SEC31A RNA-Seq in K562

General Information


RBP	SEC31A
Cell_Line	K562
Method	CRISPR
Exp_Name	SEC31A-BGKcLV33-K562
ENCODE_series_ID	ENCSR848NDO
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR218ITU
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SEC31A-BGKcLV33-37
Rep2	SEC31A-BGKcLV33-38
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	no band on the position
Rep2_WB
Antibody Cat#	A303-949A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	902

Experiment Information (Status: Released)

	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
idx	1133	1214	1216	1134	1215	1217
TRCN#_or_BGC#	BGC#0000849	BGC#0000844	BGC#0000844	BGC#0000849	BGC#0000844	BGC#0000844
shRNA_or_gRNA_sequence	AGTGGTGCTTCGATATTCAG	CTTATGGAGCTCCACCGTCT	CTTATGGAGCTCCACCGTCT	AGTGGTGCTTCGATATTCAG	CTTATGGAGCTCCACCGTCT	CTTATGGAGCTCCACCGTCT
PAM	TGG	CGG	CGG	TGG	CGG	CGG
Name	SEC31A_88	SARNP_74	SARNP_74	SEC31A_88	SARNP_74	SARNP_74
Sample_ID	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
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	SEC31A	SARNP	SARNP	SEC31A	SARNP	SARNP
qPCR_result		XX	XX		XX	XX
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	384	2178	2178	377	2195	2195
WB_result	64.6	68.0	64.6	65.7	72.0	58.9
Ave_WB	65.2	70.0	61.7
WB_DONE_date	1/26/22	3/2/22	3/23/22
MW	133kd	24kd	24kd
IP
antibody_Cat#	A302-336A	A303-209A	A303-210A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB353OXX	no id		8/4/22	8/4/22
submitted_to_DCC_date		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	5273	5356	5358	5274	5357	5359

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SARNP	Product_ID: A303-209A Lot_ID: 1 Source: Bethyl Labs Target Name: SARNP-human
SARNP	Product_ID: A303-210A Lot_ID: 1 Source: Bethyl Labs Target Name: SARNP-human

Experiment Status

	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
Sample_ID	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
Sample Name
Sample Name	SARNP-BGKcLV33-31			SARNP-BGKcLV33-32
RBP	SARNP	SEC31A	SARNP	SARNP	SEC31A	SARNP
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	10653	10717	10773	10654	10718	10774

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-31	BGKcLV33-32
Sample #	23	24
Sample Name	SARNP-BGKcLV33-31	SARNP-BGKcLV33-32
Sample_Name_Alias
Index Well Position	G03	H03
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	302	288
Peak_Molarity	57.50	45.40
libSampleQC_DNA_Well	DNA_Library_set53/set1/G7.png	DNA_Library_set53/set1/H7.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set53/set1/G3.png	RNA_Library_set53/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-31	BGKcLV33-32
RBP	SARNP	SARNP
Batch_ID	BGKcLV33	BGKcLV33
WB_result	68.000	72.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3284	3285

Sequencing Information

	BGKcLV33-31	BGKcLV33-32
Sample_ID	BGKcLV33-31	BGKcLV33-32
Sample Name	SARNP-BGKcLV33-31	SARNP-BGKcLV33-32
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	74,620,006	78,377,138
total_aligned_reads	68,296,120	70,282,760
unique_aligned_reads	62,539,994	64,071,822
percent_uniqueAligned	0.83811	0.81748
correlation_replicates	0.997446	0.997446
spikein_reads	4,712	11,336
percent_spikeins	0.00006	0.00014
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2051	2052

Data Submission Information

	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
ENCODE_alias	brenton-graveley:SARNP-BGKcLV33	brenton-graveley:SARNP-BGKcLV33-31	brenton-graveley:L-SARNP-BGKcLV33-31	brenton-graveley:SARNP-BGKcLV33-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGKcLV33-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGKcLV33-K562	brenton-graveley:SARNP-BGKcLV33-32	brenton-graveley:L-SARNP-BGKcLV33-32	brenton-graveley:SARNP-BGKcLV33-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGKcLV33-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR639XFV	ENCBS783LPC	ENCLB753EDT	ENCFF656XRO	ENCFF683OXW	ENCSR862NTU	ENCBS173FOK	ENCLB451BYR	ENCFF016BTQ	ENCFF883HUH
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	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-31	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32	BGKcLV33-32
Sample Name	SARNP-BGKcLV33-31	SARNP-BGKcLV33-31	SARNP-BGKcLV33-31	SARNP-BGKcLV33-31	SARNP-BGKcLV33-31	SARNP-BGKcLV33-31	SARNP-BGKcLV33-32	SARNP-BGKcLV33-32	SARNP-BGKcLV33-32	SARNP-BGKcLV33-32
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		SARNP-BGKcLV33-31.pdf	L-SARNP-BGKcLV33-31.pdf				SARNP-BGKcLV33-32.pdf	L-SARNP-BGKcLV33-32.pdf
ID	7482	7573	7683	7793	7903	7971	7574	7684	7794	7904

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
SARNP-BGKcLV33-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2051	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	6629
SARNP-BGKcLV33-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2051	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	6685
SARNP-BGKcLV33-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2051					GRCh38	V40	SARNP-BGKcLV33-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGKcLV33-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18106
SARNP-BGKcLV33-31_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	2051					GRCh38	V40	SARNP-BGKcLV33-31/Aligned.sortedByCoord.out.bam		ENCORE2	18162
SARNP-BGKcLV33-31_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	2051					GRCh38	V40	SARNP-BGKcLV33-31/Aligned.sortedByCoord.out.bam		ENCORE2	18218
SARNP-BGKcLV33-31_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	2051					GRCh38	V40	SARNP-BGKcLV33-31/Aligned.sortedByCoord.out.bam		ENCORE2	18274
SARNP-BGKcLV33-31_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	2051					GRCh38	V40	SARNP-BGKcLV33-31/Aligned.sortedByCoord.out.bam		ENCORE2	18330
SARNP-BGKcLV33-31_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2051					GRCh38	V40	SARNP-BGKcLV33-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGKcLV33-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18386
SARNP-BGKcLV33-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2052	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	6630
SARNP-BGKcLV33-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2052	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	6686
SARNP-BGKcLV33-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2052					GRCh38	V40	SARNP-BGKcLV33-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGKcLV33-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18107
SARNP-BGKcLV33-32_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	2052					GRCh38	V40	SARNP-BGKcLV33-32/Aligned.sortedByCoord.out.bam		ENCORE2	18163
SARNP-BGKcLV33-32_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	2052					GRCh38	V40	SARNP-BGKcLV33-32/Aligned.sortedByCoord.out.bam		ENCORE2	18219
SARNP-BGKcLV33-32_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	2052					GRCh38	V40	SARNP-BGKcLV33-32/Aligned.sortedByCoord.out.bam		ENCORE2	18275
SARNP-BGKcLV33-32_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	2052					GRCh38	V40	SARNP-BGKcLV33-32/Aligned.sortedByCoord.out.bam		ENCORE2	18331
SARNP-BGKcLV33-32_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2052					GRCh38	V40	SARNP-BGKcLV33-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGKcLV33-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18387