SAMHD1 RNA-Seq in HepG2

General Information


RBP	SAMHD1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SAMHD1-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR424OIS
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR878TRK
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SAMHD1-BGHcLV31-23
Rep2	SAMHD1-BGHcLV31-24
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	71.8
Rep2_WB	72.4
Antibody Cat#	A303-690A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCODE4
ID	923

Experiment Information (Status: Released)

	BGHcLV31-23	BGHcLV31-24
idx	941	942
TRCN#_or_BGC#	BGC#0000839	BGC#0000839
shRNA_or_gRNA_sequence	CTCGGGCTGTCATCGCAACG	CTCGGGCTGTCATCGCAACG
PAM	GGG	GGG
Name	SAMHD1_96	SAMHD1_96
Sample_ID	BGHcLV31-23	BGHcLV31-24
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SAMHD1	SAMHD1
qPCR_result	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3632	4232
WB_result	71.8	72.4
Ave_WB	72.1
WB_DONE_date	10/27/21	jess
MW	72kd
IP
antibody_Cat#	A303-690A	LOT #1
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7120	7121

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAMHD1	Product_ID: A303-690A Lot_ID: 1 Source: Bethyl Labs Target Name: SAMHD1-human

Experiment Status

	BGHcLV31-23	BGHcLV31-24
Sample_ID	BGHcLV31-23	BGHcLV31-24
Sample Name
Sample Name	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-24
RBP	SAMHD1	SAMHD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10301	10302

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-23	BGHcLV31-24
Sample #	15	16
Sample Name	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-24
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	285	286
Peak_Molarity	70.30	71.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/G9.png	DNA_Library_set52/set1/H9.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set52/set1/G2.png	RNA_Library_set52/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-23	BGHcLV31-24
RBP	SAMHD1	SAMHD1
Batch_ID	BGHcLV31	BGHcLV31
WB_result	71.800	72.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3192	3193

Sequencing Information

	BGHcLV31-23	BGHcLV31-24
Sample_ID	BGHcLV31-23	BGHcLV31-24
Sample Name	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-24
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	89,285,232	81,368,678
total_aligned_reads	79,373,702	71,537,354
unique_aligned_reads	74,693,640	67,367,434
percent_uniqueAligned	0.83657	0.82793
correlation_replicates	0.999547	0.999547
spikein_reads	4,832	6,528
percent_spikeins	0.00005	0.00008
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1989	1990

Data Submission Information

	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-24	BGHcLV31-24	BGHcLV31-24	BGHcLV31-24
ENCODE_alias	brenton-graveley:SAMHD1-BGHcLV31	brenton-graveley:SAMHD1-BGHcLV31-23	brenton-graveley:L-SAMHD1-BGHcLV31-23	brenton-graveley:SAMHD1-BGHcLV31-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGHcLV31-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGHcLV31-HepG2	brenton-graveley:SAMHD1-BGHcLV31-24	brenton-graveley:L-SAMHD1-BGHcLV31-24	brenton-graveley:SAMHD1-BGHcLV31-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGHcLV31-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR878TRK	ENCBS279YBS	ENCLB252AWJ	ENCFF581GQQ	ENCFF482UQE	ENCSR424OIS	ENCBS011AMX	ENCLB338BJP	ENCFF484PPW	ENCFF814ICT
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	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-23	BGHcLV31-24	BGHcLV31-24	BGHcLV31-24	BGHcLV31-24
Sample Name	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-23	SAMHD1-BGHcLV31-24	SAMHD1-BGHcLV31-24	SAMHD1-BGHcLV31-24	SAMHD1-BGHcLV31-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		SAMHD1-BGHcLV31-23.pdf	L-SAMHD1-BGHcLV31-23.pdf				SAMHD1-BGHcLV31-24.pdf	L-SAMHD1-BGHcLV31-24.pdf
ID	7451	7513	7621	7731	7841	7943	7514	7622	7732	7842

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
SAMHD1-BGHcLV31-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1989	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6535
SAMHD1-BGHcLV31-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1989	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6589
SAMHD1-BGHcLV31-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGHcLV31-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18456
SAMHD1-BGHcLV31-23_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	18510
SAMHD1-BGHcLV31-23_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	18564
SAMHD1-BGHcLV31-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	18618
SAMHD1-BGHcLV31-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23/Aligned.sortedByCoord.out.bam		ENCORE2	18672
SAMHD1-BGHcLV31-23_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1989					GRCh38	V40	SAMHD1-BGHcLV31-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGHcLV31-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18726
SAMHD1-BGHcLV31-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1990	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6536
SAMHD1-BGHcLV31-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1990	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6590
SAMHD1-BGHcLV31-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGHcLV31-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18457
SAMHD1-BGHcLV31-24_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	18511
SAMHD1-BGHcLV31-24_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	18565
SAMHD1-BGHcLV31-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	18619
SAMHD1-BGHcLV31-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24/Aligned.sortedByCoord.out.bam		ENCORE2	18673
SAMHD1-BGHcLV31-24_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1990					GRCh38	V40	SAMHD1-BGHcLV31-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGHcLV31-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18727