SEC62 RNA-Seq in K562

General Information


RBP	SEC62
Cell_Line	K562
Method	CRISPR
Exp_Name	SEC62-BGKcLV33-K562
ENCODE_series_ID	ENCSR936PNF
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR008ECN
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SEC62-BGKcLV33-39
Rep2	SEC62-BGKcLV33-40
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A304-176A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	903

Experiment Information (Status: Released)

	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
idx	1135	1218	1220	1136	1219	1221
TRCN#_or_BGC#	BGC#0000851	BGC#0000846	BGC#0000846	BGC#0000851	BGC#0000846	BGC#0000846
shRNA_or_gRNA_sequence	CCACCAATATGATGGGTCAC	ATGTCGGGATTGTCGCACAA	ATGTCGGGATTGTCGCACAA	CCACCAATATGATGGGTCAC	ATGTCGGGATTGTCGCACAA	ATGTCGGGATTGTCGCACAA
PAM	CGG	TGG	TGG	CGG	TGG	TGG
Name	SEC62_84	SCAF8_97	SCAF8_97	SEC62_84	SCAF8_97	SCAF8_97
Sample_ID	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	SEC62	SCAF8	SCAF8	SEC62	SCAF8	SCAF8
qPCR_result		31.2	31.2		41.4	41.4
Ave_qPCR		36.3	36.3
RT-qPCR_primer-F		gttttggccagcactaccac	gttttggccagcactaccac
RT-qPCR_primer-R		tacccacggatcaggtaagc	tacccacggatcaggtaagc
protein_conc	442	2061	2061	392	2028	2028
WB_result	95.7	80.5	91.2	98.3	76.3	94.7
Ave_WB	97.0	78.4	92.9
WB_DONE_date	1/24/22	3/14/22	3/23/22
MW	46kd	141kd	141kd
IP
antibody_Cat#	A303-981A	A301-036A	A301-037A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB569CKW	ENCAB332NQB		8/4/22	8/4/22
submitted_to_DCC_date		8/16/22	8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date		04/13/22			04/13/22
repeat_library
Note
ID	5275	5360	5362	5276	5361	5363

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SCAF8	Product_ID: A301-036A Lot_ID: 1 Source: Bethyl Labs Target Name: SCAF8-human
SCAF8	Product_ID: A301-037A Lot_ID: 1 Source: Bethyl Labs Target Name: SCAF8-human

Experiment Status

	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
Sample_ID	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
Sample Name
Sample Name	SCAF8-BGKcLV33-33			SCAF8-BGKcLV33-34
RBP	SCAF8	SEC62	SCAF8	SCAF8	SEC62	SCAF8
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	NotSatisfied	Released	NotSatisfied	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-03-30	2022-10-28	2022-03-30	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10655	10719	10775	10656	10720	10776

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-33	BGKcLV33-34
Sample #	25	26
Sample Name	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-34
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	287	292
Peak_Molarity	56.60	68.80
libSampleQC_DNA_Well	DNA_Library_set53/set1/A8.png	DNA_Library_set53/set1/B8.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set53/set1/A4.png	RNA_Library_set53/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-33	BGKcLV33-34
RBP	SCAF8	SCAF8
Batch_ID	BGKcLV33	BGKcLV33
WB_result	80.500	76.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3286	3287

Sequencing Information

	BGKcLV33-33	BGKcLV33-34
Sample_ID	BGKcLV33-33	BGKcLV33-34
Sample Name	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-34
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	122,579,810	93,368,686
total_aligned_reads	111,917,562	85,440,814
unique_aligned_reads	102,011,970	77,887,124
percent_uniqueAligned	0.83221	0.83419
correlation_replicates	0.988825	0.988825
spikein_reads	31,648	15,658
percent_spikeins	0.00026	0.00017
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2053	2054

Data Submission Information

	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
ENCODE_alias	brenton-graveley:SCAF8-BGKcLV33	brenton-graveley:SCAF8-BGKcLV33-33	brenton-graveley:L-SCAF8-BGKcLV33-33	brenton-graveley:SCAF8-BGKcLV33-33_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGKcLV33-33_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGKcLV33-K562	brenton-graveley:SCAF8-BGKcLV33-34	brenton-graveley:L-SCAF8-BGKcLV33-34	brenton-graveley:SCAF8-BGKcLV33-34_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGKcLV33-34_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR329UEC	ENCBS504VVD	ENCLB123ZJK	ENCFF808UFC	ENCFF870IVY	ENCSR184MTJ	ENCBS462NYH	ENCLB172XDC	ENCFF019YBI	ENCFF228XAQ
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	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-33	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34	BGKcLV33-34
Sample Name	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-33	SCAF8-BGKcLV33-34	SCAF8-BGKcLV33-34	SCAF8-BGKcLV33-34	SCAF8-BGKcLV33-34
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
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SCAF8-BGKcLV33-33.pdf	L-SCAF8-BGKcLV33-33.pdf				SCAF8-BGKcLV33-34.pdf	L-SCAF8-BGKcLV33-34.pdf
ID	7483	7575	7685	7795	7905	7972	7576	7686	7796	7906

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
SCAF8-BGKcLV33-33_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2053	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6631
SCAF8-BGKcLV33-33_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2053	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6687
SCAF8-BGKcLV33-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGKcLV33-33_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18108
SCAF8-BGKcLV33-33_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	18164
SCAF8-BGKcLV33-33_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	18220
SCAF8-BGKcLV33-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	18276
SCAF8-BGKcLV33-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33/Aligned.sortedByCoord.out.bam		ENCORE2	18332
SCAF8-BGKcLV33-33_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2053					GRCh38	V40	SCAF8-BGKcLV33-33_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGKcLV33-33_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18388
SCAF8-BGKcLV33-34_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2054	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6632
SCAF8-BGKcLV33-34_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2054	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6688
SCAF8-BGKcLV33-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGKcLV33-34_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18109
SCAF8-BGKcLV33-34_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	18165
SCAF8-BGKcLV33-34_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	18221
SCAF8-BGKcLV33-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	18277
SCAF8-BGKcLV33-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34/Aligned.sortedByCoord.out.bam		ENCORE2	18333
SCAF8-BGKcLV33-34_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2054					GRCh38	V40	SCAF8-BGKcLV33-34_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGKcLV33-34_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18389