non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHcLV39-1 and BGHcLV39-2

NT-BGHcLV39-1,NT-BGHcLV39-2:

DDX5-BGHcLV39-HepG2

DDX56-BGHcLV39-HepG2

DHX15-BGHcLV39-HepG2

DIAPH1-BGHcLV39-HepG2

DNAJA1-BGHcLV39-HepG2

DNAJC1-BGHcLV39-HepG2

EDF1-BGHcLV39-HepG2

EEF1G-BGHcLV39-HepG2

EIF2B4-BGHcLV39-HepG2

EIF2D-BGHcLV39-HepG2

EIF3L-BGHcLV39-HepG2

EIF3M-BGHcLV39-HepG2

Experiment Information (Status: Submitting)

	BGHcLV39-1	BGHcLV39-2
idx	1201	1202
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non- target	non- target
Sample_ID	BGHcLV39-1	BGHcLV39-2
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	2478
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7388	7389

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV39-1	BGHcLV39-2
Sample_ID	BGHcLV39-1	BGHcLV39-2
Sample Name
Sample Name	NT-BGHcLV39-1	NT-BGHcLV39-2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11974	11975

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-1	BGHcLV39-2
Sample #	1	2
Sample Name	NT-BGHcLV39-1	NT-BGHcLV39-2
Sample_Name_Alias
Index Well Position	A01	B01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	278	271
Peak_Molarity	20.30	29.90
libSampleQC_DNA_Well	DNA_Library_set63/set1/A9.png	DNA_Library_set63/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/A9.png	RNA_Library_set63/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-1	BGHcLV39-2
RBP	NT	NT
Batch_ID	BGHcLV39	BGHcLV39
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3744	3745

Sequencing Information

	BGHcLV39-1	BGHcLV39-2
Sample_ID	BGHcLV39-1	BGHcLV39-2
Sample Name	NT-BGHcLV39-1	NT-BGHcLV39-2
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	40,200,458	28,148,262
total_aligned_reads	31,795,596	21,851,381
unique_aligned_reads	30,012,838	20,577,152
percent_uniqueAligned	0.74658	0.73103
correlation_replicates	0.999735	0.999735
spikein_reads	59,008	38,472
percent_spikeins	0.00147	0.00137
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2643	2644

Data Submission Information DCC submission information was not avaliable

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	Project	FILE_ID
NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2643	NovaSeq6000	100	paired-ended	1				ENCORE2	8654
NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2643	NovaSeq6000	100	paired-ended	2				ENCORE2	8680
NT-BGHcLV39-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9951
NT-BGHcLV39-1_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1/Aligned.sortedByCoord.out.bam	ENCORE2	9977
NT-BGHcLV39-1_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1/Aligned.sortedByCoord.out.bam	ENCORE2	10003
NT-BGHcLV39-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1/Aligned.sortedByCoord.out.bam	ENCORE2	10029
NT-BGHcLV39-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1/Aligned.sortedByCoord.out.bam	ENCORE2	10055
NT-BGHcLV39-1_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2643					GRCh38	V40	NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10081
NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2644	NovaSeq6000	100	paired-ended	1				ENCORE2	8655
NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2644	NovaSeq6000	100	paired-ended	2				ENCORE2	8681
NT-BGHcLV39-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9952
NT-BGHcLV39-2_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2/Aligned.sortedByCoord.out.bam	ENCORE2	9978
NT-BGHcLV39-2_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2/Aligned.sortedByCoord.out.bam	ENCORE2	10004
NT-BGHcLV39-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2/Aligned.sortedByCoord.out.bam	ENCORE2	10030
NT-BGHcLV39-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2/Aligned.sortedByCoord.out.bam	ENCORE2	10056
NT-BGHcLV39-2_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2644					GRCh38	V40	NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10082