RPL28 RNA-Seq in HepG2

General Information


RBP	RPL28
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPL28-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR662PKM
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR687ITW
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	RPL28-BGHcLV18-41
Rep2	RPL28-BGHcLV18-42
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	36.7
Rep2_qPCR	29.5
Rep1_WB	91.6
Rep2_WB	93.4
Antibody Cat#	LS-C352792
Antibody Lot#
Antibody DCC ID	ENCAB131AOZ
Status	Released
Project	ENCODE4
ID	116

Experiment Information (Status: Released)

	BGHcLV18-41	BGHcLV18-42
idx	534	535
TRCN#_or_BGC#	BGC#0000365	BGC#0000365
shRNA_or_gRNA_sequence	AGCCGACGGCAAAGGTGTCG	AGCCGACGGCAAAGGTGTCG
PAM	TGG	TGG
Name	RPL28-85	RPL28-85
Sample_ID	BGHcLV18-41	BGHcLV18-42
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	RPL28	RPL28
qPCR_result	36.7	29.5
Ave_qPCR	33.1
RT-qPCR_primer-F	TCCGCTACAACGGACTGATT
RT-qPCR_primer-R	ACATAGGAGGTGGCAGGCTT
protein_conc	3958	3837
WB_result	91.6	93.4
Ave_WB	92.5
WB_DONE_date	9/16/19
MW	16KD
IP	Rabbit / I
antibody_Cat#	LS-C352792
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	997	0
Rep2_TPM	280	0
Action	Question	Question
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6689	6690

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV18-41	BGHcLV18-42
Sample_ID	BGHcLV18-41	BGHcLV18-42
Sample Name
Sample Name	RPL28-BGHcLV18-41	RPL28-BGHcLV18-42
RBP	RPL28	RPL28
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5649	5650

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-41	BGHcLV18-42
Sample #	155	156
Sample Name	RPL28-BGHcLV18-41	RPL28-BGHcLV18-42
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-G1	5-H1
Tecan	23.06	42.70
Tecan_date	2019-12-16	2019-12-16
Size_bp	284	271
Peak_Molarity	28.40	31.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A9.png	DNA_Library_set43-44/set2/B9.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/E10.png	RNA_Library_set43-44/set4/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-41	BGHcLV18-42
RBP	RPL28	RPL28
Batch_ID	BGHcLV18	BGHcLV18
WB_result	91.600	93.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	731	732

Sequencing Information

	BGHcLV18-41	BGHcLV18-42
Sample_ID	BGHcLV18-41	BGHcLV18-42
Sample Name	RPL28-BGHcLV18-41	RPL28-BGHcLV18-42
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	205,460,942	210,993,564
total_aligned_reads	201,602,676	205,654,308
unique_aligned_reads	188,825,976	192,595,368
percent_uniqueAligned	0.91904	0.91280
correlation_replicates	0.994075	0.994075
spikein_reads	412,614	373,592
percent_spikeins	0.00201	0.00177
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	237	238

Data Submission Information

	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-42	BGHcLV18-42	BGHcLV18-42	BGHcLV18-42
ENCODE_alias	brenton-graveley:RPL28-BGHcLV18	brenton-graveley:RPL28-BGHcLV18-41	brenton-graveley:L-RPL28-BGHcLV18-41	brenton-graveley:RPL28-BGHcLV18-41_S67_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGHcLV18-41_S67_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGHcLV18-HepG2	brenton-graveley:RPL28-BGHcLV18-42	brenton-graveley:L-RPL28-BGHcLV18-42	brenton-graveley:RPL28-BGHcLV18-42_S68_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL28-BGHcLV18-42_S68_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR687ITW	ENCBS484PMS	ENCLB930MCV	ENCFF050XKH	ENCFF354EVY	ENCSR662PKM	ENCBS282WMO	ENCLB188NOL	ENCFF824OCM	ENCFF440WRR
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	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-41	BGHcLV18-42	BGHcLV18-42	BGHcLV18-42	BGHcLV18-42
Sample Name	RPL28-BGHcLV18-41	RPL28-BGHcLV18-41	RPL28-BGHcLV18-41	RPL28-BGHcLV18-41	RPL28-BGHcLV18-41	RPL28-BGHcLV18-41	RPL28-BGHcLV18-42	RPL28-BGHcLV18-42	RPL28-BGHcLV18-42	RPL28-BGHcLV18-42
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV44H_library_protocol					LV44H_library_protocol
protocol_URL			L-RPL28-BGHcLV18-41.pdf					L-RPL28-BGHcLV18-42.pdf
ID	63	206	372	622	674	7308	207	373	623	675

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-BGHcLV18-41_S67_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	237	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	209
RPL28-BGHcLV18-41_S67_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	237	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	261
RPL28-BGHcLV18-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41_S67_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGHcLV18-41_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24929
RPL28-BGHcLV18-41_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41/Aligned.sortedByCoord.out.bam		ENCORE2	24981
RPL28-BGHcLV18-41_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41/Aligned.sortedByCoord.out.bam		ENCORE2	25033
RPL28-BGHcLV18-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41/Aligned.sortedByCoord.out.bam		ENCORE2	25085
RPL28-BGHcLV18-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41/Aligned.sortedByCoord.out.bam		ENCORE2	25137
RPL28-BGHcLV18-41_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	237					GRCh38	V40	RPL28-BGHcLV18-41_S67_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGHcLV18-41_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25189
RPL28-BGHcLV18-42_S68_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	238	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	210
RPL28-BGHcLV18-42_S68_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	238	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	262
RPL28-BGHcLV18-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42_S68_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGHcLV18-42_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24930
RPL28-BGHcLV18-42_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42/Aligned.sortedByCoord.out.bam		ENCORE2	24982
RPL28-BGHcLV18-42_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42/Aligned.sortedByCoord.out.bam		ENCORE2	25034
RPL28-BGHcLV18-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42/Aligned.sortedByCoord.out.bam		ENCORE2	25086
RPL28-BGHcLV18-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42/Aligned.sortedByCoord.out.bam		ENCORE2	25138
RPL28-BGHcLV18-42_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	238					GRCh38	V40	RPL28-BGHcLV18-42_S68_R1_001.filtered.trimmed.paired.fastq.gz,RPL28-BGHcLV18-42_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25190