RPL28 RNA-Seq in K562

General Information


RBP	RPL28
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL28-BGKcLV15-K562
ENCODE_series_ID	ENCSR602SLK
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR234FWR
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	RPL28-BGKcLV15-53
Rep2	RPL28-BGKcLV15-54
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	50.7
Rep2_qPCR	53.5
Rep1_WB	64.3
Rep2_WB	52.0
Antibody Cat#	LS-C352792
Antibody Lot#
Antibody DCC ID	ENCAB131AOZ
Status	Released
Project	ENCODE4
ID	135

Experiment Information (Status: Released)

	BGKcLV15-53	BGKcLV15-54
idx	591	592
TRCN#_or_BGC#	BGC#0000366	BGC#0000366
shRNA_or_gRNA_sequence	CGCAATTCCTTCCGCTACAA	CGCAATTCCTTCCGCTACAA
PAM	CGG	CGG
Name	RPL28-91	RPL28-91
Sample_ID	BGKcLV15-53	BGKcLV15-54
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	RPL28	RPL28
qPCR_result	50.7	53.5
Ave_qPCR	52.1
RT-qPCR_primer-F	TCCGCTACAACGGACTGATT
RT-qPCR_primer-R	ACATAGGAGGTGGCAGGCTT
protein_conc	5604	6121
WB_result	64.3	52.0
Ave_WB	58.2
WB_DONE_date	4/9/19
MW	16KD
IP	Rabbit / I
antibody_Cat#	LS-C352792
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	1509.7	0
Rep2_TPM	1350.9	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4703	4704

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL28	Product_ID: LS-C352792 Lot_ID: NotAvailable Source: LSBio Target Name: RPL28-human

Experiment Status

	BGKcLV15-53	BGKcLV15-54
Sample_ID	BGKcLV15-53	BGKcLV15-54
Sample Name	RPL28-BGKcLV15-53	RPL28-BGKcLV15-54
Sample Name	RPL28-BGKcLV15-53	RPL28-BGKcLV15-54
RBP	RPL28	RPL28
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5359	5360

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-53	BGKcLV15-54
Sample #	29	30
Sample Name	RPL28-BGKcLV15-53	RPL28-BGKcLV15-54
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-E2	2-F2
Tecan	33.20	40.16
Tecan_date	2019-12-10	2019-12-10
Size_bp	266	269
Peak_Molarity	18.80	22.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E4.png	DNA_Library_set43-44/set1/F4.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/E4.png	RNA_Library_set43-44/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-53	BGKcLV15-54
RBP	RPL28	RPL28
Batch_ID	BGKcLV15	BGKcLV15
WB_result	64.300	52.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	605	606

Sequencing Information

	BGKcLV15-53	BGKcLV15-54
Sample_ID	BGKcLV15-53	BGKcLV15-54
Sample Name	RPL28-BGKcLV15-53	RPL28-BGKcLV15-54
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	335,562,896	88,616,646
total_aligned_reads	301,336,950	79,176,880
unique_aligned_reads	273,421,170	72,235,984
percent_uniqueAligned	0.81481	0.81515
correlation_replicates	0.997976	0.997976
spikein_reads	150,188	50,458
percent_spikeins	0.00045	0.00057
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	111	112

Data Submission Information

	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-54	BGKcLV15-54	BGKcLV15-54	BGKcLV15-54
ENCODE_alias	brenton-graveley:RPL28-BGKcLV15	brenton-graveley:RPL28-BGKcLV15-53	brenton-graveley:L-RPL28-BGKcLV15-53	brenton-graveley:RPL28-BGKcLV15-53_S29_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGKcLV15-53_S29_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGKcLV15-K562	brenton-graveley:RPL28-BGKcLV15-54	brenton-graveley:L-RPL28-BGKcLV15-54	brenton-graveley:RPL28-BGKcLV15-54_S30_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGKcLV15-54_S30_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR234FWR	ENCBS412RPC	ENCLB692GKG	ENCFF377XYQ	ENCFF775WYI	ENCSR602SLK	ENCBS591WUS	ENCLB521IAP	ENCFF945JZG	ENCFF769KCN
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	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-53	BGKcLV15-54	BGKcLV15-54	BGKcLV15-54	BGKcLV15-54
Sample Name	RPL28-BGKcLV15-53	RPL28-BGKcLV15-53	RPL28-BGKcLV15-53	RPL28-BGKcLV15-53	RPL28-BGKcLV15-53	RPL28-BGKcLV15-53	RPL28-BGKcLV15-54	RPL28-BGKcLV15-54	RPL28-BGKcLV15-54	RPL28-BGKcLV15-54
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
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		RPL28-BGKcLV15-53.pdf	L-RPL28-BGKcLV15-53.pdf				RPL28-BGKcLV15-54.pdf	L-RPL28-BGKcLV15-54.pdf
ID	31	144	308	506	558	7309	145	309	507	559

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
RPL28-BGKcLV15-53_S29_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	111	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	107
RPL28-BGKcLV15-53_S29_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	111	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	159
RPL28-BGKcLV15-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53_S29_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGKcLV15-53_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24398
RPL28-BGKcLV15-53_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53/Aligned.sortedByCoord.out.bam		ENCORE2	24450
RPL28-BGKcLV15-53_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53/Aligned.sortedByCoord.out.bam		ENCORE2	24502
RPL28-BGKcLV15-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53/Aligned.sortedByCoord.out.bam		ENCORE2	24554
RPL28-BGKcLV15-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53/Aligned.sortedByCoord.out.bam		ENCORE2	24606
RPL28-BGKcLV15-53_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	111					GRCh38	V40	RPL28-BGKcLV15-53_S29_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGKcLV15-53_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24658
RPL28-BGKcLV15-54_S30_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	112	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	108
RPL28-BGKcLV15-54_S30_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	112	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	160
RPL28-BGKcLV15-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54_S30_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGKcLV15-54_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24399
RPL28-BGKcLV15-54_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54/Aligned.sortedByCoord.out.bam		ENCORE2	24451
RPL28-BGKcLV15-54_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54/Aligned.sortedByCoord.out.bam		ENCORE2	24503
RPL28-BGKcLV15-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54/Aligned.sortedByCoord.out.bam		ENCORE2	24555
RPL28-BGKcLV15-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54/Aligned.sortedByCoord.out.bam		ENCORE2	24607
RPL28-BGKcLV15-54_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	112					GRCh38	V40	RPL28-BGKcLV15-54_S30_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGKcLV15-54_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24659