MDM2 RNA-Seq in K562

General Information


RBP	MDM2
Cell_Line	K562
Method	CRISPR
Exp_Name	MDM2-BGKcLV19-K562
ENCODE_series_ID	ENCSR285NGS
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR943CXG
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	MDM2-BGKcLV19-19
Rep2	MDM2-BGKcLV19-20
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	16
Rep2_qPCR	0
Rep1_WB	70.1
Rep2_WB	76.0
Antibody Cat#	MA1-113
Antibody Lot#	LOT#TG267046
Antibody DCC ID	ENCAB000YUG
Status	Released
Project	ENCODE4
ID	52

Experiment Information (Status: Released)

	BGKcLV19-19	BGKcLV19-19	BGKcLV19-20	BGKcLV19-20
idx	689	691	690	692
TRCN#_or_BGC#	BGC#0000398	BGC#0000398	BGC#0000398	BGC#0000398
shRNA_or_gRNA_sequence	GTGGTTACAGCACCATCAGT	GTGGTTACAGCACCATCAGT	GTGGTTACAGCACCATCAGT	GTGGTTACAGCACCATCAGT
PAM	agg	agg	agg	agg
Name	MDM2_81	MDM2_81	MDM2_81	MDM2_81
Sample_ID	BGKcLV19-19	BGKcLV19-19	BGKcLV19-20	BGKcLV19-20
transduction_Date	11/6/19	11/6/19	11/6/19	11/6/19
days	Day 6	Day 6	Day 6	Day 6
RBP_name	MDM2	MDM2	MDM2	MDM2
qPCR_result	16		0
Ave_qPCR	8.0
RT-qPCR_primer-F	TGTTGGTGCACAAAAAGACACTT	TGTTGGTGCACAAAAAGACACTT
RT-qPCR_primer-R	TTTTGATCACTCCCACCTTCA	TTTTGATCACTCCCACCTTCA
protein_conc	4478	4478	4384	4384
WB_result	70.1	69.2	76.0	73.1
Ave_WB	73.1	71.2
WB_DONE_date	12/5/19	12/5/19
MW	90KD	55KD
IP	Mouse / Ig	Mouse / Ig
antibody_Cat#	MA1-113	MA1-113	LOT#TG267046
Antibody DCC ID	no ID
submitted_to_DCC_date
Rep1_TPM	22.6	0	0	0
Rep2_TPM	21.3	0	0	0
Action	Ready		Ready
Library_start_date	09/24/20		09/24/20
repeat_library
Note
ID	4809	4811	4810	4812

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV19-19	BGKcLV19-20
Sample_ID	BGKcLV19-19	BGKcLV19-20
Sample Name
Sample Name	MDM2-BGKcLV19-19	MDM2-BGKcLV19-20
RBP	MDM2	MDM2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5697	5698

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-19	BGKcLV19-20
Sample #	11	12
Sample Name	MDM2-BGKcLV19-19	MDM2-BGKcLV19-20
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	299	310
Peak_Molarity	101.00	102.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E1.png	DNA_Library_set45/set1/F1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set45/set1/E1.png	RNA_Library_set45/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-19	BGKcLV19-20
RBP	MDM2	MDM2
Batch_ID	BGKcLV19	BGKcLV19
WB_result	70.100	76.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	785	786

Sequencing Information

	BGKcLV19-19	BGKcLV19-20
Sample_ID	BGKcLV19-19	BGKcLV19-20
Sample Name	MDM2-BGKcLV19-19	MDM2-BGKcLV19-20
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	98,935,872	91,786,824
total_aligned_reads	94,757,794	88,096,600
unique_aligned_reads	86,524,688	80,562,212
percent_uniqueAligned	0.87455	0.87771
correlation_replicates	0.989691	0.989691
spikein_reads	78,426	86,062
percent_spikeins	0.00079	0.00094
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	416	417

Data Submission Information

	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-20	BGKcLV19-20	BGKcLV19-20	BGKcLV19-20
ENCODE_alias	brenton-graveley:MDM2-BGKcLV19	brenton-graveley:MDM2-BGKcLV19-19	brenton-graveley:L-MDM2-BGKcLV19-19	brenton-graveley:MDM2-BGKcLV19-19_S5_R1_001.fastq.gz	brenton-graveley:MDM2-BGKcLV19-19_S5_R2_001.fastq.gz	brenton-graveley:MDM2-BGKcLV19-K562	brenton-graveley:MDM2-BGKcLV19-20	brenton-graveley:L-MDM2-BGKcLV19-20	brenton-graveley:MDM2-BGKcLV19-20_S6_R1_001.fastq.gz	brenton-graveley:MDM2-BGKcLV19-20_S6_R2_001.fastq.gz
ENCODE_accession	ENCSR943CXG	ENCBS899OZI	ENCLB709TXV	ENCFF449PEW	ENCFF681OOQ	ENCSR285NGS	ENCBS736JGG	ENCLB608SYZ	ENCFF690FUP	ENCFF936RIA
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	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-19	BGKcLV19-20	BGKcLV19-20	BGKcLV19-20	BGKcLV19-20
Sample Name	MDM2-BGKcLV19-19	MDM2-BGKcLV19-19	MDM2-BGKcLV19-19	MDM2-BGKcLV19-19	MDM2-BGKcLV19-19	MDM2-BGKcLV19-19	MDM2-BGKcLV19-20	MDM2-BGKcLV19-20	MDM2-BGKcLV19-20	MDM2-BGKcLV19-20
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV45K_library_protocol					LV45K_library_protocol
protocol_URL			L-MDM2-BGKcLV19-19.pdf					L-MDM2-BGKcLV19-20.pdf
ID	2092	2139	2209	2279	2349	7252	2140	2210	2280	2350

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
MDM2-BGKcLV19-19_S5_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	416	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1228
MDM2-BGKcLV19-19_S5_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	416	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1278
MDM2-BGKcLV19-19_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19_S5_R1_001.filtered.trimmed.paired.fastq.gz,MDM2-BGKcLV19-19_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25221
MDM2-BGKcLV19-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19_S5_R1_001.filtered.trimmed.paired.fastq.gz,MDM2-BGKcLV19-19_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27175
MDM2-BGKcLV19-19_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19/Aligned.sortedByCoord.out.bam		ENCORE2	27225
MDM2-BGKcLV19-19_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19/Aligned.sortedByCoord.out.bam		ENCORE2	27275
MDM2-BGKcLV19-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19/Aligned.sortedByCoord.out.bam		ENCORE2	27325
MDM2-BGKcLV19-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	416					GRCh38	V40	MDM2-BGKcLV19-19/Aligned.sortedByCoord.out.bam		ENCORE2	27375
MDM2-BGKcLV19-20_S6_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	417	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1229
MDM2-BGKcLV19-20_S6_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	417	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1279
MDM2-BGKcLV19-20_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20_S6_R1_001.filtered.trimmed.paired.fastq.gz,MDM2-BGKcLV19-20_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25222
MDM2-BGKcLV19-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20_S6_R1_001.filtered.trimmed.paired.fastq.gz,MDM2-BGKcLV19-20_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27176
MDM2-BGKcLV19-20_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20/Aligned.sortedByCoord.out.bam		ENCORE2	27226
MDM2-BGKcLV19-20_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20/Aligned.sortedByCoord.out.bam		ENCORE2	27276
MDM2-BGKcLV19-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20/Aligned.sortedByCoord.out.bam		ENCORE2	27326
MDM2-BGKcLV19-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	417					GRCh38	V40	MDM2-BGKcLV19-20/Aligned.sortedByCoord.out.bam		ENCORE2	27376