.bam		ENCORE2	25092
SMAD5-BGHcLV18-48_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	244					GRCh38	V40	SMAD5-BGHcLV18-48/Aligned.sortedByCoord.out.bam		ENCORE2	25144
SMAD5-BGHcLV18-48_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	244					GRCh38	V40	SMAD5-BGHcLV18-48_S74_R1_001.filtered.trimmed.paired.fastq.gz,SMAD5-BGHcLV18-48_S74_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25196