title: S05P4P150692UOXZP11E01.R1.star.bam


title: S41P4P150692UOXZP11A06.R1.star.bam

status: Public on Aug 20 2018

type: SRA

city: Cardiff

first: Viola

last: Volpato

address: Maindy Rd

department: UK DRI

country: United Kingdom

institute: Cardiff University

library_source: transcriptomic

data_processing:
SC alignment: RNA-seq data were mapped to the hg19 assembly via STAR version 2.2.0. Read alignments were merged in single BAM file output per sample.
SC filtering: Reads were filtered to remove those not uniquely mapped and all ribosomal and mitochondrial RNA reads. We excluded libraries with: less than 2000 expressed genes; low complexity, where the % of 200 most expressed features (genes and ERCC-spike in) represented more than 50% of total number of counts; low % of endogenous RNA, for which the % of  ERCC spike-in > 14%; low number of mapped read for which the total counts < 10e-6.
SC generation of abundances measures: Gene-level read counts were obtained using FeatureCount (Liao et al., 2014).
SC normalisation: We computed the normalized log-expression values with R package scran (1.0.4) by adding one to each count, dividing by the size factor for that cell, and log transforming.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalised values for filtered Samples

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Single cell suspensions were generated using accutase dissociation followed by single cell filtration of iPSC-derived cortical neurons. The single cell suspension was sorted into a 96-well PCR plate containing a lysis mix. Sorting gates were set to include only live (DAPI negative) single cells. Stream alignment and sort efficiency was checked using Accudrop beads (Becton Dickinson). Single iPSC derived cortical neurons were isolated by FACS onto 96-well plates in 2ul lysis buffer.
Libraries were prepared following the Smart-Seq2 protocol. Libraries were pooled in 288- or 384-plexes and each pool sequenced on 1 lane of HiSeq4000 at 75bp paired end

tag: cell type

value: iPSC-derived neurons

tag: time point

tag: site

value: E

tag: well

tag: batch

tag: cell line


title: S64P2P150692UOXZC11H08.R1.star.bam


title: S17P4P150692UOXZP11A03.R1.star.bam


title: S52P2P150692UOXZC11D07.R1.star.bam


title: S18P4P150692UOXZP11B03.R1.star.bam


title: S28P2P150692UOXZC11D04.R1.star.bam


title: S88P4P150692UOXZP11H11.R1.star.bam


title: S16P2P150692UOXZC11H02.R1.star.bam


title: S40P2P150692UOXZC11H05.R1.star.bam


title: S64P4P150692UOXZP11H08.R1.star.bam


title: S04P2P150692UOXZC11D01.R1.star.bam


title: S76P4P150692UOXZP11D10.R1.star.bam


title: S16P4P150692UOXZP11H02.R1.star.bam


title: S04P4P150692UOXZP11D01.R1.star.bam


title: S28P4P150692UOXZP11D04.R1.star.bam


title: S75P2P150692UOXZC11C10.R1.star.bam


title: S87P2P150692UOXZC11G11.R1.star.bam


title: S40P4P150692UOXZP11H05.R1.star.bam


title: S27P2P150692UOXZC11C04.R1.star.bam


title: S63P2P150692UOXZC11G08.R1.star.bam


title: S52P4P150692UOXZP11D07.R1.star.bam


title: S51P2P150692UOXZC11C07.R1.star.bam


title: S03P2P150692UOXZC11C01.R1.star.bam


title: S87P4P150692UOXZP11G11.R1.star.bam


title: S15P2P150692UOXZC11G02.R1.star.bam


title: S39P2P150692UOXZC11G05.R1.star.bam


title: S39P4P150692UOXZP11G05.R1.star.bam


title: S51P4P150692UOXZP11C07.R1.star.bam


title: S75P4P150692UOXZP11C10.R1.star.bam


title: S27P4P150692UOXZP11C04.R1.star.bam


title: S15P4P150692UOXZP11G02.R1.star.bam


title: S86P2P150692UOXZC11F11.R1.star.bam


title: S74P2P150692UOXZC11B10.R1.star.bam


title: S50P2P150692UOXZC11B07.R1.star.bam


title: S38P2P150692UOXZC11F05.R1.star.bam


title: S14P2P150692UOXZC11F02.R1.star.bam


title: S26P2P150692UOXZC11B04.R1.star.bam


title: S86P4P150692UOXZP11F11.R1.star.bam


title: S74P4P150692UOXZP11B10.R1.star.bam


title: S62P4P150692UOXZP11F08.R1.star.bam


title: S38P4P150692UOXZP11F05.R1.star.bam


title: S50P4P150692UOXZP11B07.R1.star.bam


title: S14P4P150692UOXZP11F02.R1.star.bam


title: S85P2P150692UOXZC11E11.R1.star.bam


title: S26P4P150692UOXZP11B04.R1.star.bam


title: S02P4P150692UOXZP11B01.R1.star.bam


title: S61P2P150692UOXZC11E08.R1.star.bam


title: S73P2P150692UOXZC11A10.R1.star.bam


title: S49P2P150692UOXZC11A07.R1.star.bam


title: S37P2P150692UOXZC11E05.R1.star.bam


title: S63P4P150692UOXZP11G08.R1.star.bam


title: S03P4P150692UOXZP11C01.R1.star.bam


title: S62P2P150692UOXZC11F08.R1.star.bam


title: S25P2P150692UOXZC11A04.R1.star.bam


title: hydrogen peroxide treated sample 3 + TEX enzyme

city: Chicago

first: H

middle: Steven

last: Seifert

state: IL

address: 303 East Chicago Ave.

department: Microbiology-Immunology

country: USA

institute: Northwestern University Feinberg School of Medicine

description:
RNA harvested from liquid culture treated with enzyme that preferentially degrades RNA with 5 prime monophosphate moiety
h202_Tex_rep3

data_processing:
3’ adapters, if present in raw reads, were trimmed from raw data reads using fastx_clipper, part of the FastX toolkit (using the following flags: -Q 33 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Low quality reads were filtered using fastq_quality_filter, filtering out reads where more than 50% of bases in the read have a phred quality score less than 20 (using the following flags: -Q 33 -q 20-p 50)
Bowtie (version 1.1.0) was first used to filter rRNA sequences by aligning against an index file containing only rRNA sequences and filtering out positive hits
Reads that did not map to the rRNAs were ran through Kallisto (version 0.42.3) and aligned to an index of either all coding sequences (to quantify transcript abundances) or to the entire genome (for visualization of peaks)
Genome_build: NC_002946
Supplementary_files_format_and_content: .wig files were generated from the pseudo-bam option of kallisto when reads were aligned against the entire genome. Transcript abundance file was generated from Kallisto/Sleuth aligning reads against the annotated coding sequences.

molecule: total RNA

organism: Neisseria gonorrhoeae

source_name: hydrogen peroxide treated sample + TEX enzyme

growth_protocol: Exponential growth in liquid media was achieved using a three day protocol: Day one, Gc was streaked from a freezer stock onto Gc medium base (Difco) agar + Kellogg Supplement I (22.2 mM glucose, 0.68 mM glutamine, 0.45 mM cocarboxylase) and II [1.23 mM Fe(NO3)3] (GCB+) and incubated at 37 degrees C, 5% CO2 for 16 hours. Day two, 20 colonies were picked and used to streak heavy lawns of bacteria on GCB+ on plates that were freshly poured the day before, and incubated at 37 degrees C, 5% CO2 for ten hours. The lawns were collected using sterile Dacron swabs and inoculated into six mls of liquid GCB+ with 0.042% sodium bicarbonate (GCBL) to an OD600 of ~0.05 in 15 ml conical tubes (Sarstedt) These cultures were incubated at 30 degrees C with shaking for 16 hours. Day three, piliated bacteria from these tubes were allowed to pellet at the bottom of the tube. The pellets were collected by sterile pipette and added into 20 mls of fresh GCBL in a 50 ml conical tube (Sarstedt) and grown for three hours at 37 degrees C with shaking at 220 rpm. At three hours, 2.5 mls of culture was added to 22.5 mls of fresh liquid GCBL and grown for another three hours at 37 degrees C with shaking at 220 rpm. 50 mls of culture was added to 380 mls fresh GCBL and grown for three hours at 37 degrees C with shaking at 220 rpm to reach mid-log phase for HP treatment.

extract_protocol:
All water used to make reagents used in RNA isolation was DEPC-treated. After treatment, 500 mls of Gc in mid-log liquid culture were added to one half volume of ice in plastic bottles to stop growth, and centrifuged at 10,000 rpm for 20 minutes at four degrees C. Pellets were resuspended in 500 ul of ice cold phosphate buffered saline solution (PBS), pelleted and washed once with 1X ice cold PBS, then resuspended in 500 ul PBS and stored overnight at -80 degrees C. Cells were lysed by addition of 50 ul of one mg/ml lysozyme (Sigma) then flash frozen in liquid nitrogen for five minutes and thawed for five minutes in a 37 degrees C water bath. Samples were treated with 15 ul of 15 mM sodium deoxycholate and the freeze-thaw process was repeated. Insoluble materials were pelleted for ten minutes at 15,000 rpm at four degrees C in a table top centrifuge and supernatants were treated with Qiagen RNeasy Mini Kit (#74104) according to the manufacturer’s instructions, eluting the total RNA into 50 ul RNase-free H2O. RNA was precipitated overnight at -80 degrees C with isopropanol and sodium acetate precipitation. RNA quality was determined by 23S/16S ratio using Biorad Experion StdSens kit (#7007104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Liquid cultures were treated with 15 mM hydrogen peroxide for 15 minutes at mid-log phase. Untreated controls were treated with an equal volume of water.

tag: strain

tag: piliation state

value: piliated

tag: locked piliation

value: GCM77 is a derivative of strain FA1090 containing a mutation in the pilE G4 region preventing pilin antigenic variation and a mutation in pilC1 coding sequence preventing pilus phase variation


title: S13P2P150692UOXZC11E02.R1.star.bam


title: S01P2P150692UOXZC11A01.R1.star.bam


title: untreated control 3 + TEX enzyme

description:
RNA harvested from liquid culture treated with enzyme that preferentially degrades RNA with 5 prime monophosphate moiety
control_Tex_rep3

source_name: untreated control + TEX enzyme


title: untreated control 2 + TEX enzyme

description:
RNA harvested from liquid culture treated with enzyme that preferentially degrades RNA with 5 prime monophosphate moiety
control_Tex_rep2


title: S85P4P150692UOXZP11E11.R1.star.bam


title: S02P2P150692UOXZC11B01.R1.star.bam


title: S73P4P150692UOXZP11A10.R1.star.bam


title: untreated control 1 + TEX enzyme

description:
RNA harvested from liquid culture treated with enzyme that preferentially degrades RNA with 5 prime monophosphate moiety
control_Tex_rep1


title: hydrogen peroxide treated sample 3

description:
RNA harvested from liquid culture
h202_noTex_rep3

source_name: hydrogen peroxide treated sample


title: S61P4P150692UOXZP11E08.R1.star.bam


title: S49P4P150692UOXZP11A07.R1.star.bam


title: untreated control 3

description:
RNA harvested from liquid culture
control_noTex_rep3

source_name: untreated control


title: hydrogen peroxide treated sample 2

description:
RNA harvested from liquid culture
h202_noTex_rep2


title: untreated control 2

description:
RNA harvested from liquid culture
control_noTex_rep2


title: hydrogen peroxide treated sample 1

description:
RNA harvested from liquid culture
h202_noTex_rep1


title: S13P4P150692UOXZP11E02.R1.star.bam


title: S25P4P150692UOXZP11A04.R1.star.bam


title: S37P4P150692UOXZP11E05.R1.star.bam


title: S01P4P150692UOXZP11A01.R1.star.bam


title: S84P3P150692UOXCP11D11.R1.star.bam

value: D


title: S72P3P150692UOXCP11H09.R1.star.bam


title: untreated control 1

description:
RNA harvested from liquid culture
control_noTex_rep1


title: hydrogen peroxide treated sample 2 + TEX enzyme

description:
RNA harvested from liquid culture treated with enzyme that preferentially degrades RNA with 5 prime monophosphate moiety
h202_Tex_rep2


title: S48P3P150692UOXCP11H06.R1.star.bam


title: S36P3P150692UOXCP11D05.R1.star.bam


title: S60P3P150692UOXCP11D08.R1.star.bam


title: FANCF-M-c, MSSK1-M-a, MSSK1-M-b, MSSK1-M-c, PDL1-M-a, PDL1-M-b, VEGFA-M-b NT rep 3

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description:
Sample 125
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150

library_source: genomic

data_processing:
Library strategy: DNA-seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Files for Indels (Indels.xls) and Base Subtitutions (*variation.txt)

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: HEK293T from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free.

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq X ten and NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, HEK293T cells were seeded in a 24-well plate at a density of 160 k per well and transfected with 200 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg BE3 expression vector (or hA3A-BE3, hA3A-BE3-Y130F, hA3A-BE3-D131Y, hA3A-BE3-Y132D, hA3A-BE3-C101S, hA3A-BE3-C106S, hA3A-eBE-Y130F, hA3A-eBE-Y132D expression vector) and 0.68 μg sgRNA expression vector.

tag: type

value: DNA

tag: treatment

value: NT


title: FANCF-M-c, MSSK1-M-a, MSSK1-M-c, PDL1-M-a, PDL1-M-b NT rep 2; MAGEA1-M-a, VEGFA-M-a NT rep 3

description:
Sample 124
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c,MSSK1-M-a,c,PDL1-M-a,PDL1-M-b NT rep 1;MAGEA1-M-a,MSSK1-M-b,VEGFA-M-a,b NT rep 2;FANCF-M-b NT rep 3

description:
Sample 123
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S24P3P150692UOXCP11H03.R1.star.bam


title: S12P3P150692UOXCP11D02.R1.star.bam


title: MAGEA1-M-a, MSSK1-M-b, VEGFA-M-a, VEGFA-M-b NT rep 1; FANCF-M-b NT rep 2; FANCF-M-a NT rep 3

description:
Sample 122
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S96P1P150692UOXCC1BULK2NA.R1.star.bam


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b hA3A-BE3 rep 2 and PDL1-M-b hA3A-BE3 rep 3

description:
Sample 56
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c, PDL1-M-a hA3A-BE3 rep 3

description:
Sample 46
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: MSSK1-M-a hA3A-BE3 rep 1

description:
Sample 49
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b hA3A-BE3 rep 3

description:
Sample 48
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b, VEGFA-M-a hA3A-BE3 rep 2

description:
Sample 45
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S72P1P150692UOXCC11H09.R1.star.bam


title: FANCF-M-b, VEGFA-M-a hA3A-BE3 rep 3

description:
Sample 47
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S96P3P150692UOXCP1BULK2NA.R1.star.bam


title: S60P1P150692UOXCC11D08.R1.star.bam


title: S84P1P150692UOXCC11D11.R1.star.bam


title: S48P1P150692UOXCC11H06.R1.star.bam


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c, PDL1-M-a hA3A-BE3 rep 2

description:
Sample 43
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S36P1P150692UOXCC11D05.R1.star.bam


title: FANCF-M-b, VEGFA-M-a hA3A-BE3 rep 1

description:
Sample 42
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1_hA3A-BE3 rep 2; PDL1-M-a dCas9-DNMT3_hA3A-BE3 rep 2

description:
Sample 39
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b hA3A-BE3 rep 1 and PDL1-M-b hA3A-BE3 rep 2

description:
Sample 57
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S24P1P150692UOXCC11H03.R1.star.bam


title: FANCF-M-c,MSSK1-M-b dCas9-TET1_hA3A-BE3 rep1;VEGFA-M-b dCas9-DNMT3_hA3A-BE3 rep1;PDL1-M-b dCas9-DNMT3_hA3A-BE3 rep2

description:
Sample 38
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S12P1P150692UOXCC11D02.R1.star.bam


title: FANCF-M-b dCas9-TET1_hA3A-BE3 rep 1; VEGFA-M-a dCas9-DNMT3_hA3A-BE3 rep 1

description:
Sample 37
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S83P3P150692UOXCP11C11.R1.star.bam


title: S71P3P150692UOXCP11G09.R1.star.bam


title: S95P3P150692UOXCP1BULK1NA.R1.star.bam


title: FANCF-M-c, MSSK1-M-b dCas9-TET1_hA3A-BE3 rep 3; VEGFA-M-b dCas9-DNMT3_hA3A-BE3 rep 3

description:
Sample 36
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b dCas9-TET1_hA3A-BE3 rep 3; VEGFA-M-a dCas9-DNMT3_hA3A-BE3 rep 3

description:
Sample 34
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1_hA3A-BE3 rep 1; PDL1-M-a dCas9-DNMT3_hA3A-BE3 rep 1

description:
Sample 35
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1_hA3A-BE3 rep 3; PDL1-M-a dCas9-DNMT3_hA3A-BE3 rep 3

description:
Sample 33
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S59P3P150692UOXCP11C08.R1.star.bam


title: S47P3P150692UOXCP11G06.R1.star.bam


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c, PDL1-M-a hA3A-BE3 rep 1

description:
Sample 44
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S35P3P150692UOXCP11C05.R1.star.bam


title: FANCF-M-c,MSSK1-M-b dCas9-TET1_hA3A-BE3 rep2;VEGFA-M-b dCas9-DNMT3_hA3A-BE3 rep2;PDL1-M-b dCas9-DNMT3_h3A3A-BE3 rep3

description:
Sample 32
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b dCas9-TET1_hA3A-BE3 rep 2; VEGFA-M-a dCas9-DNMT3_hA3A-BE3 rep 2

description:
Sample 31
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S23P3P150692UOXCP11G03.R1.star.bam


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1-BE3 rep 3; PDL1-M-a dCas9-DNMT3-BE3 rep 3

description:
Sample 30
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150

value: dCas9-TET1-BE3 or dCas9-DNMT3-BE3


title: FANCF-M-c, MSSK1-M-b dCas9-TET1_BE3 rep 1; VEGFA-M-b dCas9-DNMT3_BE3 rep 1; PDL1-M-b dCas9-DNMT3_BE3 rep 2

description:
Sample 29
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150

value: dCas9-TET1_BE3 or dCas9-DNMT3_BE3


title: S11P3P150692UOXCP11C02.R1.star.bam


title: FANCF-M-c, MSSK1-M-b dCas9-TET1_BE3 rep 3; VEGFA-M-b dCas9-DNMT3_BE3 rep 3

description:
Sample 28
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S83P1P150692UOXCC11C11.R1.star.bam


title: S71P1P150692UOXCC11G09.R1.star.bam


title: FANCF-M-b dCas9-TET1_BE3 rep 3; VEGFA-M-a dCas9-DNMT3_BE3 rep 3

description:
Sample 27
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S59P1P150692UOXCC11C08.R1.star.bam


title: FANCF-M-b dCas9-TET1_BE3 rep 2; VEGFA-M-a dCas9-DNMT3_BE3 rep 2

description:
Sample 24
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b dCas9-TET1_BE3 rep 2; VEGFA-M-b dCas9-DNMT3_BE3 rep 2; PDL1-M-b dCas9-DNMT3_BE3 rep 3

description:
Sample 25
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1_BE3; PDL1-M-a dCas9-DNMT3_BE3 rep 1

description:
Sample 26
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S47P1P150692UOXCC11G06.R1.star.bam


title: S95P1P150692UOXCC11G12.R1.star.bam


title: S35P1P150692UOXCC11C05.R1.star.bam


title: S23P1P150692UOXCC11G03.R1.star.bam


title: S11P1P150692UOXCC11C02.R1.star.bam


title: S82P3P150692UOXCP11B11.R1.star.bam


title: FANCF-M-b, VEGFA-M-a BE3 rep 3

description:
Sample 9
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-a BE3 rep 3

description:
Sample 11
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b BE3 rep 3

description:
Sample 10
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S58P3P150692UOXCP11B08.R1.star.bam


title: FANCF-M-b, VEGFA-M-a BE3 rep 2

description:
Sample 6
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S46P3P150692UOXCP11F06.R1.star.bam


title: PDL1-M-a BE3 rep 2; FANCF-M-a, MAGEA1-M-a, MSSK1-M-c BE3 rep 3

description:
Sample 8
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b BE3 rep 2; PDL1-M-b BE3 rep 3

description:
Sample 7
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-a BE3 rep1; FANCF-M-a, MAGEA1-M-a, MSSK1-M-c BE3 rep 2

description:
Sample 5
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S22P3P150692UOXCP11F03.R1.star.bam


title: S10P3P150692UOXCP11B02.R1.star.bam


title: S94P1P150692UOXCC11F12.R1.star.bam


title: S34P3P150692UOXCP11B05.R1.star.bam


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c BE3 rep1

description:
Sample 4
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-c, MSSK1-M-b, VEGFA-M-b BE3 rep1; PDL1-M-b BE3 rep 2

description:
Sample 3
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S70P1P150692UOXCC11F09.R1.star.bam


title: S82P1P150692UOXCC11B11.R1.star.bam


title: S58P1P150692UOXCC11B08.R1.star.bam


title: S70P3P150692UOXCP11F09.R1.star.bam


title: FANCF-M-b, VEGFA-M-a dCas9-DNMT3_BE3 rep 1

description:
Sample 22
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S10P1P150692UOXCC11B02.R1.star.bam


title: S34P1P150692UOXCC11B05.R1.star.bam


title: S93P3P150692UOXCP11E12.R1.star.bam


title: S22P1P150692UOXCC11F03.R1.star.bam


title: S69P3P150692UOXCP11E09.R1.star.bam


title: S81P3P150692UOXCP11A11.R1.star.bam


title: S57P3P150692UOXCP11A08.R1.star.bam


title: S33P3P150692UOXCP11A05.R1.star.bam


title: S93P1P150692UOXCC11E12.R1.star.bam


title: S81P1P150692UOXCC11A11.R1.star.bam


title: S09P3P150692UOXCP11A02.R1.star.bam


title: S69P1P150692UOXCC11E09.R1.star.bam


title: S21P3P150692UOXCP11E03.R1.star.bam


title: FANCF-M-b, VEGFA-M-a BE3 rep 1

description:
Sample 2
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S46P1P150692UOXCC11F06.R1.star.bam


title: S68P3P150692UOXCP11D09.R1.star.bam


title: S33P1P150692UOXCC11A05.R1.star.bam


title: S80P3P150692UOXCP11H10.R1.star.bam


title: S21P1P150692UOXCC11E03.R1.star.bam


title: S45P1P150692UOXCC11E06.R1.star.bam


title: S09P1P150692UOXCC11A02.R1.star.bam


title: S56P3P150692UOXCP11H07.R1.star.bam


title: S44P3P150692UOXCP11D06.R1.star.bam


title: S92P1P150692UOXCC11D12.R1.star.bam


title: S08P3P150692UOXCP11H01.R1.star.bam


title: S68P1P150692UOXCC11D09.R1.star.bam


title: S20P3P150692UOXCP11D03.R1.star.bam


title: S45P3P150692UOXCP11E06.R1.star.bam


title: S32P3P150692UOXCP11H04.R1.star.bam


title: S44P1P150692UOXCC11D06.R1.star.bam


title: S32P1P150692UOXCC11H04.R1.star.bam


title: FANCF-M-a, MAGEA1-M-a, MSSK1-M-c dCas9-TET1_BE3 rep 2; PDL1-M-a dCas9-DNMT3_BE3 rep 2

description:
Sample 23
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: S20P1P150692UOXCC11D03.R1.star.bam


title: S57P1P150692UOXCC11A08.R1.star.bam


title: S56P1P150692UOXCC11H07.R1.star.bam


title: S79P3P150692UOXCP11G10.R1.star.bam


title: S67P3P150692UOXCP11C09.R1.star.bam


title: S08P1P150692UOXCC11H01.R1.star.bam


title: S55P3P150692UOXCP11G07.R1.star.bam


title: S43P3P150692UOXCP11C06.R1.star.bam


title: S92P3P150692UOXCP11D12.R1.star.bam


title: S31P3P150692UOXCP11G04.R1.star.bam


title: S80P1P150692UOXCC11H10.R1.star.bam


title: S19P3P150692UOXCP11C03.R1.star.bam


title: S67P1P150692UOXCC11C09.R1.star.bam


title: S07P3P150692UOXCP11G01.R1.star.bam


title: S55P1P150692UOXCC11G07.R1.star.bam


title: S91P1P150692UOXCC11C12.R1.star.bam


title: S79P1P150692UOXCC11G10.R1.star.bam


title: S07P1P150692UOXCC11G01.R1.star.bam


title: S43P1P150692UOXCC11C06.R1.star.bam


title: S90P3P150692UOXCP11B12.R1.star.bam


title: S31P1P150692UOXCC11G04.R1.star.bam


title: S19P1P150692UOXCC11C03.R1.star.bam


title: S78P3P150692UOXCP11F10.R1.star.bam


title: S66P3P150692UOXCP11B09.R1.star.bam


title: S91P3P150692UOXCP11C12.R1.star.bam


title: S42P3P150692UOXCP11B06.R1.star.bam


title: S54P3P150692UOXCP11F07.R1.star.bam


title: MGH42_112414_1.bam

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
summary read counts by featureCounts v1.5.1
Genome_build: hg19
Supplementary_files_format_and_content: csv of the read counts matrix generated by featureCounts

source_name: metastatic melanoma

extract_protocol:
RNA was purified from patients' frozen or formalin-fixed tumor specimens using the TRIzol protocol.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 250 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment state

value: On Immune Checkpoint Blockade Therapy

tag: timepoint

tag: antibody

tag: response

value: NR

tag: age at the baseline

tag: tumor type

value: metastatic melanoma

tag: patient id

value: MGH Patient 42


title: MGH42_122914-1.bam


title: MGH42_122914-2_1.bam


title: S18P3P150692UOXCP11B03.R1.star.bam

tag: cell type

tag: time point


title: S30P3P150692UOXCP11F04.R1.star.bam

tag: site

tag: well


title: MGH42_112414.bam

tag: batch


title: MGH42_122914_1.bam


title: S06P3P150692UOXCP11F01.R1.star.bam

tag: cell line


title: MGH39_103114.bam

value: MGH Patient 39


title: MGH42_101714.bam

value: PRE Immune Checkpoint Blockade Therapy (On dabrafenib+trametinib)


title: MGH42_101714_1.bam


title: MGH39_082514-5.bam


title: MGH39_082514-4.bam


title: S90P1P150692UOXCC1BULK1NA.R1.star.bam


title: S66P1P150692UOXCC11B09.R1.star.bam


title: MGH39_082514-2.bam


title: S54P1P150692UOXCC11F07.R1.star.bam


title: S78P1P150692UOXCC11F10.R1.star.bam


title: MGH39_082514-1.bam


title: S30P1P150692UOXCC11F04.R1.star.bam


title: MGH39_033114.bam

value: PRE Immune Checkpoint Blockade Therapy


title: MGH208_051315.bam

value: MGH Patient 208


title: S18P1P150692UOXCC11B03.R1.star.bam

value: iPSC-derived neurons


title: S06P1P150692UOXCC11F01.R1.star.bam


title: MGH208_031115-2.bam


title: MGH208_031115-1.bam


title: MGH422-110515.bam

value: R

value: MGH Patient 422


title: S65P3P150692UOXCP11A09.R1.star.bam


title: S77P3P150692UOXCP11E10.R1.star.bam


title: MGH422-092815.bam


title: MGH272-121914.bam

value: MGH Patient 272


title: S53P3P150692UOXCP11E07.R1.star.bam

value: D


title: MGH272-020415.bam


title: S29P3P150692UOXCP11E04.R1.star.bam


title: 115-041514

value: MGH Patient 115


title: S41P3P150692UOXCP11A06.R1.star.bam


title: MGH39_082514-3.bam


title: S17P3P150692UOXCP11A03.R1.star.bam


title: S05P3P150692UOXCP11E01.R1.star.bam


title: 115-031814


title: S89P1P150692UOXCC11A12.R1.star.bam


title: S42P1P150692UOXCC11B06.R1.star.bam


title: S53P1P150692UOXCC11E07.R1.star.bam


title: S77P1P150692UOXCC11E10.R1.star.bam


title: S65P1P150692UOXCC11A09.R1.star.bam


title: S41P1P150692UOXCC11A06.R1.star.bam


title: S89P3P150692UOXCP11A12.R1.star.bam


title: S05P1P150692UOXCC11E01.R1.star.bam


title: S64P3P150692UOXCP11H08.R1.star.bam


title: S76P3P150692UOXCP11D10.R1.star.bam


title: S17P1P150692UOXCC11A03.R1.star.bam


title: S52P3P150692UOXCP11D07.R1.star.bam


title: L/L, cre rep2 [TruSeq]

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description:
KO216
M4WHEARTRNAKO216_HLFFWAFXX_GTCCGC

data_processing:
Raw reads from technical replicates for each sample were pooled and aligned to the NumtS-masked mouse genome (mm10) with HISAT2 v2.0.5 using default parameters.
Alignments were filtered to retain only properly paired, primary alignments with SAMtools v1.5{Li:2009ka}.
Read pairs that aligned to the mitochondria were realigned to the mitochondrial genome sequence with the --no-spliced-alignment parameter enabled, to avoid introducing spurious splice junctions into mitochondrial alignments.
The mitochondrial and nuclear alignments were combined, and gene-level counts were produced with featureCounts v1.5.1 (–largestOverlap -s 2) using the GENCODE vM14 annotation and an in-house mitochondrial annotation.
Differential expression analysis was performed using DESeq2 v1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalised counts and differential expression results

organism: Mus musculus

source_name: Elac2 -/-_heart

growth_protocol: To generate conditional ELAC2 knockout mice, an exon of this gene was loxP-flanked (Taconic Artemis GmbH, Cologne, Germany) and excised by breeding to mice expressing cre from the muscle creatinine kinase promoter.

extract_protocol:
RNA was isolated from total hearts using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyser.
RNA sequencing libraries were constructed using the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: Elac2 -/-

tag: tissue

value: Heart


title: L/L, cre rep3 [TruSeq]

description:
KO245
M4WHEARTRNAKO245_HLFFWAFXX_GTGAAA


title: L/L rep2 [TruSeq]

description:
P95
M4WHEARTRNAP_P95_HLFFWAFXX_AGTCAA

source_name: Elac2 +/+_heart

value: Elac2 +/+


title: L/L rep1 [TruSeq]

description:
P103
M4WHEARTRNAP_P103_HLFFWAFXX_ATGTCA


title: L/L rep3 [TruSeq]

description:
P96
M4WHEARTRNAP_P96_HLFFWAFXX_AGTTCC


title: L/L, cre rep1 [TruSeq]

description:
KO203
M4WHEARTRNAKO203_HLFFWAFXX_CCGTCC


title: S28P3P150692UOXCP11D04.R1.star.bam


title: S16P3P150692UOXCP11H02.R1.star.bam


title: L/L, cre rep2 [miRNA-seq]

description:
KO216
M4WHEARTRNAKO216_sRNA_HKMVWAFXX_GGCTAC

data_processing:
Raw paired-end reads from the miRNA sequencing library were merged with BBMap v37.02 [ref], removing the adapter sequences, and technical replicates were pooled.
Merged and pooled reads with a length of at least 15 nt were aligned the mouse genome (mm10) with Bowtie 2 v2.2.9 [ref] with the parameters: -D 20 -R 3 -N 0 -L 15 -i S,1,0.50 -k 100 (equivalent to the --very-sensitive preset, with the seed substring shortened to 15 nt and up to 100 alignments reported).
In order to account for the presence of non-template 3′-CCA found on tRF-3s, all unaligned and non-exactly aligning reads were extracted and cutadapt v1.1.4 used to detect and trim up to a single -CCA triplet anchored at the 3′ end. Trimmed reads were subsequently aligned to the mouse genome and filtered for exact alignments as above.
Multimapping reads (those with equally top scoring primary and secondary alignments) that mapped to genomic tRNA loci were retained only if all equally-scoring secondary alignments were also mapped to tRNA loci from, which the primary alignment was retained. Primary alignments were also retained for multimappers outside of tRNA loci and non-multimappers.
tRNA fragments were identified according to the mapped position of their 5′ and 3′ terminal nucleotides: tRF-5s by the 5′ terminal nucleotide of a read mapping to the 5′ end of a tRNA; tRF-3s by the 3′ end from the CCA-trimmed data mapping to the 3′ end of a tRNA; and tRF-1s if the 5′ end mapped to a tRNA 3′+1 position.
Reads from these sets of alignments was extracted and collapsed by sequence to identify the most abundant fragments, irrespective of mapping location (ambiguous in the case of multimappers).
Differential expression analysis was performed with the set of unique sequences using DESeq2 v1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalised counts and differential expression results

extract_protocol:
RNA was isolated from crude hearts using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyser.
RNA sequencing libraries were constructed using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15 - 35 nt RNAs. Paired-end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.


title: L/L rep3 [miRNA-seq]

description:
P96
M4WHEARTRNAP_P96_sRNA_HKMVWAFXX_ACTTGA


title: L/L, cre rep1 [miRNA-seq]

description:
KO203
M4WHEARTRNAKO203_sRNA_HKMVWAFXX_TAGCTT


title: L/L rep2 [miRNA-seq]

description:
P95
M4WHEARTRNAP_P95_sRNA_HKMVWAFXX_CAGATC


title: S29P1P150692UOXCC11E04.R1.star.bam


title: L/L rep1 [miRNA-seq]

description:
P103
M4WHEARTRNAP_P103_sRNA_HKMVWAFXX_GATCAG


title: S88P1P150692UOXCC11H11.R1.star.bam


title: S64P1P150692UOXCC11H08.R1.star.bam


title: S76P1P150692UOXCC11D10.R1.star.bam


title: S88P3P150692UOXCP11H11.R1.star.bam


title: S52P1P150692UOXCC11D07.R1.star.bam


title: L/L, cre rep1

description:
KO203
M4WHEARTRNAKO203_sRNA

data_processing:
Raw reads were trimmed of adapter sequences (5′-AGATCGGAAGAGCACACG-TCTGAACTCCAGTCAC-3′) with cutadapt v1.14, discarding reads with a trimmed length of less than 15 nt. Only reads with successfully trimmed adapters were retained for subsequent analysis.
Trimmed reads for technical replicates were pooled for each sample and alignment to the NumtS-masked mouse genome (mm10) plus a set of mature tRNA sequences, using Bowtie 2 v2.2.9 with the parameters: -D 20 -R 3 -N 0 -L 15 -i S,1,0.50 -k 100 (equivalent to the --very-sensitive preset, with the seed substring shortened to 15 nt and up to 100 alignments reported). The mature tRNA sequences were derived from the genomic tRNA database (GtRNAdb), by removing intronic sequences, adding a 3′-CCA to each tRNA and a 5′ G nucleotide to each histidine tRNA, and collapsing the set to unique sequences.
Prior to differential expression, a single alignment for each read was retained according to the alignment scores of the highest scoring primary and secondary alignments, and their mapping locations (secondary alignments with scores lower than the primary were not considered). All primary alignments with a higher alignment score than any secondaries were retained. Primary alignments with one or more secondaries with equal scores (ambiguous multimappers) were retained if none mapped to precursor or mature tRNA sequences, or the mitochondrial chromosome. Those that did map to a tRNA sequence were retained according to their mapping locations: if all alignments mapped either to precursor or mature tRNA, then the primary precursor or mature alignment was retained, respectively; if the alignments were mapped to both precursor and mature tRNA, but nowhere else, then a mature tRNA alignment was randomly selected (to improve the specificity of precursor alignments); if the alignments mapped to a precursor or mature tRNA and chrM, a mitochondrial alignment was randomly retained (under the rationale that a mitochondrial tRNA is the most likely source due to the high amount of mitochondrial RNA in cardiomyocytes); if the equally-scoring alignments mapped to multiple locations on chrM, or if they mapped to other nuclear genomic locations in addition to tRNAs, they were excluded from further analysis.
Gene-level read counts were produced using featureCounts v1.5.1(--largestOverlap -s 1) with the GENCODE vM14 annotation limited to small ncRNA annotations (miRNA, snoRNA, snRNA, sRNA, scaRNA, scRNA, rRNA and misc_RNA) combined with the GtRNAdb-derived precursor and mature tRNA annotations, and an in-house mitochondrial annotation.
Differential expression was performed with DESeq2 v1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalised counts and differential expression results

extract_protocol:
RNA was isolated from crude hearts using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyser.
RNA sequencing libraries were constructed using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15 - 100 nt RNAs. Paired-end deep sequencing of the mitochondrial RNAs was performed on an Illumina NextSeq 500 according to the manufacturer’s instructions.


title: S40P3P150692UOXCP11H05.R1.star.bam


title: S40P1P150692UOXCC11H05.R1.star.bam


title: L/L, cre rep3 [miRNA-seq]

description:
KO245
M4WHEARTRNAKO245_sRNA_HKMVWAFXX_CTTGTA


title: S28P1P150692UOXCC11D04.R1.star.bam


title: S04P1P150692UOXCC11D01.R1.star.bam


title: S51P3P150692UOXCP11C07.R1.star.bam


title: S63P3P150692UOXCP11G08.R1.star.bam


title: L/L rep3

description:
P96
M4WHEARTRNAP_P96_sRNA


title: L/L rep1

description:
P103
M4WHEARTRNAP_P103_sRNA


title: S75P3P150692UOXCP11C10.R1.star.bam


title: S39P3P150692UOXCP11G05.R1.star.bam


title: S04P3P150692UOXCP11D01.R1.star.bam


title: S27P3P150692UOXCP11C04.R1.star.bam


title: L/L rep2

description:
P95
M4WHEARTRNAP_P95_sRNA


title: S15P3P150692UOXCP11G02.R1.star.bam


title: S87P3P150692UOXCP11G11.R1.star.bam


title: L/L, cre rep3

description:
KO245
M4WHEARTRNAKO245_sRNA


title: L/L, cre rep2

description:
KO216
M4WHEARTRNAKO216_sRNA


title: S51P1P150692UOXCC11C07.R1.star.bam


title: S75P1P150692UOXCC11C10.R1.star.bam


title: S03P3P150692UOXCP11C01.R1.star.bam


title: S87P1P150692UOXCC11G11.R1.star.bam


title: S63P1P150692UOXCC11G08.R1.star.bam


title: S27P1P150692UOXCC11C04.R1.star.bam


title: S94P3P150692UOXCP11F12.R1.star.bam


title: S15P1P150692UOXCC11G02.R1.star.bam


title: S03P1P150692UOXCC11C01.R1.star.bam


title: KB42_DKO

city: MADRID

first: Alfonsina

last: Trento

state: Madrid

address: Darwin 3

department: DIO

country: Spain

institute: Centro Nacional de Microbiologia - CSIC

description: DKO rep1

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).
Sequencing adaptor contaminations were removed from reads using cutadapt software and the resulting reads were mapped and quantified on the transcriptome (Ensembl GRCm38, gene-build 82) using RSEM v1.2.3
Genes with at least 1 counts per million in at least 2 samples were considered for statistical analysis
Data were TMM normalized
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized raw count values for each Sample ...

source_name: Spleen

growth_protocol: Mature B lymphocytes  were sorted from spleen and were cultured (105 cells/well) in RPMI 1640 medium with 15% FBS, 2-Mercaptoethanol, penicillin/streptomycin and activated with LPS (20 μg/ml; Sigma-Aldrich) and IL-4 (20 ng/ml; R&D Systems).

extract_protocol:
Activated B cells were harvested after 72h. Total RNA from was isolated with RNeasy Micro Kit (Cat No./ID: 74004, QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Double knock-out

value: B lymphocytes

tag: age

value: 8 -10 weeks

value: Spleen


title: KB37_MYC_KO

description: MYC_KO rep2

value: Myc knock-out


title: KB44_MYC_KO

description: DKO rep2


title: S16P1P150692UOXCC11H02.R1.star.bam


title: KB32_DKO

description: MYC_KO rep1


title: S86P3P150692UOXCP11F11.R1.star.bam


title: KB43_MAX_KO

description: MAX_KO rep2

value: Max knock-out


title: S74P3P150692UOXCP11B10.R1.star.bam


title: S62P3P150692UOXCP11F08.R1.star.bam


title: S38P3P150692UOXCP11F05.R1.star.bam


title: E5.75-Section7VE

city: Cambridge

first: Christos

last: Kyprianou

address: Downing Street

department: Physiology Development and Neuroscience

institute: University of Cambridge

description:
E5.75-Section7VE were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Samples with low quality, including E5.75-Section9 and E5.75-Section13 has few expressed genes, were removed in the further analysis.
In E5.5 sections, the expression level of A and B were taken average as each section's expression.
Genome_build: mm10
Supplementary_files_format_and_content: Textfiles include FPKM values for each sample

growth_protocol: Recovered fresh from the mother. Embryos removed from deciduas at specific stages and immediately embedded in OCT in cryomolds. First frozen in dry ice and then kept at -80 degrees

extract_protocol:
Samples were harvested by laser capture microdissection (LCM), and then RNA isolation.
Low-input RNA-seq was performed using the Smart-seq2 protocol.

treatment_protocol: no treatment

tag: developmental stage


title: E5.75-Section6VE

description:
E5.75-Section6VE were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S50P3P150692UOXCP11B07.R1.star.bam


title: S02P3P150692UOXCP11B01.R1.star.bam


title: S26P3P150692UOXCP11B04.R1.star.bam


title: KB34_HET

description: CONTROL rep1

value: heterozygous


title: E5.75-Section18

description:
E5.75-Section18 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S39P1P150692UOXCC11G05.R1.star.bam


title: E5.75-Section16

description:
E5.75-Section16 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section19

description:
E5.75-Section19 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S86P1P150692UOXCC11F11.R1.star.bam


title: S14P3P150692UOXCP11F02.R1.star.bam


title: KB38_HET

description: CONTROL rep2


title: E5.75-Section17

description:
E5.75-Section17 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: KB35_MAX_KO

description: MAX_KO rep1


title: S62P1P150692UOXCC11F08.R1.star.bam


title: S50P1P150692UOXCC11B07.R1.star.bam


title: E5.75-Section14

description:
E5.75-Section14 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S38P1P150692UOXCC11F05.R1.star.bam


title: E5.75-Section12

description:
E5.75-Section12 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section13

description:
E5.75-Section13 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S26P1P150692UOXCC11B04.R1.star.bam


title: E5.75-Section11

description:
E5.75-Section11 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S14P1P150692UOXCC11F02.R1.star.bam


title: S85P3P150692UOXCP11E11.R1.star.bam


title: E5.75-Section9

description:
E5.75-Section9 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section10

description:
E5.75-Section10 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S02P1P150692UOXCC11B01.R1.star.bam


title: S74P1P150692UOXCC11B10.R1.star.bam


title: S37P3P150692UOXCP11E05.R1.star.bam


title: S49P3P150692UOXCP11A07.R1.star.bam


title: E5.75-Section5

description:
E5.75-Section5 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section8

description:
E5.75-Section8 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S25P3P150692UOXCP11A04.R1.star.bam


title: S73P3P150692UOXCP11A10.R1.star.bam


title: S13P3P150692UOXCP11E02.R1.star.bam


title: S01P3P150692UOXCP11A01.R1.star.bam


title: E5.75-Section15

description:
E5.75-Section15 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section6

description:
E5.75-Section6 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section1

description:
E5.75-Section1 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section2

description:
E5.75-Section2 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.75-Section7

description:
E5.75-Section7 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S85P1P150692UOXCC11E11.R1.star.bam


title: S73P1P150692UOXCC11A10.R1.star.bam


title: E5.75-Section4

description:
E5.75-Section4 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: S61P1P150692UOXCC11E08.R1.star.bam


title: E5.5-Section10-B

description:
E5.5-Section11 were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: S49P1P150692UOXCC11A07.R1.star.bam


title: E5.5-Section10-A

description:
E5.5-Section10 were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: S61P3P150692UOXCP11E08.R1.star.bam


title: E5.5-Section9-A

description:
E5.5-Section9A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: S37P1P150692UOXCC11E05.R1.star.bam


title: S25P1P150692UOXCC11A04.R1.star.bam


title: E5.5-Section8-B

description:
E5.5-Section8B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: S13P1P150692UOXCC11E02.R1.star.bam


title: S01P1P150692UOXCC11A01.R1.star.bam


title: E5.75-Section3

description:
E5.75-Section3 were collected by laser capture microdissection from the E5.75 mouse embryo
Genes.FPKM.Norm.E5.75.txt


title: E5.5-Section8-A

description:
E5.5-Section8A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: SB808_3_FP.55_D

data_processing:
Alignment: RNA-seq data were mapped to the hg19 assembly via STAR version 2.2.0. Read alignments were merged in single BAM file output per sample (57 in total).
Filtering: Reads were filtered to remove those not uniquely mapped (mapping quality equal to 255) and all ribosomal and mitochondrial RNA reads.
Generation of abundances: Gene-level read counts were obtained using FeatureCount (Liao et al., 2014). Cuffquant and Cuffnorm tools from Cufflinks program (Trapnell et al., 2010) were used to calculate fragments per kilobase per million reads (FPKM) from the merged BAM files.
Normalisation: Upper quartile (UQ) normalisation has been applied (in-house code) on raw gene counts to correct for library size differences. RUVs was used to infer factors explaining transcriptome-wide variance components that were regressed out from the UQ-normalised gene counts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalised values for each Sample

extract_protocol:
Pooled cells from three wells were detached in ice-cold PBS and total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: detachment

tag: hearly harvest

tag: independend day

value: B

tag: cell number

tag: maturity

value: Y


title: SB808_3_FP.55_B

tag: cell type

value: iPSC-derived neurons

value: A

value: N


title: SB808_3_FP.25_D

value: D

tag: time point


title: E5.5-Section7-A

description:
E5.5-Section7A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section5-A

description:
E5.5-Section5A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section7-B

description:
E5.5-Section7B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section6-B

description:
E5.5-Section6B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section5-B

description:
E5.5-Section5B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section4-B

description:
E5.5-Section4B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section6-A

description:
E5.5-Section6A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: SB808_3_FP.55_C

tag: site

value: C


title: E5.5-Section9-B

description:
E5.5-Section9B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section4-A

description:
E5.5-Section4A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: SB808_3_FP.55_A


title: SB808_3_FP.25_C


title: SB808_3_FP.25_B


title: SB808_3_FP.25_A


title: E5.5-Section2-A

description:
E5.5-Section2A were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: E5.5-Section2-B

description:
E5.5-Section2B were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: SB808_2_FP.55_D


title: E5.5-Section1

description:
E5.5-Section1 were collected by laser capture microdissection from the E5.5 mouse embryo
Genes.FPKM.Norm.E5.5.txt


title: SB808_2_FP.55_B


title: SB808_2_FP.55_A


title: E5.25-Section7

description:
E5.25-Section7 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: SB808_2_FP.55_C


title: E5.25-Section6

description:
E5.25-Section6 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: E5.25-Section8

description:
E5.25-Section8 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: E5.25-Section4

description:
E5.25-Section4 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: E5.25-Section2

description:
E5.25-Section2 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: E5.25-Section1

description:
E5.25-Section1 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt


title: 62-7-8-14_S8

tag: treatment state

value: On Immune Checkpoint Blockade Therapy

tag: timepoint

tag: antibody

tag: response

value: NR

tag: age at the baseline

tag: tumor type

value: metastatic melanoma

tag: patient id

value: MGH Patient 62


title: 62-5-27-14_S7

tag: batch


title: 62-10-2-13_S6

value: PRE Immune Checkpoint Blockade Therapy


title: SB808_2_FP.25_E

value: E

tag: cell line


title: SB808_2_FP.55_E

tag: detachment


title: 42-12-30-14_S5

value: MGH Patient 42


title: SB808_1_FP.55_C

tag: hearly harvest


title: SB808_1_FP.55_E

tag: independend day


title: 42-11-24-14_S4


title: SB808_1_FP.55_A

tag: cell number


title: SB808_2_FP.25_A

tag: maturity


title: SB808_2_FP.25_C

tag: cell type


title: SB808_1_FP.25_E

tag: time point


title: SB808_2_FP.25_B

tag: site


title: SB808_1_FP.55_D


title: 42-10-17-14_S3

tag: treatment state

value: PRE Immune Checkpoint Blockade Therapy (On dabrafenib+trametinib)


title: SB808_1_FP.55_B


title: 39-8-25-14_S16

tag: timepoint

value: MGH Patient 39


title: SB808_1_FP.25_D


title: 39-3-31-14_S15

tag: antibody


title: 39-10-31-14_S17

tag: response


title: SB808_1_FP.25_C


title: SB808_1_FP.25_B


title: 208-9-10-14_S11

tag: age at the baseline

value: MGH Patient 208


title: E5.25-Section3

description:
E5.25-Section3 were collected by laser capture microdissection from the E5.25 mouse embryo
Genes.FPKM.Norm.E5.25.txt

tag: developmental stage


title: SB808_1_FP.25_A


title: SB808_2_FP.25_D

value: B


title: 208-3-11-15_S13

tag: tumor type

tag: patient id


title: SBAD3_3_FP.55_D

source_name: CTR

tag: cell line

value: CTR

value: Y


title: SBAD3_3_FP.55_E

value: iPSC-derived neurons

tag: detachment

value: A


title: 148-6-5-14_S9

value: R

tag: batch

value: MGH Patient 148


title: SBAD3_3_FP.55_B

tag: hearly harvest

tag: independend day

value: N


title: 208-10-22-14_S12

value: On Immune Checkpoint Blockade Therapy

value: NR


title: SBAD3_3_FP.55_C

value: C

tag: cell number

tag: maturity


title: FANCF-M-d, MAGEA1-M-b, EMX1, RNF2, SITE2, SITE3, SITE4 NT rep 3

description:
Sample 128
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

tag: type

value: DNA

tag: treatment

value: NT


title: SBAD3_3_FP.25_D

tag: cell type

tag: site

value: D

tag: time point


title: SBAD3_3_FP.25_C


title: SBAD3_3_FP.25_B


title: FANCF-M-d, MAGEA1-M-b, EMX1, RNF2, SITE2, SITE3, SITE4 NT rep 2

description:
Sample 127
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-a NT rep 1

description:
Sample 120
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_3_FP.55_A


title: SBAD3_3_FP.25_E

value: E


title: FANCF-M-b NT rep 1; FANCF-M-a NT rep 2

description:
Sample 121
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b, MAGEA1-M-b hA3A-eBE-Y132D rep a

description:
Sample 118
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-d, MAGEA1-M-b, EMX1, RNF2, SITE2, SITE3, SITE4 NT rep 1

description:
Sample 126
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-b, MAGEA1-M-b hA3A-eBE-Y132D rep b

description:
Sample 119
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: 208-5-13-15_S14

tag: treatment state

tag: timepoint

tag: antibody

tag: response

value: metastatic melanoma


title: FANCF-M-b, PDL1-M-c, VEGFA-M-c hA3A-eBE-Y132D rep c

description:
Sample 117
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_3_FP.25_A


title: PDL1-M-c, VEGFA-M-c hA3A-eBE-Y132D rep b

description:
Sample 116
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_2_FP.55_D


title: SBAD3_2_FP.55_C


title: SBAD3_2_FP.55_A


title: SBAD3_2_FP.55_B


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-eBE-Y130F rep b

description:
Sample 114
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-c, VEGFA-M-c hA3A-eBE-Y132D rep a; MAGEA1-M-b hA3A-eBE-Y132D rep c

description:
Sample 115
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_2_FP.25_E


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-eBE-Y130F rep a

description:
Sample 113
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_2_FP.25_D


title: SBAD3_2_FP.25_C


title: PDL1-M-c hA3A-eBE-Y130F rep b

description:
Sample 111
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b, PDL1-M-c hA3A-eBE-Y130F rep c

description:
Sample 112
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_1_FP.55_E


title: PDL1-M-c hA3A-eBE-Y130F rep a; MAGEA1-M-b, VEGFA-M-c hA3A-eBE-Y130F rep c

description:
Sample 110
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_1_FP.55_D


title: FANCF-M-b, MSSK1-M-a hA3A-BE3-Y132D rep1; PDL1-M-c NT rep 1

description:
Sample 107
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3-Y132D or NT


title: FANCF-M-b, MSSK1-M-a hA3A-BE3-Y132D rep2; PDL1-M-c NT rep 2

description:
Sample 108
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-b, MSSK1-M-a hA3A-BE3-Y132D rep3;  PDL1-M-c NT rep 3

description:
Sample 109
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: SBAD3_1_FP.55_A


title: SBAD3_1_FP.55_C

value: B


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-BE3-Y132D rep a

description:
Sample 104
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_2_FP.25_B

value: CTR


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-BE3-Y132D rep b

description:
Sample 105
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_1_FP.25_E


title: FANCF-M-d hA3A-BE3-Y132D rep 1

description:
Sample 101
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-a, PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y132D rep 3

description:
Sample 100
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: SBAD3_1_FP.25_B


title: SBAD3_1_FP.25_C

value: Y


title: FANCF-M-a hA3A-BE3-Y132D rep 1; PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y132D rep 2

description:
Sample 99
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y132D rep 1; FANCF-M-d hA3A-BE3-Y132D rep 3

description:
Sample 98
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-d hA3A-BE3-Y132D rep 2

description:
Sample 97
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: SBAD3_2_FP.25_A

value: iPSC-derived neurons


title: MAGEA1-M-b hA3A-BE3-Y132D rep 3

description:
Sample 96
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MAGEA1-M-b hA3A-BE3-Y132D rep 2

description:
Sample 95
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MAGEA1-M-b hA3A-BE3-Y132D rep 1

description:
Sample 94
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c hA3A-BE3-Y132D rep b

description:
Sample 106
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_1_FP.55_B

value: A


title: FANCF-M-b hA3A-BE3-Y130F rep1; VEGFA-M-c NT rep 2

description:
Sample 93
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3-Y130F or NT


title: SBAD3_1_FP.25_D


title: FANCF-M-b, PDL1-M-c, VEGFA-M-c hA3A-BE3-Y132D rep c

description:
Sample 103
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: MSSK1-M-a hA3A-BE3-Y130F rep3; VEGFA-M-c NT rep 1

description:
Sample 92
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-b, PDL1-M-c hA3A-BE3-Y130F rep c

description:
Sample 90
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-c hA3A-BE3-Y132D rep a; MAGEA1-M-b hA3A-BE3-Y132D rep c

description:
Sample 102
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: SBAD3_1_FP.25_A


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-BE3-Y130F rep b

description:
Sample 88
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-c hA3A-BE3-Y130F rep a and MAGEA1-M-b, VEGFA-M-c hA3A-BE3-Y130F rep c

description:
Sample 89
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-c hA3A-BE3-Y130F rep b

description:
Sample 87
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-b, MAGEA1-M-b, VEGFA-M-c hA3A-BE3-Y130F rep a

description:
Sample 86
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: FANCF-M-a, PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y130F rep 3

description:
Sample 84
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-a hA3A-BE3-Y130F rep 2

description:
Sample 83
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MSSK1-M-a hA3A-BE3-Y130F rep 2

description:
Sample 85
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MSSK1-M-a hA3A-BE3-Y130F rep1; PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-D131Y rep 3

description:
Sample 91
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3-Y130F or hA3A-BE3-D131Y


title: FANCF-M-d hA3A-BE3-Y130F rep 1

description:
Sample 82
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-a hA3A-BE3-Y130F rep1; PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y130F rep 2

description:
Sample 81
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MY-LA Day 8 unt 385250

type: RNA

city: Boulder

first: Aimee

last: Jackson

state: CO

address: 6200 Lookout Rd.

institute: miRagen Therapeutics

description: Gene expression from MY-LA cell line at day 8, untreated

hyb_protocol: 15 ug of cRNA were hybridized for 16 hr at 45C Affymetrix Human U133 plus 2.0 array. GeneChips were washed and stained according to manufacturer instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix MAS 5.0, Array Studio

label: biotin

source_name: MY-LA cell line at day 8, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Flat-bottomed 6 well plates were seeded with 200K/ml of cells per well.

extract_protocol: Suspension cells are harvested with centrifugation into Eppendorf tubes. Qiagen RNeasy kit is used for isolation of total RNA from the cells, per manufacturer’s instructions.

treatment_protocol: Oligos were added directly to the growth media at the indicated concentration.  96 hours following administration of antimiR, the untreated wells were counted, the dilution factor for returning the untreated cells to 200K/ml was calculated, then all groups were split back using the same dilution factor. Cell passaging was performed with medium containing antimiR, and 48 hours later an equal volume of fresh medium was added to the wells to provide additional growth nutrients.

value: MY-LA

value: untreated

tag: time

value: day 8


title: MY-LA Day 8 11667 385248

description: Gene expression from MY-LA cell line at day 8, MRG-106

source_name: MY-LA cell line at day 8, MRG-106


title: MY-LA Day 4 unt 385244

description: Gene expression from MY-LA cell line at day 4, untreated

source_name: MY-LA cell line at day 4, untreated

value: day 4


title: FANCF-M-d hA3A-BE3-Y130F rep 2

description:
Sample 79
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

tag: cell line

value: DNA


title: MY-LA Day 8 unt 385249


title: MY-LA Day 8 unt 385251


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-Y130F rep1; FANCF-M-d hA3A-BE3 -Y130F rep 3

description:
Sample 80
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MY-LA Day 8 11667 385246


title: MAGEA1-M-b hA3A-BE3-Y130F rep 2

description:
Sample 77
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MY-LA Day 4 unt 385241


title: MY-LA Day 4 unt 385242


title: MY-LA Day 8 unt 385252


title: MAGEA1-M-b hA3A-BE3-Y130F rep 3

description:
Sample 78
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MY-LA Day 8 11667 385247


title: MY-LA Day 8 11667 385245


title: MY-LA Day 4 unt 385243


title: MY-LA Day 4 11667 385239

description: Gene expression from MY-LA cell line at day 4, MRG-106

source_name: MY-LA cell line at day 4, MRG-106


title: MAGEA1-M-b hA3A-BE3-Y130F rep 1

description:
Sample 76
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MY-LA Day 4 11667 385238


title: MY-LA Day 4 11667 385237


title: MY-LA Day 4 11667 385240


title: HuT78 Day 8 11667 385236

description: Gene expression from HuT-78 cell line at day 8, MRG-106

source_name: HuT-78 cell line at day 8, MRG-106


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-D131Y rep2; FANCF-M-a hA3A-BE3-Y132D rep 2

description:
Sample 75
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3-D131Y or hA3A-BE3-Y132D


title: MAGEA1-M-b hA3A-BE3-D131Y rep 1

description:
Sample 74
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-D131Y rep1; MAGEA1-M-b hA3A-BE3-D131Y rep 3

description:
Sample 73
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: HuT78 Day 8 11667 385234


title: MAGEA1-M-b hA3A-BE3-D131Y rep 2

description:
Sample 72
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MSSK1-M-a BE3 rep2; PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C106S rep 3

description:
Sample 70
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C106S rep 2

description:
Sample 69
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C106S rep 1; MAGEA1-M-b hA3A-BE3-C106S rep 3

description:
Sample 68
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: HuT78 Day 8 unt 385235

description: Gene expression from HuT-78 cell line at day 8, untreated

source_name: HuT-78 cell line at day 8, untreated


title: MAGEA1-M-b hA3A-BE3-C106S rep 2

description:
Sample 67
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: HuT78 Day 8 11667 385232


title: MSSK1-M-a BE3 rep1; PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C101S rep 3

description:
Sample 65
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MAGEA1-M-b hA3A-BE3-C106S rep 1

description:
Sample 71
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C101S rep 2

description:
Sample 64
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3-C101S rep 1; MAGEA1-M-b hA3A-BE3-C101S rep 3

description:
Sample 63
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: HuT78 Day 8 unt 385233


title: HuT78 Day 8 unt 385229


title: CS3-2

city: Shenyang

first: Zhiyong

last: Liu

institute: Shenyang Agriculture University

data_processing:
Libraries were sequenced on an Illumina Hiseq platform (San Diego, CA, USA)
The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12.
Gene expression levels were calculated based on reads per kb per million reads. Differential expression analysis of eight samples (three biological replicates per condition) was performed using DESeq R package v.1.10.1. The false discovery rate (FDR) method was used to determine the threshold P value in multiple tests to identify DEGs; an adjusted log2 ratio ≥ 5 and FDR ≤ 0.001 were set as the threshold for differential expression.
Genome_build: the genome website （http://cucurbitgenomics.org/）
Supplementary_files_format_and_content: DESeq output

organism: Cucumis sativus

source_name: leaves

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
In total, of 3 μg RNA per sample from four time points each with three independent biological replicates were used to construct 12 cDNA libraries designated as CS0, CS0-1, CS0-2, CS1, CS1-1, CS1-2, CS2, CS2-1, CS2-2, CS3, CS3-1, and CS3-2.

tag: strain

tag: tissue

value: leaves

tag: developmental stage

value: trifoliate

value: exposed to an air temperature of 6°C for 12 h


title: CS3


title: MJ Day 8 11667 351314

description: Gene expression from MJ cell line at day 8, MRG-106

source_name: MJ cell line at day 8, MRG-106

value: MJ


title: HuT78 Day 8 11667 385230


title: MJ Day 8 unt 351312

description: Gene expression from MJ cell line at day 8, untreated

source_name: MJ cell line at day 8, untreated


title: HuT78 Day 8 unt 385231


title: MJ Day 8 11667 351311


title: MJ Day 8 unt 351306


title: MJ Day 8 11667 351308


title: CS1-1

value: exposed to an air temperature of 6°C for 2 h


title: MSSK1-M-a hA3A-BE3; FANCF-M-b hA3A-BE3-Y130F rep 2; VEGFA-M-c NT rep 3

description:
Sample 61
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3 or hA3A-BE3-Y130F or NT


title: CS2

value: exposed to an air temperature of 6°C for 6 h


title: CS1-2


title: CS2-1


title: CS0


title: MAGEA1-M-b hA3A-BE3-C101S rep 2

description:
Sample 62
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: CS0-1


title: CS1


title: MJ Day 8 11667 351305


title: MSSK1-M-a hA3A-BE3 rep 3 and FANCF-M-b hA3A-BE3-Y130F rep 3

description:
Sample 60
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: hA3A-BE3 or hA3A-BE3-Y130F


title: MAGEA1-M-b hA3A-BE3 rep 3

description:
Sample 59
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MAGEA1-M-b hA3A-BE3 rep 1

description:
Sample 58
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3 rep 3

description:
Sample 55
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MJ Day 4 11667 351302

description: Gene expression from MJ cell line at day 4, MRG-106

source_name: MJ cell line at day 4, MRG-106


title: FANCF-M-d hA3A-BE3 rep 1

description:
Sample 53
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MJ Day 8 unt 351309


title: MJ Day 4 unt 351297

description: Gene expression from MJ cell line at day 4, untreated

source_name: MJ cell line at day 4, untreated


title: MJ Day 4 unt 351300


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3 rep 2

description:
Sample 54
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

source_name: HEK293T cells


title: MJ Day 4 11667 351299


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 hA3A-BE3 rep 1 and FANCF-M-d hA3A-BE3 rep 3

description:
Sample 52
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-d hA3A-BE3 rep 2 and VEGFA-M-c hA3A-BE3 rep 3

description:
Sample 51
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MJ Day 4 11667 351296


title: BLCA_LNM_335

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

description:
Paired tumor sample in GSE83586 : SAMPLE 166 : p1404_166.CEL
GEO accession of paired tumor: GSM2213066

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

tag: sample type

value: Lymph node metastasis

tag: labeling batch


title: BLCA_LNM_332

description:
Paired tumor sample in GSE83586 : SAMPLE 15 : 15.CEL
GEO accession of paired tumor: GSM2212915


title: BLCA_LNM_331

description:
Paired tumor sample in GSE83586 : SAMPLE 41 : p1404_41.CEL
GEO accession of paired tumor: GSM2212941


title: BLCA_LNM_333

description:
Paired tumor sample in GSE83586 : SAMPLE 120 : p1404_120_re.CEL
GEO accession of paired tumor: GSM2213020


title: BLCA_LNM_330

description:
Paired tumor sample in GSE83586 : SAMPLE 216 : p1419_216.CEL
GEO accession of paired tumor: GSM2213122


title: MAGEA1-M-b hA3A-BE3 rep 2

description:
Sample 50
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: BLCA_LNM_334

description:
Paired tumor sample in GSE83586 : SAMPLE 12 : 12.CEL
GEO accession of paired tumor: GSM2212912


title: MJ Day 4 unt 351291


title: PDL1-M-b hA3A-BE3 rep 1

description:
Sample 41
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: HuT102 Day 8 unt 351288

description: Gene expression from HuT-102 cell line at day 8, untreated

source_name: HuT-102 cell line at day 8, untreated


title: BLCA_LNM_324

description:
Paired tumor sample in GSE83586 : SAMPLE 266 : p1419_266.CEL
GEO accession of paired tumor: GSM2213172


title: BLCA_LNM_325

description:
Paired tumor sample in GSE83586 : SAMPLE 246 : p1419_246.CEL
GEO accession of paired tumor: GSM2213152


title: BLCA_LNM_328

description:
Paired tumor sample in GSE83586 : SAMPLE 162 : p1404_162.CEL
GEO accession of paired tumor: GSM2213062


title: PDL1-M-b dCas9-DNMT3_hA3A-BE3 rep 1

description:
Sample 40
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: PDL1-M-b dCas9-DNMT3_BE3 rep1

description:
Sample 21
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: MJ Day 4 11667 351293

description: Gene expression from MJ cell line at day 4, MRG-106


title: BLCA_LNM_326

description:
Paired tumor sample in GSE83586 : SAMPLE 235 : p1419_235.CEL
GEO accession of paired tumor: GSM2213141


title: MJ Day 4 unt 351294

description: Gene expression from MJ cell line at day 4, untreated


title: BLCA_LNM_321

description:
Paired tumor sample in GSE83586 : SAMPLE 264 : p1419_264.CEL
GEO accession of paired tumor: GSM2213170


title: BLCA_LNM_329

description:
Paired tumor sample in GSE83586 : SAMPLE 293 : p1419_312.CEL
GEO accession of paired tumor: GSM2213199


title: BLCA_LNM_327

description:
Paired tumor sample in GSE83586 : SAMPLE 59 : p1404_59.CEL
GEO accession of paired tumor: GSM2212959


title: BLCA_LNM_322

description:
Paired tumor sample in GSE83586 : SAMPLE 256 : p1419_256.CEL
GEO accession of paired tumor: GSM2213162


title: HuT102 Day 8 11667 351287

description: Gene expression from HuT-102 cell line at day 8, MRG-106

source_name: HuT-102 cell line at day 8, MRG-106


title: HuT102 Day 8 unt 351285


title: BLCA_LNM_323

description:
Paired tumor sample in GSE83586 : SAMPLE 60 : p1404_60.CEL
GEO accession of paired tumor: GSM2212960


title: BLCA_LNM_320

description:
Paired tumor sample in GSE83586 : SAMPLE 26 : p1404_26.CEL
GEO accession of paired tumor: GSM2212926


title: BLCA_LNM_319

description:
Paired tumor sample in GSE83586 : SAMPLE 124 : p1404_124_re.CEL
GEO accession of paired tumor: GSM2213024


title: BLCA_LNM_318

description:
Paired tumor sample in GSE83586 : SAMPLE 255 : p1419_255.CEL
GEO accession of paired tumor: GSM2213161


title: HuT102 Day 8 unt 351282

description: Gene expression from HuT-102 cell line at day 8, untreated


title: HuT102 Day 8 11667 351284


title: MSSK1-M-a BE3 rep 3

description:
Sample 19
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 BE3 rep 3

description:
Sample 18
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: SITE3 BE3 rep1; FANCF-M-d BE3 rep 2

description:
Sample 20
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: FANCF-M-d BE3 rep 1; VEGFA-M-c BE3 rep 3

description:
Sample 15
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE3, SITE4 BE3 rep 2

description:
Sample 17
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-c, VEGFA-M-c, EMX1, RNF2, SITE2, SITE4 BE3 rep 1; FANCF-M-d BE3 rep 3

description:
Sample 16
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: BLCA_LNM_317

description:
Paired tumor sample in GSE83586 : SAMPLE 279 : p1419_289.CEL
GEO accession of paired tumor: GSM2213185


title: HuT102 Day 8 11667 351281


title: MAGEA1-M-b BE3 rep1

description:
Sample 14
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: BLCA_LNM_312

description:
Paired tumor sample in GSE83586 : SAMPLE 114 : p1404_114.CEL
GEO accession of paired tumor: GSM2213014


title: BLCA_LNM_316

description:
Paired tumor sample in GSE83586 : SAMPLE 102 : p1404_102.CEL
GEO accession of paired tumor: GSM2213002


title: BLCA_LNM_313

description:
Paired tumor sample in GSE83586 : SAMPLE 278 : p1419_288.CEL
GEO accession of paired tumor: GSM2213184


title: HuT102 Day 8 unt 351279


title: BLCA_LNM_314

description:
Paired tumor sample in GSE83586 : SAMPLE 277 : p1419_284.CEL
GEO accession of paired tumor: GSM2213183


title: BLCA_LNM_310

description:
Paired tumor sample in GSE83586 : SAMPLE 302 : p1419_322.CEL
GEO accession of paired tumor: GSM2213208


title: HuT102 Day 4 11667 351272

description: Gene expression from HuT-102 cell line at day 4, MRG-106

source_name: HuT-102 cell line at day 4, MRG-106


title: HuT102 Day 4 11667 351275


title: HuT102 Day 4 unt 351273

description: Gene expression from HuT-102 cell line at day 4, untreated

source_name: HuT-102 cell line at day 4, untreated


title: BLCA_LNM_308

description:
Paired tumor sample in GSE83586 : SAMPLE 137 : p1404_137_re.CEL
GEO accession of paired tumor: GSM2213037


title: MAGEA1-M-b BE3 rep 3

description:
Sample 13
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: BLCA_LNM_315

description:
Paired tumor sample in GSE83586 : SAMPLE 221 : p1419_221.CEL
GEO accession of paired tumor: GSM2213127


title: HuT102 Day 4 unt 351276


title: HuT102 Day 4 11667 351278


title: MAGEA1-M-b BE3 rep 2

description:
Sample 12
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: MAGEA1-M-b hA3A-BE3-C101S rep 1

description:
Sample 66
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: PDL1-M-b BE3 rep 1

description:
Sample 1
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 120-150


title: 4410-FFB-0016_miRNAseq

city: Auburn

first: Frank

middle: F

last: Bartol

state: Alabama

address: 1130 Wire Road

department: College of Veterinary Medicine

institute: Auburn University

description:
SL255973_0
4410-FFB-0016-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx

data_processing:
For RNAseq data, raw reads were imported on Avadis NGS and mapped to the Sscrofa 11.1 build of the porcine genome  (National Center for Biotechnology Information [NCBI]) with default settings that allowed only two mismatches per read. Samples  were grouped according to their respective identifiers. Normalized gene expression was quantified using the trimmed mean of M-values method. Human orthologs of unannotated differentially expressed genes (DEGs) were identified using the Reciprocal Best Hits method.
For miRNAseq data, raw reads were imported on Avadis NGS Quality control checks, adapter trimming, and read filtering were performed. Filtered reads were used to extract and count miRNAs which were annotated with miRBase release 21 database. Sample were grouped according to their respective identifiers followed by quantification of miRNA abundance.  Differentially expressed mRNAs and miRNAs, based on fold change (≥ ± 1.5), were identified with respect to neonatal immunocrit (high iCrit versus low iCrit). Probability values for each differentially expressed mRNA and miRNA were estimated by z-score calculations using a false discovery rate of 0.05.
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: normalized expression values

organism: Sus scrofa domesticus

source_name: High Immunocrit_endometrium

growth_protocol: Gilts (Sus scrofa domesticus) were born and raised from a herd of crossbred maternal line (Landrace and Yorkshire genetics) pigs at the U. S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. All procedures involving animals were reviewed and approved by the USMARC Institutional Animal Care and Use Committee and conducted in accordance with the Federation of Animal Science Societies (2010) guidelines for the care and use of agricultural animals in research.

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen) following the manufacturer's protocol.  RNA quality was assessed using Agilent Bioanalyzer and Qbit Fluorometer. Samples with an RNA integrity number (RIN) ≥ 7.5 were used for library preparation for RNA sequencing RNAseq) and miRNA sequencing (miRNAseq).
Briefly, total RNA (500 ng) from each endometrial sample was used for mRNA and miRNA library preparation. For mRNAseq, polyadenylated (polyA) RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads (New England BioLabs, Inc.). After polyA selection, RNA was fragmented and primed for first-strand synthesis using the NEBNext First Strand Synthesis Module, followed by second-strand synthesis using the NEBNext Second Strand Synthesis Module. Samples followed standard library preparation protocol using NEBNext DNA Library Prep Master Mix Set for Illumina. For miRNAseq, the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs Inc., Ipswich, MA, USA) was followed according to the manufacturer’s protocol. Final mRNA and miRNA library quantities were assessed using a Qubit® 2.0 Fluorometer and library quality was determined using a DNA High Sense chip on Agilent 2100 Bioanalyzer. Further library quantification was completed using the qPCR-based KAPA Biosystem Library Quantification kit (Kapa Biosystems Inc., Woburn, MA, USA). For mRNAseq, each library was diluted to a final concentration of 12.5 nM. For miRNAseq, individual sample libraries were diluted to a final concentration of 1.25 nM. Equimolar amounts of individual barcoded  samples from each group were pooled prior to sequencing. Paired-end (50bp) RNAseq at over 25 million reads per individual barcoded sample  was performed using a HiSeq 2500 (Illumina, Inc., San Diego, CA, USA). miRNAseq was conducted using an Illumina HiSeq 2500 instrument (Illumina Inc., San Diego, CA, USA) at 50bp Single End condition generating approximately 15 million reads per sample.

treatment_protocol: On the day of birth (PND 0), piglets were processed (ear notch, tail dock, needle teeth clipped, penicillin and iron dextran injection) using standard operating procedures and a jugular blood sample was collected from each gilt offspring. On day 15 of age, all gilts received creep feed and were weaned on approximately day 24. At weaning, gilts were housed in the USMARC nursery for 4 weeks and fed the USMARC standard nursery ration. After 4 weeks, gilts were moved to finishing barns and fed standard USMARC grower and finisher diets. At 170 days of age, gilts were moved to the gilt breeding area and were observed daily for estrous behavior. Following at least one estrous cycle of normal duration (17-23 days), gilts were mated at subsequent estrus by artificial insemination using commercial maternal line semen, and mated again 24 h later if still in estrus. On day 13 of pregnancy (PxD 13), gilts were humanely slaughtered at the USMARC abattoir and reproductive tracts were collected. Corpora lutea were counted as an indicator of ovulation rate. Uteri were trimmed free of the broad ligament and uterine lengths (cm) and wet weights (g) were recorded. Each uterine horn was opened longitudinally, and endometrial tissue was collected from approximately the middle of the horn. Endometrial samples were frozen in liquid nitrogen and stored at -80°C until total RNA was extracted. One low iCrit animal was not pregnant and removed from the study (final sample size:  low iCrit, n = 7; high iCrit, n = 8).

tag: breed

value: Crossbred (Landrace, Yorkshire, Duroc)

tag: feeding

value: High Immunocrit

tag: age (days)

value: Pregnancy Day 13

value: endometrium


title: 4410-FFB-0014_miRNAseq

description:
SL255971_0
4410-FFB-0014-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0013_miRNAseq

description:
SL255970_0
4410-FFB-0013-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0015_miRNAseq

description:
SL255972_0
4410-FFB-0015-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: BLCA_LNM_311

description:
Paired tumor sample in GSE83586 : SAMPLE 138 : p1404_138.CEL
GEO accession of paired tumor: GSM2213038


title: 4410-FFB-0012_miRNAseq

description:
SL255969_0
4410-FFB-0012-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: MJ Day 8 unt 351303

description: Gene expression from MJ cell line at day 8, untreated

tag: cell type

tag: treatment

value: untreated

value: day 8


title: HuT102 Day 4 unt 351270

value: day 4


title: 4410-FFB-0009_miRNAseq

description:
SL255966_0
4410-FFB-0009-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: BLCA_LNM_309

description:
Paired tumor sample in GSE83586 : SAMPLE 265 : p1419_265.CEL
GEO accession of paired tumor: GSM2213171


title: 4410-FFB-0010_miRNAseq

description:
SL255967_0
4410-FFB-0010-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: HuT102 Day 4 11667 351269

description: Gene expression from HuT-102 cell line at day 4, MRG-106


title: HuT102 Day 4 unt 351267

description: Gene expression from HuT-102 cell line at day 4, untreated


title: 4410-FFB-0007_miRNAseq

description:
SL255964_0
4410-FFB-0007-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx

source_name: Low Immunocrit_endometrium

value: Low Immunocrit


title: 4410-FFB-0011_miRNAseq

description:
SL255968_0
4410-FFB-0011-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0008_miRNAseq

description:
SL255965_0
4410-FFB-0008-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0005_miRNAseq

description:
SL255963_0
4410-FFB-0005-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0003_miRNAseq

description:
SL255961_0
4410-FFB-0003-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0002_miRNAseq

description:
SL255960_0
4410-FFB-0002-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0004_miRNAseq

description:
SL255962_0
4410-FFB-0004-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0001_miRNAseq

description:
SL255959_0
4410-FFB-0001-miRNA
processed data file: Normalized_expression_values_Bartol_miRNAseq.xlsx


title: 4410-FFB-0015_RNA-seq

description:
SL220821_1
4410-FFB-0015
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0014_RNA-seq

description:
SL220820_1
4410-FFB-0014
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: KrasG12D Dox 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Expression arrays were processed and RMA normalized using BioConductor affy package.

source_name: human primary bronchial epithelial cell line (HBEC)

label_protocol: According to Affymetix protocol.

growth_protocol: HBEC cells were a gift from J. Minna (University of Texas-Southwestern Medical center, and were cultured in KSFM medium (Life Technologies). All cell lines were propagated at 37°C and 5% CO2 in humidified atmosphere.

extract_protocol: Briefly, RNA was extracted and 5 µg of total RNA was used for first- and second-strand cDNA synthesis, according to Affymetrix protocol.

treatment_protocol: The Dox-regulatable KRASG12D HBEC cell line was constructed using the pInducer system. The HBEC-iKRAS (WT) cell line and HBEC-iKRASG12D  (MUT)  cell line were propagated with or without Doxycycline (500ng/ml) respectively.

tag: genotype/variation

tag: agent

value: Dox


title: KrasG12D Dox 3


title: 4410-FFB-0013_RNA-seq

description:
SL220819_1
4410-FFB-0013
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: KrasG12D no Dox 3


title: 4410-FFB-0012_RNA-seq

description:
SL220818_1
4410-FFB-0012
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0010_RNA-seq

description:
SL220816_1
4410-FFB-0010
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0016_RNA-seq

description:
SL220822_1
4410-FFB-0016
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0009_RNA-seq

description:
SL220815_1
4410-FFB-0009
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: KrasWT Dox 1

value: KrasWT


title: 4410-FFB-0008_RNA-seq

description:
SL220814_1
4410-FFB-0008
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: HuT102 Day 8 11667 351290

description: Gene expression from HuT-102 cell line at day 8, MRG-106


title: KrasWT Dox 3


title: KrasWT Dox 2


title: KrasG12D no Dox 1


title: 4410-FFB-0005_RNA-seq

description:
SL220811_1
4410-FFB-0005
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0002_RNA-seq

description:
SL220808_1
4410-FFB-0002
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: KrasG12D Dox 1


title: KrasWT no Dox 1


title: KrasG12D no Dox 2


title: KrasWT no Dox 3


title: 4410-FFB-0011_RNA-seq

description:
SL220817_1
4410-FFB-0011
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0004_RNA-seq

description:
SL220810_1
4410-FFB-0004
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0003_RNA-seq

description:
SL220809_1
4410-FFB-0003
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 4410-FFB-0007_RNA-seq

description:
SL220813_1
4410-FFB-0007
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 101P

city: New Haven

first: Lajos

last: Pusztai

state: CT

address: 300 George St., Suite 120

institute: Yale University

hyb_protocol: RNA was hybridized to capture probes by nCounter analysis system

scan_protocol: nCounter analysis system

data_processing: The expression values were normalized using housekeeping genes using the nSolver 2.6 package following the manufacturer’s recommendations

label: nanostring

source_name: primary breast cancer

label_protocol: NanoString manufactuerer's protocol

extract_protocol: RNA was extracted from 3, 10 micron FFPE sections of each cancer using the High Pure RNA Paraffin Kit from Roche Applied Science.

tag: localization

value: breast


title: 35P


title: 99P


title: 38M

source_name: metastatic breast cancer

value: bone marrow


title: 4410-FFB-0001_RNA-seq

description:
SL220807_1
4410-FFB-0001
processed data file : Normalized_expression_values_Bartol_RNAseq.xlsx


title: 18M

value: brain


title: KMT2D-depleted cells a

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

state: CA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

hyb_protocol: Hybridize at 45C for 16 hours with rotation at 60rpm (GeneChip Hybridization Oven 645)

scan_protocol: Affymetrix GeneChip Scanner 7G with default settings

data_processing: Affymetrix Expression Console

source_name: MIA PaCa-2

label_protocol: Ambion MessageAmp Premier protocol

extract_protocol: RNA was isolated using  TRIzol (Invitrogen product name) and subsequently the Qiagen  RNeasy mini Kit (cat 74104).  Column based.

treatment_protocol: MIA PaCa-2 cells were trypsinized and transfected with 50nΜ siRNA for KMT2D or scramble siRNA. Lipofectamine ® RNAiMAX was used as transfection reagent. RNA-Lipofectamine complexes were made in Opti-MEM (serum free). Cells were plated at a 50% confluence in serum and antibiotic-containing media. 24h later double transfection was performed with the same amounts of siRNAs and cells were incubated for 24h before RNA isolation.

value: KMT2D depleted


title: KrasWT no Dox 2


title: KMT2D-depleted cells b


title: control cells b

value: control


title: 18P


title: 10M

value: pericardium


title: 17P


title: 39M1

value: lung


title: 39M2

value: aorta


title: 14P


title: 21P


title: 39P


title: 17M


title: 115P


title: 10P


title: 32P


title: control cells a


title: 27P


title: 24P


title: 16M

value: ovary


title: 31M

value: soft tissue


title: 31P


title: 13M


title: 13P


title: 4P


title: 97M


title: 7P2


title: 1P


title: Patients with T cell mediated rejection [S16]

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
TCMR
S16
Small RNA-Seq

data_processing:
MicroRNAs were identified and quantified using miRDeep2.0.0.8.
Differential expression was analyzed using DESeq2 1.18.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include number of miRNA raw read counts.

source_name: Blood

growth_protocol: Kidney transplanted patients with stable graft function, antibody-mediated rejection or T cell-mediated rejection episodes.

extract_protocol:
Total RNA (tRNA) was isolated from blood cells contained in PAXgene Blood RNA Tubes with the PAXgene blood miRNA Kit (PreAnalytix, Qiagen, Hilden, Germany) according to the manufacturer's instruction. Total RNA concentration and quality of each sample were determined with the NanoDrop ND-Lite (peqlab, Erlangen, Germany) and Qubit fluorometer (ThermoFisher Scientific, Darmstadt, Germany). Dependent on quantity and quality of RNA, six samples from patients with ABMR, six samples from patients with SGF and 4 samples from patients with TCMR were chosen for high-throughput sequencing.
The "TruSeq® small RNA library Prep" kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries for small RNA sequencing from a maximum of 1µg of total RNA isolated from the whole blood of patients with Tx according to manufacturer’s instruction. RNA quality was assessed on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and only RNA with a RIN >8 was considered for further processing. After quality control (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany) the resulting cDNA libraries were purified by gel-electrophoresis for the small RNA containing cDNA fraction at ~150 bp. The final small RNA cDNA libraries were quality checked (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany) and quantified (Qubit dsDNA HS Assay Kit, Invitrogen, Darmstadt, Germany). The final libraries were single-end (50 bp) sequenced on a HiSeq2500 Illumina Next Generation Sequencing Device (Illumina, San Diego, CA, USA).

value: Blood

value: Whole blood cells

value: Kidney transplant

tag: transplant result

value: T cell-mediated rejection


title: Patients with T cell mediated rejection [S15]

description:
TCMR
S15
Small RNA-Seq


title: Patients with T cell mediated rejection [S14]

description:
TCMR
S14
Small RNA-Seq


title: Pkm2-/- 3D

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

data_processing:
Quality control: The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads  for subsequent analysis.  The steps of sequencing data filtering:  1) removing reads containing adapter;  2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%;  3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire  read);  All the downstream analyses were based on clean data with high quality.
Mapping to the reference genome: The reference genome and gene model annotation files were downloaded directly from the  genome website. The reference genome index was built using Bowtie2 (v2.2.9)[1], and paired-end  clean reads were aligned to the reference genome using TopHat (v2.1.1)[2]
Transcriptome assembly: The mapped reads of each sample were assembled using Cufflinks (v2.2.1)[3] with a  reference-based approach. This method employed spliced reads to determine exon connectivity.  Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression levels  of a minimal set of isoforms, which provides a maximum likelihood explanation of the expression  data in a given locus.
Quantification of gene expression levels: Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample. Gene FPKMs  were computed by summing the FPKMs of the transcripts in each gene group. FPKM stands for  “fragments per kilobase of exon per million fragments mapped”, and it is calculated based on the  length of the fragments and the reads count mapped to each fragment.
Differential expression analysis: Cuffdiff (v2.2.1)[3] provides statistical routines for determining differential expression in digital  transcript or gene expression datasets using a model based on a negative binomial distribution.  Genes with corrected p values less than 0.05 and the absolute value of log2 (fold change) < 1 were  assigned as significantly differentially expressed.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: colon epithelial cells

extract_protocol:
colon epithelial cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.the VAHTS mRNA-seq v2 Library  Prep Kit for Illumina® (Vazyme, NR601)  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: colon epithelium

value: treated with  2.5% DSS for 3 days


title: 29M

value: liver


title: Patients with stable graft function [S12]

description:
SGF
S12
Small RNA-Seq

value: stable graft function