RPL29 RNA-Seq in K562

General Information


RBP	RPL29
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL29-BGKcLV30-K562
ENCODE_series_ID	ENCSR384WTS
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR036ZTN
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RPL29-BGKcLV30-47
Rep2	RPL29-BGKcLV30-48
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	2.8
Rep2_qPCR	1.0
Rep1_WB	52.8
Rep2_WB	51.4
Antibody Cat#	A305-056A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB581HIJ
Status	Submitted
Project	ENCODE4
ID	877

Experiment Information (Status: Released)

	BGKcLV30-47	BGKcLV30-48
idx	1076	1077
TRCN#_or_BGC#	BGC#0000794	BGC#0000794
shRNA_or_gRNA_sequence	AGGGCCCAAAAAACTTACAC	AGGGCCCAAAAAACTTACAC
PAM	TGG	TGG
Name	RPL29_81	RPL29_81
Sample_ID	BGKcLV30-47	BGKcLV30-48
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RPL29	RPL29
qPCR_result	2.8	1.0
Ave_qPCR	1.9
RT-qPCR_primer-F	accccgatcacaaagatacg
RT-qPCR_primer-R	attgttggcctgcatcttct
protein_conc	2881	2370
WB_result	52.8	51.4
Ave_WB	52.1
WB_DONE_date	9/13/21
MW	18KD
IP
antibody_Cat#	A305-056A	LOT #1
Antibody DCC ID	ENCAB581HIJ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/10/21	11/10/21
repeat_library
Note
ID	5216	5217

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL29	Product_ID: A305-056A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL29-human

Experiment Status

	BGKcLV30-47	BGKcLV30-48
Sample_ID	BGKcLV30-47	BGKcLV30-48
Sample Name
Sample Name	RPL29-BGKcLV30-47	RPL29-BGKcLV30-48
RBP	RPL29	RPL29
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10079	10080

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-47	BGKcLV30-48
Sample #	69	70
Sample Name	RPL29-BGKcLV30-47	RPL29-BGKcLV30-48
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	293	295
Peak_Molarity	43.80	30.70
libSampleQC_DNA_Well	DNA_Library_set50/set2/A12.png	DNA_Library_set50/set2/B12.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set50/set2/A12.png	RNA_Library_set50/set2/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-47	BGKcLV30-48
RBP	RPL29	RPL29
Batch_ID	BGKcLV30	BGKcLV30
WB_result	52.800	51.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3156	3157

Sequencing Information

	BGKcLV30-47	BGKcLV30-48
Sample_ID	BGKcLV30-47	BGKcLV30-48
Sample Name	RPL29-BGKcLV30-47	RPL29-BGKcLV30-48
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	47,827,938	94,571,662
total_aligned_reads	45,239,008	87,572,300
unique_aligned_reads	41,604,836	80,241,364
percent_uniqueAligned	0.86989	0.84847
correlation_replicates	0.991976	0.991976
spikein_reads	13,522	16,958
percent_spikeins	0.00028	0.00018
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1941	1942

Data Submission Information

	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-48	BGKcLV30-48	BGKcLV30-48	BGKcLV30-48
ENCODE_alias	brenton-graveley:RPL29-BGKcLV30	brenton-graveley:RPL29-BGKcLV30-47	brenton-graveley:L-RPL29-BGKcLV30-47	brenton-graveley:RPL29-BGKcLV30-47_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGKcLV30-47_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGKcLV30-K562	brenton-graveley:RPL29-BGKcLV30-48	brenton-graveley:L-RPL29-BGKcLV30-48	brenton-graveley:RPL29-BGKcLV30-48_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGKcLV30-48_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR036ZTN	ENCBS540NPH	ENCLB041BKJ	ENCFF957XVL	ENCFF263NRY	ENCSR384WTS	ENCBS919IEY	ENCLB426GTV	ENCFF830RWT	ENCFF761RYT
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	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-47	BGKcLV30-48	BGKcLV30-48	BGKcLV30-48	BGKcLV30-48
Sample Name	RPL29-BGKcLV30-47	RPL29-BGKcLV30-47	RPL29-BGKcLV30-47	RPL29-BGKcLV30-47	RPL29-BGKcLV30-47	RPL29-BGKcLV30-47	RPL29-BGKcLV30-48	RPL29-BGKcLV30-48	RPL29-BGKcLV30-48	RPL29-BGKcLV30-48
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RPL29-BGKcLV30-47.pdf	L-RPL29-BGKcLV30-47.pdf				RPL29-BGKcLV30-48.pdf	L-RPL29-BGKcLV30-48.pdf
ID	5876	5945	6017	6089	6161	6198	5946	6018	6090	6162

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
RPL29-BGKcLV30-47_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1941	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5869
RPL29-BGKcLV30-47_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1941	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5899
RPL29-BGKcLV30-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGKcLV30-47_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18770
RPL29-BGKcLV30-47_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47/Aligned.sortedByCoord.out.bam		ENCORE2	18800
RPL29-BGKcLV30-47_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47/Aligned.sortedByCoord.out.bam		ENCORE2	18830
RPL29-BGKcLV30-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47/Aligned.sortedByCoord.out.bam		ENCORE2	18860
RPL29-BGKcLV30-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47/Aligned.sortedByCoord.out.bam		ENCORE2	18890
RPL29-BGKcLV30-47_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1941					GRCh38	V40	RPL29-BGKcLV30-47_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGKcLV30-47_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18920
RPL29-BGKcLV30-48_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1942	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5870
RPL29-BGKcLV30-48_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1942	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5900
RPL29-BGKcLV30-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGKcLV30-48_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18771
RPL29-BGKcLV30-48_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48/Aligned.sortedByCoord.out.bam		ENCORE2	18801
RPL29-BGKcLV30-48_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48/Aligned.sortedByCoord.out.bam		ENCORE2	18831
RPL29-BGKcLV30-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48/Aligned.sortedByCoord.out.bam		ENCORE2	18861
RPL29-BGKcLV30-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48/Aligned.sortedByCoord.out.bam		ENCORE2	18891
RPL29-BGKcLV30-48_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1942					GRCh38	V40	RPL29-BGKcLV30-48_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGKcLV30-48_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18921