RRP8 RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14
idx	1115	1190	1116	1191
TRCN#_or_BGC#	BGC#0000832	BGC#0000823	BGC#0000832	BGC#0000823
shRNA_or_gRNA_sequence	AATCTCACGACCTCCGCCTG	TTCGGGCCCCCACCTCACCC	AATCTCACGACCTCCGCCTG	TTCGGGCCCCCACCTCACCC
PAM	CGG	TGG	CGG	TGG
Name	RRP8_91	RPS28_55	RRP8_91	RPS28_55
Sample_ID	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	RRP8	RPS28	RRP8	RPS28
qPCR_result		61.1		46.5
Ave_qPCR		53.8
RT-qPCR_primer-F		accggttctcagggacagt
RT-qPCR_primer-R		tttacattgcggatgatgga
protein_conc	278	2091	409	2300
WB_result	0.0	74.4	0.0	68.8
Ave_WB	0.0	71.6
WB_DONE_date		3/22/22
MW	52KD	7.8kd
IP
antibody_Cat#	A304-202A	A305-095A	LOT #1	LOT #1
Antibody DCC ID		NO ID		8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5255	5330	5256	5331

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS28	Product_ID: A305-095A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS28-human

Experiment Status

	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14
Sample_ID	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14
Sample Name
Sample Name	RPS28-BGKcLV33-13		RPS28-BGKcLV33-14
RBP	RPS28	RRP8	RPS28	RRP8
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10643	10699	10644	10700

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-13	BGKcLV33-14
Sample #	13	14
Sample Name	RPS28-BGKcLV33-13	RPS28-BGKcLV33-14
Sample_Name_Alias
Index Well Position	E02	F02
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	291	294
Peak_Molarity	62.00	70.80
libSampleQC_DNA_Well	DNA_Library_set53/set1/E6.png	DNA_Library_set53/set1/F6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set53/set1/E2.png	RNA_Library_set53/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-13	BGKcLV33-14
RBP	RPS28	RPS28
Batch_ID	BGKcLV33	BGKcLV33
WB_result	74.400	68.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3274	3275

Sequencing Information

	BGKcLV33-13	BGKcLV33-14
Sample_ID	BGKcLV33-13	BGKcLV33-14
Sample Name	RPS28-BGKcLV33-13	RPS28-BGKcLV33-14
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	96,934,162	107,426,702
total_aligned_reads	86,978,854	100,265,882
unique_aligned_reads	79,679,038	92,020,660
percent_uniqueAligned	0.82199	0.85659
correlation_replicates	0.995856	0.995856
spikein_reads	6,712	7,848
percent_spikeins	0.00007	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2041	2042

Data Submission Information

	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14	BGKcLV33-14	BGKcLV33-14
ENCODE_alias	brenton-graveley:RPS28-BGKcLV33	brenton-graveley:RPS28-BGKcLV33-13	brenton-graveley:L-RPS28-BGKcLV33-13	brenton-graveley:RPS28-BGKcLV33-13_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS28-BGKcLV33-13_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS28-BGKcLV33-K562	brenton-graveley:RPS28-BGKcLV33-14	brenton-graveley:L-RPS28-BGKcLV33-14	brenton-graveley:RPS28-BGKcLV33-14_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS28-BGKcLV33-14_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR928XFZ	ENCBS387CRZ	ENCLB435SIW	ENCFF624IUV	ENCFF679WJY	ENCSR355OJK	ENCBS359SKL	ENCLB307ZVV	ENCFF910RMI	ENCFF441ZCE
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	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-13	BGKcLV33-14	BGKcLV33-14	BGKcLV33-14	BGKcLV33-14
Sample Name	RPS28-BGKcLV33-13	RPS28-BGKcLV33-13	RPS28-BGKcLV33-13	RPS28-BGKcLV33-13	RPS28-BGKcLV33-13	RPS28-BGKcLV33-13	RPS28-BGKcLV33-14	RPS28-BGKcLV33-14	RPS28-BGKcLV33-14	RPS28-BGKcLV33-14
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		RPS28-BGKcLV33-13.pdf	L-RPS28-BGKcLV33-13.pdf				RPS28-BGKcLV33-14.pdf	L-RPS28-BGKcLV33-14.pdf
ID	7477	7563	7673	7783	7893	7966	7564	7674	7784	7894

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
RPS28-BGKcLV33-13_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2041	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	6619
RPS28-BGKcLV33-13_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2041	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	6675
RPS28-BGKcLV33-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2041					GRCh38	V40	RPS28-BGKcLV33-13_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGKcLV33-13_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18096
RPS28-BGKcLV33-13_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	2041					GRCh38	V40	RPS28-BGKcLV33-13/Aligned.sortedByCoord.out.bam		ENCORE2	18152
RPS28-BGKcLV33-13_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	2041					GRCh38	V40	RPS28-BGKcLV33-13/Aligned.sortedByCoord.out.bam		ENCORE2	18208
RPS28-BGKcLV33-13_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	2041					GRCh38	V40	RPS28-BGKcLV33-13/Aligned.sortedByCoord.out.bam		ENCORE2	18264
RPS28-BGKcLV33-13_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	2041					GRCh38	V40	RPS28-BGKcLV33-13/Aligned.sortedByCoord.out.bam		ENCORE2	18320
RPS28-BGKcLV33-13_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2041					GRCh38	V40	RPS28-BGKcLV33-13_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGKcLV33-13_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18376
RPS28-BGKcLV33-14_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2042	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	6620
RPS28-BGKcLV33-14_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2042	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	6676
RPS28-BGKcLV33-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2042					GRCh38	V40	RPS28-BGKcLV33-14_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGKcLV33-14_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18097
RPS28-BGKcLV33-14_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	2042					GRCh38	V40	RPS28-BGKcLV33-14/Aligned.sortedByCoord.out.bam		ENCORE2	18153
RPS28-BGKcLV33-14_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	2042					GRCh38	V40	RPS28-BGKcLV33-14/Aligned.sortedByCoord.out.bam		ENCORE2	18209
RPS28-BGKcLV33-14_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	2042					GRCh38	V40	RPS28-BGKcLV33-14/Aligned.sortedByCoord.out.bam		ENCORE2	18265
RPS28-BGKcLV33-14_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	2042					GRCh38	V40	RPS28-BGKcLV33-14/Aligned.sortedByCoord.out.bam		ENCORE2	18321
RPS28-BGKcLV33-14_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2042					GRCh38	V40	RPS28-BGKcLV33-14_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGKcLV33-14_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18377