SART1 RNA-Seq in K562

General Information


RBP	SART1
Cell_Line	K562
Method	CRISPR
Exp_Name	SART1-BGKcLV21-K562
ENCODE_series_ID	ENCSR876MPH
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR208AJS
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	SART1-BGKcLV21-39
Rep2	SART1-BGKcLV21-40
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	56.3
Rep2_qPCR	45.1
Rep1_WB	75.8
Rep2_WB	74.8
Antibody Cat#	A301-422A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB301DST
Status	Released
Project	ENCODE4
ID	72

Experiment Information (Status: Released)

	BGKcLV21-39	BGKcLV21-40
idx	772	773
TRCN#_or_BGC#	BGC#0000539	BGC#0000539
shRNA_or_gRNA_sequence	TATGGCCTTGCGACAGCGAG	TATGGCCTTGCGACAGCGAG
PAM	AGG	AGG
Name	SART1_96	SART1_96
Sample_ID	BGKcLV21-39	BGKcLV21-40
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	SART1	SART1
qPCR_result	56.3	45.1
Ave_qPCR	50.7
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5592	5429
WB_result	75.8	74.8
Ave_WB	75.3
WB_DONE_date	9/17/29	JESS
MW	90.3kDa
IP	Rabbit / I
antibody_Cat#	A301-422A	lot# 1
Antibody DCC ID	ENCAB301DST
submitted_to_DCC_date	11/16/20
Rep1_TPM	32.7	0
Rep2_TPM	21.3	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4892	4893

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SART1	Product_ID: A301-422A Lot_ID: 1 Source: Bethyl Labs Target Name: SART1-human

Experiment Status

	BGKcLV21-39	BGKcLV21-40
Sample_ID	BGKcLV21-39	BGKcLV21-40
Sample Name
Sample Name	SART1-BGKcLV21-39	SART1-BGKcLV21-40
RBP	SART1	SART1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6135	6136

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-39	BGKcLV21-40
Sample #	53	54
Sample Name	SART1-BGKcLV21-39	SART1-BGKcLV21-40
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	304	294
Peak_Molarity	85.20	93.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/G6.png	DNA_Library_set45/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set45/set1/G6.png	RNA_Library_set45/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-39	BGKcLV21-40
RBP	SART1	SART1
Batch_ID	BGKcLV21	BGKcLV21
WB_result	75.800	74.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	827	828

Sequencing Information

	BGKcLV21-39	BGKcLV21-40
Sample_ID	BGKcLV21-39	BGKcLV21-40
Sample Name	SART1-BGKcLV21-39	SART1-BGKcLV21-40
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	142,999,012	103,102,256
total_aligned_reads	142,376,646	99,828,302
unique_aligned_reads	130,032,890	91,055,152
percent_uniqueAligned	0.90933	0.88315
correlation_replicates	0.984111	0.984111
spikein_reads	94,582	101,364
percent_spikeins	0.00066	0.00098
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	458	459

Data Submission Information

	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-40	BGKcLV21-40	BGKcLV21-40	BGKcLV21-40
ENCODE_alias	brenton-graveley:SART1-BGKcLV21	brenton-graveley:SART1-BGKcLV21-39	brenton-graveley:L-SART1-BGKcLV21-39	brenton-graveley:SART1-BGKcLV21-39_S47_R1_001.fastq.gz	brenton-graveley:SART1-BGKcLV21-39_S47_R2_001.fastq.gz	brenton-graveley:SART1-BGKcLV21-K562	brenton-graveley:SART1-BGKcLV21-40	brenton-graveley:L-SART1-BGKcLV21-40	brenton-graveley:SART1-BGKcLV21-40_S48_R1_001.fastq.gz	brenton-graveley:SART1-BGKcLV21-40_S48_R2_001.fastq.gz
ENCODE_accession	ENCSR208AJS	ENCBS257WRR	ENCLB909ITK	ENCFF597ZJB	ENCFF539URZ	ENCSR876MPH	ENCBS845NMN	ENCLB414SMO	ENCFF450EYQ	ENCFF153KJC
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	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-39	BGKcLV21-40	BGKcLV21-40	BGKcLV21-40	BGKcLV21-40
Sample Name	SART1-BGKcLV21-39	SART1-BGKcLV21-39	SART1-BGKcLV21-39	SART1-BGKcLV21-39	SART1-BGKcLV21-39	SART1-BGKcLV21-39	SART1-BGKcLV21-40	SART1-BGKcLV21-40	SART1-BGKcLV21-40	SART1-BGKcLV21-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		SART1-BGKcLV21-39.pdf	L-SART1-BGKcLV21-39.pdf				SART1-BGKcLV21-40.pdf	L-SART1-BGKcLV21-40.pdf
ID	2113	2181	2251	2321	2391	7319	2182	2252	2322	2392

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
SART1-BGKcLV21-39_S47_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	458	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1248
SART1-BGKcLV21-39_S47_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	458	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1298
SART1-BGKcLV21-39_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39_S47_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGKcLV21-39_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25241
SART1-BGKcLV21-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39_S47_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGKcLV21-39_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27195
SART1-BGKcLV21-39_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39/Aligned.sortedByCoord.out.bam		ENCORE2	27245
SART1-BGKcLV21-39_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39/Aligned.sortedByCoord.out.bam		ENCORE2	27295
SART1-BGKcLV21-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39/Aligned.sortedByCoord.out.bam		ENCORE2	27345
SART1-BGKcLV21-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	458					GRCh38	V40	SART1-BGKcLV21-39/Aligned.sortedByCoord.out.bam		ENCORE2	27395
SART1-BGKcLV21-40_S48_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	459	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1249
SART1-BGKcLV21-40_S48_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	459	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1299
SART1-BGKcLV21-40_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40_S48_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGKcLV21-40_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25242
SART1-BGKcLV21-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40_S48_R1_001.filtered.trimmed.paired.fastq.gz,SART1-BGKcLV21-40_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27196
SART1-BGKcLV21-40_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40/Aligned.sortedByCoord.out.bam		ENCORE2	27246
SART1-BGKcLV21-40_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40/Aligned.sortedByCoord.out.bam		ENCORE2	27296
SART1-BGKcLV21-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40/Aligned.sortedByCoord.out.bam		ENCORE2	27346
SART1-BGKcLV21-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	459					GRCh38	V40	SART1-BGKcLV21-40/Aligned.sortedByCoord.out.bam		ENCORE2	27396