LIN28B RNA-Seq in HepG2

General Information


RBP	LIN28B
Cell_Line	HepG2
Method	shRNA
Exp_Name	LIN28B-BGHLV18-HepG2
ENCODE_series_ID	ENCSR820HTF
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR927SLP
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	LIN28B_BGHLV18_21
Rep2	LIN28B_BGHLV18_22
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	67.5
Rep2_qPCR	71.0
Rep1_WB	79.3
Rep2_WB	74.6
Antibody Cat#	A303-588A
Antibody Lot#	A303-588A
Antibody DCC ID	ENCAB006PLV
Status	Released
Project	ENCODE3
ID	449

Experiment Information (Status: Released)

	BGHLV18-21	BGHLV18-22
idx	321	322
TRCN#_or_BGC#	TRCN0000144508	TRCN0000144508
shRNA_or_gRNA_sequence	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA
PAM
Name	LIN28B	LIN28B
Sample_ID	BGHLV18-21	BGHLV18-22
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	LIN28B	LIN28B
qPCR_result	67.5	71.0
Ave_qPCR	69.2
RT-qPCR_primer-F	ggagcccctgtttaggaagt
RT-qPCR_primer-R	gcacttctttggctgaggag
protein_conc	4505	4211
WB_result	79.3	74.6
Ave_WB	76.9
WB_DONE_date	3/27/2015
MW	27kDa
IP	1	1
antibody_Cat#	A303-588A	A303-588A
Antibody DCC ID	ENCAB006PLV	ENCAB006PLV
submitted_to_DCC_date	5/6/2015
Rep1_TPM	5.7	0
Rep2_TPM	4.8	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2386	2387

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LIN28B	Product_ID: A303-588A Lot_ID: 1 Source: Bethyl Labs Target Name: LIN28B-human

Experiment Status

	BGHLV18-21	BGHLV18-22
Sample_ID	BGHLV18-21	BGHLV18-22
Sample Name	LIN28B_BGHLV18_21	LIN28B_BGHLV18_22
Sample Name	LIN28B_BGHLV18_21	LIN28B_BGHLV18_22
RBP	LIN28B	LIN28B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	626	627

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-21	BGHLV18-22
Sample #
Sample Name	LIN28B-BGHLV18-21	LIN28B-BGHLV18-22
Sample_Name_Alias	LIN28B_BGHLV18_21	LIN28B_BGHLV18_22
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E2.png	DNA_Library_LV18-19/set1/F2.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/C9.png	RNA_Library_LV18-19/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-21	BGHLV18-22
RBP	LIN28B	LIN28B
Batch_ID	BGHLV18	BGHLV18
WB_result	79.300	74.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2310	2311

Sequencing Information

	BGHLV18-21	BGHLV18-22
Sample_ID	BGHLV18-21	BGHLV18-22
Sample Name	LIN28B_BGHLV18_21	LIN28B_BGHLV18_22
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	54,040,000	54,140,000
total_aligned_reads	48,310,442	49,305,252
unique_aligned_reads	45,653,390	46,580,432
percent_uniqueAligned	0.84481	0.86037
correlation_replicates	0.998911	0.998911
spikein_reads	270,022	271,936
percent_spikeins	0.00500	0.00502
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	952	953

Data Submission Information

	BGHLV18-21	BGHLV18-21
ENCODE_alias	brenton-graveley:LIN28B_BGHLV18	brenton-graveley:LIN28B-BGHLV18-HepG2
ENCODE_accession	ENCSR927SLP	ENCSR820HTF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-21	BGHLV18-21
Sample Name	LIN28B_BGHLV18_21	LIN28B_BGHLV18_21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2830	6799

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
LIN28B_BGHLV18_21_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	952	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14800
LIN28B_BGHLV18_21_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	952	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14838
LIN28B_BGHLV18_21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21_AGTCAA_L002_R1_001.fastq.gz,LIN28B_BGHLV18_21_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	14876
LIN28B_BGHLV18_21_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21/Aligned.sortedByCoord.out.bam		ENCORE2	14914
LIN28B_BGHLV18_21_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21/Aligned.sortedByCoord.out.bam		ENCORE2	14952
LIN28B_BGHLV18_21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21/Aligned.sortedByCoord.out.bam		ENCORE2	14990
LIN28B_BGHLV18_21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21/Aligned.sortedByCoord.out.bam		ENCORE2	15028
LIN28B_BGHLV18_21_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	952					GRCh38	V40	LIN28B_BGHLV18_21_AGTCAA_L002_R1_001.fastq.gz,LIN28B_BGHLV18_21_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	15066
LIN28B_BGHLV18_22_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	953	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14801
LIN28B_BGHLV18_22_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	953	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14839
LIN28B_BGHLV18_22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22_AGTTCC_L002_R1_001.fastq.gz,LIN28B_BGHLV18_22_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	14877
LIN28B_BGHLV18_22_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22/Aligned.sortedByCoord.out.bam		ENCORE2	14915
LIN28B_BGHLV18_22_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22/Aligned.sortedByCoord.out.bam		ENCORE2	14953
LIN28B_BGHLV18_22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22/Aligned.sortedByCoord.out.bam		ENCORE2	14991
LIN28B_BGHLV18_22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22/Aligned.sortedByCoord.out.bam		ENCORE2	15029
LIN28B_BGHLV18_22_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	953					GRCh38	V40	LIN28B_BGHLV18_22_AGTTCC_L002_R1_001.fastq.gz,LIN28B_BGHLV18_22_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	15067