title: NSPCs from wild-type mouse treated with Cr-GFPe virus and maintained in FGF and EGF NSPCs_YKO3

city: Köln

first: Matteo

last: Bergami

address: Joseph Stelzmann Str 26

institute: CECAD Research Center

data_processing:
Analysis was performed with the nf-core RNA-seq pipeline version 3.0, commands are provided below see: https://doi.org/10.5281/zenodo.1400710
nextflow pull nf-core/rnaseq -r 3.0    nextflow run nf-core/rnaseq \      --input design_P-Q.csv \      --fasta ftp://ftp.ensembl.org/pub/release-103/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz \      --gff ftp://ftp.ensembl.org/pub/release-103/gff3/mus_musculus/Mus_musculus.GRCm39.103.gff3.gz \      --gtf_count_type exon --gtf_group_features gene_id --gtf_extra_attributes Name --skip_biotype_qc \      --save_reference \      --aligner star_salmon \      -profile docker \      -r 3.0 --outdir ./results_P-Q
nextflow pull nf-core/rnaseq -r 3.0    nextflow run nf-core/rnaseq \      --input design_WT-YKO.csv \      --fasta ftp://ftp.ensembl.org/pub/release-103/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz \      --gff ftp://ftp.ensembl.org/pub/release-103/gff3/mus_musculus/Mus_musculus.GRCm39.103.gff3.gz \      --gtf_count_type exon --gtf_group_features gene_id --gtf_extra_attributes Name --skip_biotype_qc \      --save_reference \      --aligner star_salmon \      -profile docker \      -r 3.0 --outdir ./results_WT-YK
Differential expression analysis was performed in R v4.0.3 with DESeq2 v1.30.1 Log Fold Change shrinkage estimation was performed with apeglm v1.12.0
Genome_build: Mus musculus GRCm39 Ensembl version 103

source_name: adult NSPCs

extract_protocol:
NSPCs were harvested in TRIzol reagent (Invitrogen) and RNA was isolated according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina® Stranded TruSeq® RNA sample preparation Kit
RNA-Seq (poly-A selected)

tag: ID

tag: treatment

value: FGF and EGF; Cre-GFP adeno-associated virus


title: Brain, AD_TilingArray_M11

status: Public on Jan 19 2022

type: RNA

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing:
We used the TileShuffle algorithm (Otto C, Reiche K, Hackermuller J. Detection of differentially expressed segments in tiling array data. Bioinformatics 2012; 28: 1471–1479) to determine expressed and differentially expressed genomic intervals. Affymetrix Human Whole Genome Tiling Array 1.0 Set raw signal intensities were mapped to human genome version NCBI36 using Affymetrix BPMAP files. Expressed segments were detected with the TileShuffle parameter settings: window size = 200, the window score was defined as the arithmetic mean trimmed by the maximal and minimal values over signal intensities of all probes in a window, number of permutations = 10 000 and number of GC classes = 4. All windows with an adjusted p < 0.05 according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995) were defined to be significantly expressed. DE-TARs are differentially expressed TileShuffle intervals with adjusted p < 0.05 (window size = 200, the window score was defined as the logfold-change discarding all probes with converse behavior as observed for the relevant significantly expressed windows, number of permutations = 100 000 and number of GC classes = 1). Finally, the genome coordinates of all significantly expressed and all significantly differentially expressed segments were lifted over to GRCh37 (hg19) using liftOver (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver).
[additional results files] Ueberham_AD_K_highdiff3.bed:  significantly differentially expressed segments (adjusted p<0.05)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human brain tissue

label_protocol: The Affymetrix Human Whole Genome Tiling Array 1.0 Set consisting of 14 arrays was used according to the manufacturer’s instructions, except that separate labeling reactions were used for each array starting from 10 μg pooled total RNA.

extract_protocol: RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.

tag: disease state

value: Alzheimer's disease (AD)

tag: tissue

value: brain


title: NSPCs from wild-type mouse treated with Cr-GFPe virus and maintained in FGF and EGF NSPCs_YKO2

type: SRA

library_source: transcriptomic

organism: Mus musculus

tag: strain


title: AAV-Nd3-9577-(1), mouse_7

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

description:
mouse_7
7_S7

library_source: genomic

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38) with Bowtie2
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Genome_build: GRChm38
Supplementary_files_format_and_content: Supp Dataset 1 = excel file showing the % of base editing at individual Cs within the editing window for each sample; counts_ddCBE = xls file with Adaptor counts generated by Cutadapt

molecule: genomic DNA

source_name: heart

growth_protocol: The animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse heart samples (~50 mg) was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT
DNA resequencing

treatment_protocol: In adult experiments, 8-week-old mice were administered systemically by tail vein injection with 1 x 10*12 AAV particles of each monomer [AAV- DdCBE (L) - Nd3-9577 - G1333-C and AAV- DdCBE (H) - Nd3-9577- G1333-N]. An equal dose was applied in newborn pups (Postnatal day 1) via the temporal vein

value: heart

tag: ddcbe halves

value: L-strand:1333C ; H-strand:1333N

tag: time

value: 24 week(s) after intervention

tag: injected as

value: Adult


title: G_4_GSP_5_no_tumor_28_M.txt

city: Genova

first: Roberta

last: Resaz

address: via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Data processing, categorization, normalization, filtering, imputation and differential expression was carried out by PIPE-T galaxy tool.  Ct values falling within the range 14-32 were categorized as reliable values as recommended by the manufacturer guidelines. Global mean normalization was used to reduce any technical variability introduced in the data by the RT-qPCR experiments.    Only Exo-miR with at most 20% of missing values were retained for the analysis to reduce the bias introduced by imputation.  Mestdagh method was employed to assign a numeric expression value to missing values. The rank product method implemented by RankProd R package was used to identify significant differentially expressed microRNA.
non-normalized file reports raw Ct values. Ct value of 40 indicates a missing value. normalized data file reports delta Ct values (Ct – sample mean expression ). NA value indicates a missing value.

label: Applied Biosystems Human TaqMan Low Density Array (TLDA, v2.0) (Card A)

source_name: Plasma exosomes

label_protocol: Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM RT primers Human Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM  Pre-Amp primers Human Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiATM 7 Real-Time PCR System.

extract_protocol: Exosomes isolation and RNA extraction from plasma was performed with the exoRNeasy Serum/Plasma Midi kit (Qiagen Italia, Milano, Italy).

value: Plasma exosomes

tag: patient diagnosis

tag: molecule subtype

value: microRNA


title: G_24_GSP_38_no_tumor_29_M.txt


title: Novice_rep2

first: Chloe

last: Delepine

state: Massachusetts

address: 43 vassar st

country: USA

institute: MIT

data_processing:
Reads were aligned to the mouse mm9 genome using the TopHat sliced read mapper (Trapnell et al., 2012).
Fragment counts were obtained using the Cufflinks pipeline (Trapnell et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: Motor cortex astrocytes

extract_protocol:
RNA was purified and concentrated with proteinase K cell digestion, ethanol precipitation and washing on a silica column (Zymo, Quick-RNA FFPE)
Indexed cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 (Illumina, #634411)
Multiplexed sequencing (RNAseq) was performed on Illumina HiSeq 2000

tag: age

value: 13 wks

tag: Sex

value: M

tag: learning

value: Novice

tag: cell type

value: Motor cortex astrocytes


title: Brain, Control_TilingArray_M11

scan_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

value: Control


title: Brain_AD_sample10

hyb_protocol: 1.65 μg of labeled cRNA was used for hybridization following manufacturer’s instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) following settings for scanning: Profile: AgilentG3 GX 1Color; Channels Green; Scan Region: Agilent HD (61 × 21.6mm); Resolution 3 μm double pass; Tiff: 20 bit; Green PMT Gain: 100%. Result tables were extracted after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1)

data_processing: Differential expression analysis was performed using R and the Bioconductor package Limma. Quality control of arrays was performed by checking distribution of “bright corner”, “dark corner” probes, and relative spike-in concentration versus normalized signal. The controls confirmed high quality of the results and consequently all microarray data were included in the downstream analysis. Initially, independent filtering was performed, removing probes (i) with signal intensity above the background in less than one third of all arrays and (ii) exhibiting an interquartile range of log2 signal intensity across all samples of less than 1. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent’s 3xSLv spots). 113 047 out of 931 898 probes were retained after filtering. Signal intensities were quantile normalized but not background corrected, due to the low background intensities of Agilent arrays. Differential expression between AD and control samples was determined using a linear model that includes age because on average, individuals from the AD group were older than controls. The linear model was fitted using the R package limma and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate was controlled by a modified Benjamini-Hochberg procedure that incorporates an estimated proportion of the null p-values 23 to compute q-values using the fdrtool R package.

source_name: brain tissue

label_protocol: 1 μg of total RNA was labeled using the Quick Amp Labeling Kit (Agilent, Waldbronn, Germany), according to the manufacturer’s instructions with the adaptation of using 120 pmol of a random N6 − T7 primer (Metabion, Planegg, Germany) instead of a polyT-T7 primer. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer’s instructions.

extract_protocol: RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.

value: AD

tag: gender

value: m


title: Novice_rep1

value: 12 wks

value: F


title: Brain_AD_sample9

value: w


title: NSPCs from wild-type mouse treated with Cr-GFPe virus and maintained in FGF and EGF NSPCs_YKO1

value: FGF and EGF; Cre-GFP adeno-associated virus


title: AAV-Inactive, mouse_6

description:
mouse_6
6b_S6

value: heart

value: 3 week(s) after intervention


title: Novice_rep4


title: G_19_GSP_28_no_tumor_26_M.txt


title: Brain_AD_sample7

value: brain


title: G_20_gsp_30_no_tumor_26_F.txt


title: AAV-Nd3-9577-(1), mouse_4

description:
mouse_4
4_S4

value: L-strand:1333C ; H-strand:1333N

value: Adult


title: Brain_AD_sample13


title: Brain_AD_sample11


title: Naïve_rep5

value: 15 wks

value: Naïve


title: G_3_GSP_3_no_tumor_22_F.txt

value: Plasma exosomes

value: microRNA


title: Naïve_rep4

value: 14 wks

value: M

value: Motor cortex astrocytes


title: NSPCs from wild-type mouse treated with GFP virus and maintained in FGF and EGF NSPCs_WT2

value: FGF and EGF; GFP adeno-associated virus


title: NSPCs from wild-type mouse treated with GFP virus and maintained in FGF and EGF NSPCs_WT1


title: AAV-Nd3-9577-(1), mouse_3

description:
mouse_3
3_S3


title: G_23_GSP_36_no_tumor_22_M_BIS.txt


title: NSPCs from wild-type mouse treated with FGF and EGF NSPCs_P5

value: FGF and EGF


title: Vehicle, mouse_2

description:
mouse_2
2_S2

value: Vehicle


title: Naïve_rep2

value: 21 wks


title: Naïve_rep3

value: F


title: Brain_AD_sample6

value: AD

value: w


title: Brain_AD_sample5

value: brain


title: G_32_GSP_51_no_tumor_21_F.txt


title: NSPCs from wild-type mouse treated with FGF and EGF NSPCs_P4


title: Naïve_rep1

value: 12 wks


title: Vehicle, mouse_1

description:
mouse_1
1_S1

value: heart

value: 3 week(s) after intervention

value: Adult


title: Inactive-(4), NIH/3T3_68

description:
NIH/3T3_68
68_S12

tag: cell line

value: L-strand:1397N ; H-strand:1397C

value: 1 week(s) after intervention


title: NSPCs from wild-type mouse treated with FGF and EGF NSPCs_P1


title: Inactive-(4), NIH/3T3_8

description:
NIH/3T3_8
8_S14


title: G_34_GSP_54_no_tumor_19_M_BIS.txt

value: Plasma exosomes

value: microRNA


title: NSPCs from wild-type mouse treated with FGF and EGF NSPCs_P2


title: NSPCs from wild-type mouse treated with BMP4 NSPCs_Q4


title: 220115_Sir3-MEcoGII-overexpression-rep2_ChIP

city: Berkeley

first: Molly

last: Brothers

state: CA

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
FASTQ generation with Illumina Casava v2.2
Raw reads were mapped to SacCer3 genome modified to include  mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedGraph (normalized to genome-wide median)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 30°C in YPD except for the following: Samples 21 and 22 were grown at 25°C in YPD. Samples 23 and 24 were grown at 37°C in YPD.

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin or DNA was fragmented using sonication. V5 immunoprecipitations were performed using anti-V5 antibody (Invitrogen R960-25). m6A immunoprecipitations were performed using anti-m6A antibody (Synaptic Systems 202-003). For ChIP-seq, DNA was purified with 1X v/v SPRI Select beads (Beckman-Coulter Beckman Coulter, B23317)
For ChIP-seq: NEB Ultra II library prep kit. For MeDIP-seq: Swift Biosciences Accel-NGS 1S Plus

treatment_protocol: For ChIP-seq experiments (Samples 1 and 2), cells were fixed in 1% formaldehyde for 15 minutes at 30°C and then quenched with 300mM glycine for 10min at 30°C.

tag: ip antibody

value: anti-Sir3 antibody (gift from R. Kamakaka)

tag: condition

value: Cycling

tag: genotype

value: mat-delta::HphMX, SIR3-M.ECOGII-NatMX + pJR3526


title: AAV-Inactive, mouse_5

description:
mouse_5
5_S5

value: L-strand:1333C ; H-strand:1333N


title: 220115_Sir3-MEcoGII-overexpression-rep2_input


title: 220115_Sir3-MEcoGII-overexpression-rep1_ChIP


title: Nd3-9577-(4), NIH/3T3_67

description:
NIH/3T3_67
67_S8


title: G_51_GSP_83_no_tumor_19_F.txt


title: NSPCs from wild-type mouse treated with BMP4 NSPCs_Q3

tag: ID

tag: treatment


title: Brain_AD_sample8

tag: disease state

tag: tissue


title: G_102_GSP_155_no_tumor_20_F.txt


title: AAV-Nd3-9577-(1), mouse_15

description:
mouse_15
15_S15

tag: ddcbe halves

tag: time

value: Neonate


title: G_107_GSP_144_no_tumor_19_M.txt

tag: patient diagnosis


title: Brain_AD_sample12

value: m


title: 220115_Sir3-MEcoGII-overexpression-rep1_input

tag: strain


title: Brain_AD_sample4

value: AD

tag: age


title: NSPCs from wild-type mouse treated with BMP4 NSPCs_Q2


title: G_170_GSP_221_no_tumor_22_F.txt

tag: molecule subtype


title: CTR 46.txt

description: Healthy controls

value: healthy control


title: Brain_AD_sample3

value: brain


title: Inactive-(3), NIH/3T3_66

description:
NIH/3T3_66
66_S4

value: L-strand:1397C ; H-strand:1397N

tag: injected as


title: NSPCs from wild-type mouse treated with BMP4 NSPCs_Q1


title: CTR 41.txt

description: Healthy controls


title: Nd3-9577-(4), NIH/3T3_7

description:
NIH/3T3_7
7_S10


title: Inactive-(3), NIH/3T3_6

description:
NIH/3T3_6
6_S6


title: 220115_Sir3-MEcoGII-emptyvector-rep2_input

value: mat-delta::HphMX, SIR3-M.ECOGII-NatMX + YEp24


title: Nd3-9577-(3), NIH/3T3_56

description:
NIH/3T3_56
56_S20


title: CTR 38.txt

description: Healthy controls


title: Nd3-9577-(3), NIH/3T3_5

description:
NIH/3T3_5
5_S2


title: 220115_Sir3-MEcoGII-emptyvector-rep1_ChIP


title: CTR 39.txt

description: Healthy controls


title: B16F10-Skin rep1

city: Daejeon

first: HyunSeok

last: Kim

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

data_processing:
Raw sequencing data were quality-checked by FastQC v0.11.7 and filtered using Trimmomatic tool.
The trimmed data were subsequently aligned to mouse reference genome (mm10) using HISAT2(ver.2.1.0).
The read count data were filtered, resulting in remaining transcripts with gene IDs,read counts, FPKM(Fragments Per Kilobase of transcript per Million Mapped reads) and TPM(Transcripts Per Kilobase Million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Melanoma graft from flank skin

extract_protocol:
Tumors from primary implementation sites were removed, and RNA was extracted using RNeasy Kit (Qiagen) according to the manufacturers’ protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E

value: Foxn1-/- mice

value: Tumor(melanoma)

value: 8 weeks

tag: sample group

value: Melanoma graft from flank skin


title: 220115_Sir3-MEcoGII-emptyvector-rep1_input


title: B16F10-Skin rep3


title: B16F10-Skin rep2


title: CTR 36.txt

description: Healthy controls

value: Plasma exosomes


title: Inactive-(2), NIH/3T3_46

description:
NIH/3T3_46
46_S15

value: L-strand:1333N ; H-strand:1333C

value: 1 week(s) after intervention


title: NSPCs from wild-type mouse treated with GFP virus and maintained in FGF and EGF NSPCs_WT3

value: FGF and EGF; GFP adeno-associated virus


title: CDE3_hot

city: Turku

first: Taina

last: Tyystjärvi

address: Itäinen pitkäkatu 4

country: Finland

institute: University of Turku

data_processing:
Reads were aligned to the Synechocystis PCC sp 6803 (Moscow strain)  reference genome (Ensemble release 35) using HISAT2 (Kim et al., 2015)
HTseq-count (Anders et al., 2015) was used to calculate summarized read counts for each gene, except that the two ribosomal RNA operons were excluded from the analysis.
DESeq2 (Love et al., 2014) was used to identify differentially expressed (DE) genes
Data analysis were done with the CSC's Chipster v.4 platform (Kallio et al., 2011).
Genome_build: Synechocystis PCC sp 6803, Moscow strain, Ensemble release 35
Supplementary_files_format_and_content: Tab delimited counts of each strain in each treatment. Raw reads were trimmed with Trimmomatic program and merged with trimmed reads from different lanes in the first run. Some of the samples were re-run due to poor yield and re-run samples are also merged with previous reads

organism: Synechocystis sp. PCC 6803

source_name: cell

extract_protocol:
15-ml of cell suspension was pour to pre-frozen centrifugation tube, and cell pellet was collected by centrifugation at 7000 g for 5min at 4 °C. Cell pellets were frozen in liquid nitrogen. Isolation of total RNA was done with a hot phenol method.
Sequencing libraries for total RNA (100 ng) samples were prepared using Illumina TruSeq Stranded mRNA kit protocol.

value: glucose tolerant

value: [delta]sigC, [delta]sigD, [delta]sigE

value: 1 h at 40C


title: Inactive-(2), NIH/3T3_4

description:
NIH/3T3_4
4_S18


title: B16F10-Foot rep3

source_name: Melanoma graft from hind footpad

value: Melanoma graft from hind footpad


title: Brain_AD_sample1

value: AD

tag: gender

value: w


title: 220115_Sir3-MEcoGII-emptyvector-rep2_ChIP

value: anti-Sir3 antibody (gift from R. Kamakaka)

value: Cycling


title: CTR 33.txt

description: Healthy controls

value: healthy control

value: microRNA


title: CDE2_hot


title: CTR 32.txt

description: Healthy controls


title: Nd3-9577-(2), NIH/3T3_36

description:
NIH/3T3_36
36_S11

tag: cell line


title: B16F10-Foot rep2

value: Foxn1-/- mice

value: Tumor(melanoma)


title: B16F10-Foot rep1

value: 8 weeks


title: CTR 30.txt

description: Healthy controls

value: Plasma exosomes


title: CDE3_HL

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: Inactive-(1), NIH/3T3_26

description:
NIH/3T3_26
26_S7

value: L-strand:1333C ; H-strand:1333N

value: 1 week(s) after intervention


title: CDE2_HL

value: glucose tolerant


title: D11-anti-CTLA-4-Bhlhe40-KO

city: Houston

first: Alexander

middle: Sergeyevich

last: Shavkunov

state: Texas

address: 7455 Fannin St

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The Cell Ranger Single-Cell Software Suite available at https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome was used to perform sample demultiplexing, barcode processing and single-cell 5' counting. Cellranger mkfastq was used to demultiplex raw base call files from the NovaSeq6000 sequencer, into sample-specific fastq files. Files were demultiplexed with 81.9% to 97.1% perfect barcode match, and 90%+ q30 reads.
fastq files for each sample were processed with Cellranger count, which was used to align samples to mm10 genome, filter and quantify
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with metadata (tsv), matrices of count values (mtx) for each sample

source_name: Tumor

extract_protocol:
Established tumors were excised from mice at day 9 (D09) or Day 11 (D11) post-transplant, minced and dissociated using 1 mg/ml type IA collagenase (Sigma). Introtumoral immune cells were stained with a monoclonal anti-mouse CD45 antibody and Zombie NIR Viability dye and sorted on a BD FACSAria II fluorescence-activated cell sorter. Approximately 10,000 cells per sample were processed using Chromium Next GEM Single-cell 5' Reagent Kits v2 (10x Genomics)
Libraries were prepared using Chromium Next GEM Single-cell 5' Reagent Kits v2 according to manufacturer’s protocol (10x Genomics)

treatment_protocol: 1956 MCA sarcoma cells were subcutaneously transplanted into mice at 1 x 10^6 cells or 0.4 x 10^6 cells, respectively, in 150 ml into the flank on day 0. Mice were treated intraperitoneally with 200 mg of anti-PD-1 or anti-CTLA-4 monoclonal antibody, used alone or in combination on days 3, 6, and 9 post-tumor transplant. For controls, mice were injected with 200 mg of IgG2a isotype control antibodies.

tag: cells

value: Intratumoral CD45+ cells

tag: Sex

value: Female

value: 9 weeks old

tag: tumor cell line

value: 1956 MCA sarcoma

value: anti-CTLA-4 antibody

tag: time point

value: 11 days post-transplant


title: Inactive-(1), NIH/3T3_2

description:
NIH/3T3_2
2_S9


title: CDE1_HL

tag: genotype

value: [delta]sigC, [delta]sigD, [delta]sigE

tag: treatment


title: D11-anti-PD-1-Bhlhe40-KO

value: anti-PD-1 antibody


title: CTR 13.txt

description: Healthy controls

tag: tissue

value: healthy control

value: microRNA


title: D11-anti-CTLA-4-Bhlhe40-WT

value: wild type


title: CTR 26.txt

description: Healthy controls


title: CDE3_STD

value: untreated


title: Nd3-9577-(1), NIH/3T3_1

description:
NIH/3T3_1
1_S5

tag: ddcbe halves


title: CTR 10.txt

description: Healthy controls

value: Plasma exosomes


title: Nd3-9577-(1), NIH/3T3_16

description:
NIH/3T3_16
16_S3

tag: time


title: D11-Control-Bhlhe40-KO

value: Control antibody


title: CTR 06.txt

description: Healthy controls

tag: patient diagnosis


title: CDE2_STD

tag: strain


title: Vehicle, NIH/3T3_c6

description:
NIH/3T3_c6
c6_S19

value: Vehicle


title: CTR 05.txt

description: Healthy controls


title: CDE1_hot

value: 1 h at 40C


title: CDE1_STD

value: glucose tolerant


title: Naïve_rep6

tag: age

value: 14 wks

value: M

tag: learning

value: Naïve

tag: cell type

value: Motor cortex astrocytes


title: Nd3-9577-(2), NIH/3T3_3

description:
NIH/3T3_3
3_S13

value: L-strand:1333N ; H-strand:1333C

value: 1 week(s) after intervention

tag: injected as


title: D11-Control-Bhlhe40-WT

value: Intratumoral CD45+ cells

value: Female

value: 9 weeks old

value: 1956 MCA sarcoma

value: 11 days post-transplant


title: Vehicle, NIH/3T3_c

description:
NIH/3T3_c
c_S1


title: CTR 03.txt

description: Healthy controls

value: healthy control

tag: molecule subtype

value: microRNA


title: BCE3_hot

value: [delta]sigB, [delta]sigC, [delta]sigE


title: D09-anti-CTLA-4-Bhlhe40-KO

value: anti-CTLA-4 antibody

value: 9 days post-transplant


title: OSE3-PP_GeCKOv2

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

country: Japan

institute: The University of Tokyo

description: sgRNA fragment library

data_processing:
FASTQ files were trimmed by "cutadapt -g TTGTGGAAAGGACGAAACACCG -O 24 -m 20 --trimmed-only -e 0.1 (Version 2.1)"
Reads for each sgRNA were counted by "mageck count --list-seq human_geckov2_library_a_09mar2015.csv (Version 0.5.6)"
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO v2). Human library A sgRNA sequences deposited in Addgene #1000000049.
Supplementary_files_format_and_content: tab-delimited text files include read counts per sgRNA for each target

source_name: normal ovarian surface epithelium cell line

growth_protocol: JHOC5 and OSE3 cells were cultured in RPMI-1640, supplemented with 10% serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Genomic DNA was extracted using a QIAGEN Blood and Cell Culture DNA Midi Kit (#13343) according to the manufacturer’s protocol.
125 μg of genomic DNA from each sample was split into 2.5 μg fractions and sgRNA sequences were amplified using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene #1000000049 (Sanjana, et al Nat Methods 2014. 11(8): 783-784). Reactions were measured for fragment size using the Agilent 2200 Tapestation, and quantified using the KAPA SYBR Fast qPCR Kit (KAPA Biosystems, #7959362001).

treatment_protocol: Pooled lentiviral libraries were transduced at the multiplicity of infection (MOI) 0.3. One day after infection, a sample of 2 x 10^7 cells was pelleted and frozen under liquid nitrogen as a Day 0 sample. Cells were then passaged until they had undergone 8 doublings. To maintain sufficient sgRNA coverage, the total number of cells was maintained above 2 x 10^7 for the duration of the culture period. A second sample of 2 x 10^7 cells was taken as a final time point.

tag: cell line

tag: sgrna library

value: GeCKO v2 A library

value: T-antigen immortalized ovarian surface epithelium


title: D11-anti-PD-1-Bhlhe40-WT

tag: cells

tag: Sex

value: wild type

value: anti-PD-1 antibody


title: JHOC5-PP_GeCKOv2

description: sgRNA fragment library

source_name: ovarian cancer cell line

value: ovarian cancer


title: OSE3-Day0_GeCKOv2

description: sgRNA fragment library


title: BCE3_HL

value: glucose tolerant

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: BCE1_hot

value: 1 h at 40C


title: D09-anti-PD-1-Bhlhe40-KO

value: Intratumoral CD45+ cells

value: Female

tag: tumor cell line

tag: time point


title: D09-anti-PD-1-Bhlhe40-WT

value: 9 weeks old

tag: genotype

value: 1956 MCA sarcoma

tag: treatment


title: D09-Control-Bhlhe40-KO

value: Control antibody


title: D09-Control-Bhlhe40-WT


title: BCE1_HL


title: BCE3_STD

value: untreated


title: BT-20-SAMD9-R1293W-no-inducer-S3

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description: BT-20-SAMD9-R1293W cells without treatment

data_processing:
The 3′ adapters and low-quality bases of RNA-seq reads were trimmed by Cutadapt.
The trimmed reads with length shorter than 15 nt were excluded from analysis. The clean reads were mapped to the human transcriptome using STAR with default parameters. The annotation file downloaded from ENSEMBL database (GRCh38) was used to construct the transcriptome index file. For each gene, the transcript with longest CDS was selected. In the case of equal CDS length, the longest transcript was used. To avoid ambiguity, the reads mapped to multiple positions were disregarded for further analyses.
The reads mapped to transcript were counted. mRNAs with total reads in all conditions < 10 were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files are tab separatedread count. The first column is gene name, and the second column is read count on mRNAs.

molecule: polyA RNA

growth_protocol: BT-20 SAMD9-R1293W cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
Total cellular RNA was extracted with RNeasy plus mini kit (Qiagen). 5 μg of the total RNA was used for isolation of mRNA with the Poly(A) mRNA magnetic isolation module (NEB).
The mRNA was heat fragmented with RNA Fragmentation Reagents (Thermo Fisher Scientific). cDNA library was constructed with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: BT20 cells transduced with SAMD9-R1293W were uninduced or induced with 2 μg/ml of doxycycline for 24 hours.

tag: genotype/variation

value: transduced with SAMD9-R1293W

value: no treatment


title: BCE2_STD

value: [delta]sigB, [delta]sigC, [delta]sigE


title: BT-20-SAMD9-R1293W-with-inducer-S2

description: BT-20-SAMD9-R1293W cells treated with dox

value: +dox


title: BT-20-SAMD9-R1293W-with-inducer-S4


title: YTN16_anti-PD-L1_day_21_4

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.7.0f).
Mapped reads were counted by FeatureCounts (version 1.6.4 ).
Genome_build: mm10

source_name: tumor tissue

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and RNeasy spin columns (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep kit according to the manufacturer's protocols.

value: anti-PD-L1 antibody

value: day 21


title: BCE2_hot


title: YTN16_anti-PD-L1_day_21_5


title: BCE2_HL


title: YTN16_anti-PD-L1_day_21_3


title: AT mouse, biological rep4

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description:
Gene expression data from mice with  aP2-Cre;Tsc1Fl/Fl
MEH164

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Affymetrix Titan scanner

data_processing: Signal data was summarized by the RMA method, Z-score batch corrected and compared statistically by unequal variance t-tests for each probeset (Partek Genomics Suite 6.6).  Then a Benjamini-Hochberg multiple test correction was applied to control the false discovery rate (FDR)and statistical analysis performed with R v.3.6.1 with DESeq2 v.1.26.0 controlling the FDR at 5%. Mouse and human gene orthologs were identified using the BiomaRt Bioconductor package..

source_name: AT mouse angiosarcoma mouse tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All mice were maintained on a mixed genetic background; thus, littermate controls were used for each study. All experiments involving animal studies were reviewed and approved by the Institutional Animal Care and Use Committee at St. Jude Children’s Research Hospital.

extract_protocol: Total RNA was isolated from tumors of aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl (AKCcKO, n=4) or aP2-Cre;Tsc1Fl/Fl (ATcKO, n=4) using a bead mill TissueLyser LT (Qiagen) and the miRNEasy mini kit (Qiagen, 217004) according to manufacturer’s instructions.

treatment_protocol: Spontaneous tumors from AKC and AT mice were harvested

tag: tissue

value: KHE - angiosarcoma

tag: mouse number


title: AKC mouse, biological rep3

description:
Gene expression data from mice with  aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl
MEH159

source_name: AKC mouse angiosarcoma tumors

value: Angiosarcoma


title: AT mouse, biological rep3

description:
Gene expression data from mice with  aP2-Cre;Tsc1Fl/Fl
MEH163


title: BT-20-SAMD9-R1293W-no-inducer-S1


title: AKC mouse, biological rep4

description:
Gene expression data from mice with  aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl
MEH160


title: AT mouse, biological rep2

description:
Gene expression data from mice with  aP2-Cre;Tsc1Fl/Fl
MEH162


title: BCE1_STD

tag: strain

value: glucose tolerant


title: D09-anti-CTLA-4-Bhlhe40-WT

tag: age

value: wild type

value: anti-CTLA-4 antibody

value: 9 days post-transplant


title: BMSCs 2

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

country: China

institute: Sun Yat-sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

source_name: control BMSCs 2 (sample2)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

value: control BMSCs


title: YTN16_anti-PD-L1_day_21_1


title: BMSCs 1

source_name: control BMSCs 1 (sample1)


title: JHOC5-Day0_GeCKOv2

description: sgRNA fragment library

value: GeCKO v2 A library

value: ovarian cancer


title: AT mouse, biological rep1

description:
Gene expression data from mice with  aP2-Cre;Tsc1Fl/Fl
MEH161


title: CLEAR-CLIP_LN229_AGO2_rep1

city: Boston

first: Yanhong

last: Zhang

address: 60 Fenwood Road, Room 9006

institute: Brigham And Women's Hospital

data_processing:
For identification of miRNA-RNA chimeras, 3' and 5' adapter sequences have been removed from reads using Trimmomatic software version 0.4.0 (Bolger et al., 2014).
The trimmed sequences were collapsed with exact duplicates removal, and mapped to the hg19 reference transcriptome with BWA-MEM aligner BWA-0.7.17 (Li, 2013).
The following mapping parameters were used: seed length for 1st mapping iteration (MI) - 12; seed length for 2nd MI - 16; minimal alignment score for the 1st MI - 18; minimal alignment score for the 2nd MI - 16; matching score (MS) for 1st MI is 1; mismatch penalty (MP) for 1st MI is 4; MS for 2nd MI is 1; MP for 2nd MI is 6; gap opening penalty (GOP) for 1st MI is 6; gap extension penalty (GEP) for 1st MI is 1; GOP for 2nd MI is 100; GEP for 2nd MI is 100; maximum number of allowed multi-hits per read in 1st MI is 50; maximum number of allowed multi-hits per read in 2nd MI is 100.
Chimeric reads were extracted, and miRNA/ RNA segments were identified with ChiRA workflow version 1.3.3 (Videm et al., 2021).
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel Worksheet

source_name: Glioblastoma Cells (LN229)

growth_protocol: LN229 (human glioblastoma) cells were cultured in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) (WISENT), 1% penicillin and streptomycin (Gibco) and passaged by trypsinization (Corning®).

extract_protocol:
The cells were lysed, treated with DNase (Promega), followed by the partial RNA fragmentation using low concentrations of the RNase I (0.002 U/ml, 5 min), and treatment with the RNase inhibitor (RNAsin Plus at 0.5 U/μl) to quench RNase activity. The miRNA–RNA complexes were immunopurified using the anti-Ago-2 antibody (Millipore, #03-110) immobilized on immunoglobulin G-coated magnetic beads (Life Technologies).  The beads were washed, treated with T4 Polynucleotide Kinase (PNK, with no 3’- phosphatase activity)  (NEB, M0236S), and miRNA-RNA chimeras were produced with T4 RNA Ligase I (NEB, M0204S). The beads were further washed and subjected to alkaline phosphatase treatment (Roche, #10713023001) to remove 3’ phosphate. The 3’ linker (5′-rAppGTGTCAGTCACTTCCAGCGG-3’, Dharmacon) was added using T4 RNA Ligase 2 (NEB, M0242S), followed by the PNK (NEB, M0201S) treatment. The samples were resolved on 8% acrylamide gel (ThermoFisher Scientific), transferred to nitrocellulose membrane, followed by the purification of RNA-Ago complex, RNA isolation.
The libraries have been prepared from the low amount of RNA input using Superscript Reserve transcriptase (ThermoFisher) with first PCR amplification performed with DP3 (5’-CCGCTGGAAGTGACTGACAC-3’) and DP5 (5’-AGGGAGGACGATGCGG-3’) primers, and additional amplification with DSFP3 (5’-CAAGCAGAAGACGGCATACGACCGCTGGAAGTGACTGACAC-3’, DSFP5 (5’-AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG-3’) at maximum of 16 PCR cycles. The miR-10b chimeras have been pre-amplified with a miR-10b primer TACCCTGTAGAACCGAATTTGTG and either DP3 or DP5 primers. The products were separated from primers and primer dimers using electrophoresis on a 1% agarose gel, recovered using a QIAquick gel extraction kit (Qiagen).
CLEAR-CLIP: Covalent Ligation of Endogenous Argonaute bound RNA -Crosslinking and immunoprecipitation

treatment_protocol: LN229 cells were irradiated with UV-C light (2 times by 2400 J/m2) to covalently cross-link proteins to nucleic acids.

value: Glioblastoma Cells (LN229)

tag: antibody

value: Ago2 (Millipore, #03-110)

tag: ligation

value: Chimera ligation with T4 RNA Ligase I (NEB, M0204S)


title: AKC mouse, biological rep2

description:
Gene expression data from mice with  aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl
MEH158


title: CLEAR-CLIP_LN229_AGO2_rep2


title: LM-MSCs 2

source_name: hiPSC-derived LM-MSCs 2 (sample2)

tag: cell type

value: hiPSC-derived LM-MSCs


title: Huh7 cells-RSL3@O2-ICG NBS+LFS

city: Harbin

first: Bolin

last: Wu

state: Heilongjiang Province

address: No.150, Haping Road, Nangang District

institute: Harbin Medical University Cancer Hospital

description: D

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data(clean reads) were obtained by removing reads  containing adapter, reads on containing ploy-N and low quality reads from raw data.  At the same time, Q20, Q30 and GC content of the clean data were calculated. All the  down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using bowtie2 v2.2.8 and  paired-end clean reads were aligned to the reference genome using HISAT2(Langmead,  B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set  as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela  Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow  algorithm as well as an optional de novo assembly step to assemble and quantitate full-  length transcripts representing multiple splice variants for each gene locus.
CNCI (Coding-Non-Coding-Index) (v2) profiles adjoining nucleotide triplets to  effectively distinguish protein-coding and non-coding sequences independent of  known annotations (Sun et al. 2013). We use CNCI with default parameters.
CPC (Coding Potential Calculator) (0.9-r2) mainly through assess the extent and  quality of the ORF in a transcript and search the sequences with known protein  sequence database to clarify the coding and non-coding transcripts (Kong et al.  2007). We used the NCBI eukaryotes' protein database and set the e-value ‘1e-10’  in our analysis.
Phast (v1.3) is a software package contains much of statistical programs, most used in  phylogenetic analysis (Siepel, et al. 2005), and phastCons is a conservation scoring and  identificating program of conserved elements. We used phyloFit to compute  phylogenetic models for conserved and non-conserved regions among species and then  gave the model and HMM transition parameters to phyloP to compute a set of  conservation scores of lncRNA and coding genes.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in  each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the  FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of  exon per million fragments mapped, calculated based on the length of the fragments  and reads count mapped to this fragment.
The Ballgown suite includes functions for interactive exploration of the transcriptome  assembly, visualization of transcript structures and feature-specific abundances for  each locus, and post-hoc annotation of assembled features to annotated features(Alyssa  C. Frazee et al.2014). Transcripts with an P-adjust <0.05 were assigned as differentially  expressed.  Cuffdiff provides statistical routines for determining differential expression in digital  transcript or gene expression data using a model based on the negative binomial  distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned  as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA  target genes were implemented by the GOseq R package, in which gene length bias  was corrected(Young, M. D.et al.2010). GO terms with corrected Pvalue less than 0.05  were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the  biological system(Kanehisa, M.et al.2008), such as the cell, the organism and the  ecosystem, from molecular-level information, especially large-scale molecular datasets  generated by genome sequencing and other high-throughput experimental technologies  (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical  enrichment of differential expression genes or lncRNA target genes in KEGG  pathways(Mao, X.et al.1995).
PPI analysis of differentially expressed genes was based on the STRING database,  which known and predicted Protein-Protein Interactions. For the species existing in the  database, we construct the networks by extract the target gene list from the database;  Otherwise, Blastx (v2.2.28) was used to align the target gene sequences to the selected  reference protein sequences, and then the networks was built according to the known  interaction of selected reference species.
Alternative splicing events were classified to 12 basic types by the software Asprofile  v1.0. The number of AS events in each sample was estimated, separately.
Picard-tools v1.96 and samtools v0.1.18 were used to sort, mark duplicated reads and  reorder the bam alignment results of each sample. GATK2 software was used to  perform SNP calling(McKenna, A.et al.2010).
Genome_build: homo_sapiens_Ensembl_94

growth_protocol: Human hepatocellular carcinoma cell line HepG2 and human hepatocellular carcinoma cell line HuH7 were cultured in a moist atmosphere containing 5% CO2 at 37℃. It was cultured in DMEM medium containing 10% FBS and 1% antibiotic (penicillin-streptomycin, 10 000 U mL-1)

extract_protocol:
The treated cells were collected and RNA was extracted using Trizol reagent. The Illumina Truseq RNA Sample Prep Kit (CAT# FC-122-1001) and 1ug total RNA were used to construct the sequencing library.
The Illumina standard sequencing scheme was used to prepare RNA libraries for sequencing

treatment_protocol: Huh7 and HepG2 cells were treated with RSL3@O2-ICG NBS combined with low-frequency ultrasound for 24 h

tag: disease state

value: Hepatocellular carcinoma


title: YTN16_anti-PD-L1_day_14_5

value: day 14


title: D3_HL

value: [delta]sigD

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: D1_hot

value: 1 h at 40C


title: AKC mouse, biological rep1

description:
Gene expression data from mice with  aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl
MEH157

value: Angiosarcoma


title: LM-MSCs 1

source_name: hiPSC-derived LM-MSCs 1 (sample1)


title: YTN16_anti-PD-L1_day_14_4

value: anti-PD-L1 antibody


title: Huh7 cells

description: C

tag: cell line


title: D3_hot

value: glucose tolerant


title: HepG2 cells-RSL3@O2-ICG NBS+LFS

description: B

value: RSL3@O2-ICG NBS combined with low-frequency ultrasound for 24 h


title: D1_HL


title: LM 2

source_name: hiPSC-derived LM cells 2 (sample2)

value: hiPSC-derived LM cells


title: J_B: Jurkat_replicate_2_cDNA

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

data_processing:
Library strategy: MPRA
Barcodes were extracted from sequence files and matched to oligos using the attached barcode_oligo_tab.gz file. The barcode is the first column and the oligos attached to it are in the last column. Any barcodes matched to duplicate oligos were excluded. Oligo sequences that match the oligo ids can be found in the attached oligo_name_seq_tab.txt (column 1 is the oligo sequence, column 2 is the oligo id).
Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and a reported unnormalized in the included count file.
Supplementary_files_format_and_content: Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and a reported unnormalized in the included count file.

source_name: GFP mRNA

growth_protocol: K562 cells were grown with RPMI 1640 Complete Medium is supplemented with 2mM L-Glutamine + 10% FBS + 1% Penicillin-Streptomycin to a density of ~6*10^5 cells/ML

extract_protocol:
Twenty-four hours after transfection, cells were collected and snap frozen in liquid N2. Total RNA was extracted and GFP mRNA was isolatedand converted to cDNA Tewhey and colleagues 2016.
Following Tewhey et al. 2016, cDNA libraries were quanitified using qPCR including the plasmid pool used to transfect the cells. They were then diluted to be of equal concentration with the lowest library per cell type (15 cycles for K562 cells and 21.5 for Jurkat cells) and amplified using one fewer cycle than the lowest cycle threshold. An addition PCR was performed to add P7 indexing primers.
Libraries were than molar pooled and sequenced  with 1x50bp chemistry on a Illumina HiSeq 2500

treatment_protocol: For K562 cells 60 million cells per replicate were transfected with 60ug the MPRA library using electroporation with the Neon transfection system following the manufacturers protocol. For Jurkat cells, for each of 2 replicates 60 million cells per replicate were transfected 120ug of the MPRA library the Lonza Nucleofection system.

value: Jurkat cells


title: D2_hot


title: LM 1

source_name: hiPSC-derived LM cells 1 (sample1)


title: D3_STD

value: untreated


title: YTN16_anti-PD-L1_day_21_2

value: day 21


title: D2_STD


title: J_7: Jurkat_replicate_1_cDNA


title: K_4: K562_replicate_4_cDNA

value: K562 cells


title: YTN16_anti-PD-L1_day_14_1


title: YTN16_anti-PD-L1_day_7_5

value: day 7


title: K_3: K562_replicate_3_cDNA


title: YTN16_anti-PD-L1_day_7_4


title: K_2: K562_replicate_2_cDNA


title: B3_hot

value: [delta]sigB


title: B2_hot


title: MDMs 6 h infected Donor 3

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

data_processing:
Sequenced reads were performed quality assessment using FastQC. Reads with phred score >30 were accepted
Adapters were removed using trimomatic in the default options
Single-end reads for mRNA were mapped to the GRCh38.p13 genome using STAR with default options
Counts for RefSeq genes were obtained using Featurecounts with the default settings
DESeq2 was used to normalize expression counts.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: monocyte-derived macrophages (MDMs)

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) from blood samples of 4 healthy donors mixed with 2% EDTA, were isolated through density gradient with Lymphoprep. Monocytes were obtained from total PBMCs by adherence to the plastic and differentiation to macrophages was allowed to occur for 6 days in RPMI-1640 medium supplemented with 10% (v/v) FBS, 4 mM L-glutamine, 0.3% (v/v) NaCO3, and 1% (v/v) antibiotic-antimycotic solution 100X (complete medium), at 37 °C and 5% CO2, without growth factors

extract_protocol:
Total RNA from uninfected or CHIKV-infected MDMs was obtained using Direct-zol ™ RNA Miniprep Plus (Zymo Research, Irvine, California) following the manufacturer’s protocol. RNA samples were treated with DNase I column (Zymo Research, Irvine, California) to remove contaminating genomic DNA. RNA was quantifed, and the quality of each RNA sample was checked by spectrophotometry (Thermo Scientifc, Wilmington, DE, USA). Additionally, RNA quality was determined by analysis of ribosomal RNAs, using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Libary construction was made using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA)
RNA-seq poly A selected

treatment_protocol: CHIKV infection of human MDMs was performed at MOI 5 in serum-free RPMI-1640 medium. Samples were incubated at 37°C for 1.5 h. An hour and a half after infection, the cells were washed with PBS 1X to remove the unbound virus and fresh complete medium was added and incubated at 37°C with 5% CO2.

value: monocyte-derived macrophages (MDMs)

tag: infection

value: Chikungunya virus (CHIKV)

tag: time

value: 6 hours post infection

tag: individual

value: Donor 3


title: MDMs uninfected Donor 4

value: Uninfected

value: 0 hours post infection

value: Donor 4


title: MDMs 24 h infected Donor 3

value: 24 hours post infection


title: MDMs 6 h infected Donor 4


title: YTN16_anti-PD-L1_day_14_3

value: anti-PD-L1 antibody

value: day 14


title: D2_HL

source_name: cell

value: glucose tolerant

value: [delta]sigD

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: YTN16_anti-PD-L1_day_14_2


title: HepG2 cells

description: A

value: Hepatocellular carcinoma


title: YTN16_anti-PD-L1_day_7_2


title: MDMs uninfected Donor 3


title: YTN16_anti-PD-L1_day_7_1


title: B1_hot

value: 1 h at 40C


title: K_1: K562_replicate_1_cDNA

value: K562 cells


title: MDMs 24 h infected Donor 2

value: Donor 2


title: 8A_S2_L001

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
AFFECTED TWIN IN PAIR 14
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: skin

growth_protocol: dermal fibroblasts were maintained in complete media

extract_protocol:
100–200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. High-throughput sequencing (HTS) was performed using an Illumina HiSeq2500 with each sample sequenced to a minimum depth of ∼ 50 million reads.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: no treatment administered

tag: disease

value: SSc AFFECTED

tag: zygosity

value: MZ

tag: diffuse/limited

value: limited

tag: twins

value: fourteen


title: YTN16_anti-CTLA-4_day_21_5

tag: treatment

value: anti-CTLA-4 antibody

tag: time point

value: day 21


title: MDMs 24 h infected Donor 4

value: monocyte-derived macrophages (MDMs)

value: Chikungunya virus (CHIKV)

value: Donor 4


title: D1_STD

tag: genotype

value: untreated


title: MDMs 6 h infected Donor 2

value: 6 hours post infection


title: YTN16_anti-CTLA-4_day_21_4

tag: strain


title: 7_S1_L001

description:
HEALTHY TWIN IN PAIR 14
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: HEALTHY CONTROL


title: MDMs uninfected Donor 2

value: Uninfected

value: 0 hours post infection


title: YTN16_anti-PD-L1_day_7_3

value: anti-PD-L1 antibody

value: day 7


title: B2_HL

value: glucose tolerant

value: [delta]sigB

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: B1_HL


title: 70_S31_L008

description:
HEALTHY TWIN IN PAIR 2
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: MZ

value: two


title: YTN16_anti-CTLA-4_day_21_3

value: anti-CTLA-4 antibody


title: B3_STD


title: B2_STD


title: MDMs 6 h infected Donor 1

value: Donor 1


title: B3_HL


title: MDMs uninfected Donor 1

value: monocyte-derived macrophages (MDMs)


title: 64_S29_L008

description:
HEALTHY TWIN IN PAIR 4
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: DZ

value: four


title: 6_S7_L002

description:
HEALTHY TWIN IN PAIR 7
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: seven


title: B1_STD

value: untreated


title: 69A_S32_L008

description:
AFFECTED TWIN IN PAIR 2
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt

value: SSc AFFECTED

value: diffuse


title: YTN16_anti-CTLA-4_day_21_1

value: day 21


title: 63A_S30_L008

description:
AFFECTED TWIN IN PAIR 4
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt


title: YTN16_anti-CTLA-4_day_14_4

value: day 14


title: WT3_hot

value: wild type

value: 1 h at 40C


title: YTN16_anti-CTLA-4_day_14_5


title: WT2_hot

value: glucose tolerant


title: 62A_S22_L006

description:
AFFECTED TWIN IN PAIR 1
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt

value: one


title: Input H9 (primed) 7d+EZH2i rep3

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline: minute processing pipeline (https://github.com/NBISweden/minute)
Pipeline manager: Snakemake v5.30.1
Reads were demultiplexed using cutadapt v3.2 (Martin 2011) allowing only one mismatch per barcode. Deduplication was performed on aligned BAM files, marking duplicates using je-suite (v2.0.RC) using UMI and location of first mate. Resulting marked files were parsed and duplicate pairs were removed.
bowtie2 (v2.3.5.1) with --fast parameter
ChIP coverage tracks were generated from BAM files using deepTools (v3.5.0) bamCoverage. Quantitative scaling of the ChIP-Seq tracks amongst conditions within each pool was based on their Input-Normalized Mapped Read Count (INRC). INRC was calculated by dividing the number of unique hg38-mapped reads by the respective number of Input reads:  #mapped[ChIP] / #mapped[Input] . This essentially corrected for an uneven representation of barcodes in the Input and we could demonstrate that the INRC is proportional to the amount of epitope present in each condition.   Naïve-untreated condition pooled was chosen as the reference sample, which was scaled to 1x coverage (also termed Reads per Genome Coverage, RPGC). All other conditions were scaled relative to the reference using the ratio of INRCs multiplied by the scaling factor determined for 1x normalization of the reference: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ) * scaling factor.
Genome_build: hg38 (Homo_sapiens_UCSC_hg38.tar.gz - Illumina iGenomes: http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg38/Homo_sapiens_UCSC_hg38.tar.gz )
Supplementary_files_format_and_content: bigWig files minute-scaled to Naïve-untreated condition. Naïve-untreated condition is scaled to a  reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using hg38 genome size 3095978588

source_name: Embryonic Stem Cell

growth_protocol: Primed H9 (Wicell; WA09) p28(11) were cultured in Nutristem hESC XF medium and passaged when they reached 70-80% confluency. Naive H9 p28(8) naive p7 were grown on high-density MEF plates using NaïveCult expansion media supplemented with 10µM ROCKi. Cells were passaged every four to five days. Both hESCs were cultured at 37°C, 5% O2 and 5% CO2.

extract_protocol:
During harvesting, mouse feeder removal microbeads (Milteny Biotech; 130-095-531) were used to reduce the amount of MEFs in the naive cell samples, according to the manufacturer's protocol. Primed cells were dissociated and centrifuged directly.Three replicates of 1e6 cells per condition were collected and pellets were flash frozen.
ChIP-seq libraries were prepared using the MINUTE-ChIP protocol as described in Kumar & Elsässer 2019; PMID: 3153304 and sequenced on the Illumina NextSeq 500 (Paired End) platform. Antibodies used : H2AUb Cell signalling 8240S; lot #6 , H3K27me3 Millipore 07-449; lot #3091919 , H3K4me3 Millipore 04-745; lot #3198414.

treatment_protocol: In addition to wildtype conditions, naïve and primed H9 cells where treated with 10 uM EZH2 inhibitor (EPZ-6438; BIOV2428-5) for 7 days, with daily media changes.

tag: background

value: H9 (female)

tag: condition

value: primed

tag: minute-pool

tag: supplementary file scaling

value: RPGC 1x genome coverage


title: Input H9 (primed) 7d+EZH2i rep2

tag: antibody


title: YTN16_anti-CTLA-4_day_14_3

value: anti-CTLA-4 antibody


title: WT1_hot


title: 61_S21_L006

description:
HEALTHY TWIN IN PAIR 1
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: HEALTHY CONTROL

value: MZ


title: Input H9 (primed) 7d+EZH2i rep1


title: YTN16_anti-CTLA-4_day_14_2


title: WT3_HL

value: 1 h at PPFD of 750 μmol photons m-2 s-1


title: 60_S13_L004

description:
HEALTHY TWIN IN PAIR 12
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: twelve


title: YTN16_anti-CTLA-4_day_14_1


title: Input H9 (primed) rep3


title: MDMs 24 h infected Donor 1

tag: cell type

value: monocyte-derived macrophages (MDMs)

value: Chikungunya virus (CHIKV)

value: 24 hours post infection

value: Donor 1


title: Input H9 (primed) rep2


title: WT2_HL


title: YTN16_anti-CTLA-4_day_21_2

value: day 21


title: 59A_S14_L004

description:
AFFECTED TWIN IN PAIR 12
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

value: SSc AFFECTED

value: limited


title: YTN16_anti-CTLA-4_day_7_5

value: day 7


title: Input H9 (primed) rep1


title: WT1_HL

value: glucose tolerant

value: wild type


title: 54_S19_L005

description:
HEALTHY TWIN IN PAIR 15
Disease_vs_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: fifteen


title: 53_S25_L007

description:
HEALTHY TWIN IN PAIR 3
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: three


title: Input H9 (naïve) 7d+EZH2i rep2

value: H9 (female)

value: naive (t2iGoY)

value: RPGC 1x genome coverage


title: WT3_std

value: untreated


title: YTN16_anti-CTLA-4_day_7_2

value: anti-CTLA-4 antibody


title: WT2_std


title: Input H9 (naïve) 7d+EZH2i rep3


title: 4A_S28_L007

description:
AFFECTED TWIN IN PAIR 5
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt

value: MZ

value: diffuse

value: five


title: YTN16_anti-CTLA-4_day_7_3


title: Input H9 (naïve) 7d+EZH2i rep1


title: Input H9 (naïve) rep3


title: WT1_std


title: YTN16_anti-CTLA-4_day_7_1


title: Input H9 (naïve) rep2


title: Colonic LP macrophagessample 14

first: Izabel

last: Patik

address: 300 Longwood Ave

department: Division of Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

data_processing:
fastq files were generated using Illumina bcl2fastq v2.20 software.
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and raw gene counts were quantified using STAR (v2.5.1b)[1].
Genes names were harmonized using bioMART R API.
Gene counts were normalized and tested for differential expression using edgeR (v3.34.0)[2,3].
Visualizations were created by R packages, ggplot2 (v3.3.5) and EnhancedVolcano (v1.10.0)
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized counts

source_name: sorted Ly6C- colonic lamina propria macrophages

growth_protocol: Mice were kept under SPF conditions to induce sponteneious colitis development.

extract_protocol:
Animals were euthanized in a CO2 chamber, Colonic lamina propria cells were isolated. Briefly, colons were dissected and epithelial cells were stripped by agitation in 10mM EDTA for 30 min at 37°C. Remaining tissue was transferred to 50 ml conical tubes and digested using Collagenase VIII (Sigma-Aldrich, C2139-5G) in HBSS (with Ca /Mg) for 30-45 min at 37°C.  Cells were then filtered through 70µm cell strainers and washed twice in 1xPBS.  Cells viability and numbers were determined using automated cell counter (TECAN) and stained with the antibodies cocktails as indicated and analyzed using a LSRFortessa (BioLegend, San Diego, CA, USA ). Live CD45+, Ly6G-, CD103-, CD64+, CD11b+, MHCII+, Ly6C- scells were directly sorted into RLT buffer (Qiagen) and RNA prepared.
cDNA was sythesized using Takara SmartSeq v4 reagents from 1 ng of RNA. Full length cDNA was fragmented to a mean size of 200bp with Covaris M220 ultrasonicator and Illumina sequencing were prepared from 2ng of sheared cDNA using Swift 2S Acel reagents on a Beckman Coulter Biomek i7 according to manufacturer's protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200 and RT-qPCR using the Roche Kapa library qualification kit. Uniquely dual indexed libraries were pooled in equimolar ratios and evaluated for cluster efficiency and pool balance with shallow seqencing n an Illumina MiSeq. Final sequencing was performed on an Illumina NovaSeq6000 with paired-end 150bp reads at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: tissue

value: lamina propria from colon and cecum tissue


title: YTN16_anti-CTLA-4_day_7_4


title: 50A_S26_L007

description:
AFFECTED TWIN IN PAIR 3
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt


title: Colonic LP macrophages sample 13


title: 49A_S10_L003

description:
AFFECTED TWIN IN PAIR 6
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

value: six


title: DU145_Dox_pos_ve_3

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.9a).
The number of fragments in each known gene from GENCODE (version 33) was quantified using STAR QuantMode (GeneCounts) function.
Raw feature counts were normalized and differential expression analysis using DESeq2.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first columns represent Ensembl gene id, gene symbol and gene length. The other columns are raw counts for all the samples.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

tag: cell line

value: Prostate Cancer Cell Line


title: DU145_Dox_pos_ve_1


title: Input H9 (naïve) rep1


title: 44A_S20_L005

description:
AFFECTED TWIN IN PAIR 15
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_All_vs_Limited_All_Control.txt

value: SSc AFFECTED

value: limited


title: Colonic LP macrophages sample 12


title: Colonic LP macrophages sample 11


title: 37_S23_L006

description:
HEALTHY TWIN IN PAIR 11
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: HEALTHY CONTROL

value: DZ

value: eleven


title: DU145_Dox_neg_ve_3


title: DU145_Dox_neg_ve_2


title: 34A_S12_L003

description:
AFFECTED TWIN IN PAIR 9
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

value: nine


title: 36_S3_L001

description:
HEALTHY TWIN IN PAIR 16
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: sixteen


title: DU145_Dox_neg_ve_1


title: Colonic LP macrophages sample 10


title: Ptch1 positive subpopulation rep1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: PTC 1801

data_processing:
Quality control of reads using fastQC and Fastq-scren analysis
Genome mapping with STAR_2.4.0a versus hg38 following ENCODE RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20"
Transcripts counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCh38.76 release.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts.txt : tab-delimited text file with gene counting using featureCount

source_name: Adrenocortical carcinoma (ACC)

growth_protocol: Parental H295R cells and Ptch1 positive H295R were  cultured in DMEM/F12 supplemented with 2% NuSerum (BD), 1% ITS+ (BD) and penicillin/streptomycin (Invitrogen) at 37°C in a 5% CO2/95% air water-saturated atmosphere.

extract_protocol:
Total RNA was extracted using the RNA extraction kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.
Truseq Stranded Total RNA Libraries were generated from 500ng of total RNAs using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with Qubit and pooled. 4nM of this pool were loaded on a High Output Flowcell and sequenced on a NextSeq500 platform (Illumina) with 2x75bp paired-end chemistry.

value: adrenocortical carcinoma cells

tag: cell population

value: Ptch1 subpopulation


title: Ptch1 positive subpopulation rep2

description: PTC 3001


title: Ptch1 positive subpopulation rep3

description: PTC 3101


title: Parental H295R cells rep3

description: WT 3101

value: Parental ACC cells


title: RNAseq_GBM4_ASO_U6_inhibitor_rep3

description: ASO_U6_inhibitor vs Scr_for_U6.Alternative splicing_summary.txt

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing  adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
The data filtering included removing adaptors, removing reads containing N > 10% (N represents base that could not be determined), the Qscore (Quality value) of over 50% bases of the read is <= 5.
Alternative splicing analysis was performed by the software rMATS, a statistical method for robust and flexible detection of differential AS from replicate  RNA-Seq data. It identifies alternative splicing events corresponding to all major types of alternative splicing patterns and calculates the P value and FDR for  differential splicing. These types include exon skipping (SE), alternative 5′splice sites (A5SS), alternative 3′splice sites (A3SS), mutually exclusive exons (MXE), and  retained introns (RI).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Text Document

growth_protocol: GBM4 cells were cultured as neurospheres in Neurobasal medium (Gibco) supplemented with 0.5% N-2 (Gibco), 2% B-27 (Gibco), 1.5% glutamine (Gibco), 0.02 ng/ml epidermal growth factor (EGF) (Gibco), and 20 ng/ml fibroblast growth factor (FGF) (PeproTech) in ultralow attachment flasks or plates. GSC neurospheres were passaged using the NeuroCult chemical dissociation kit (Stemcell Technologies). All cells were maintained at 37 ºC and 5% CO2.

extract_protocol:
RNA was extracted using the Total RNA Purification Kit (Norgen Biotek, Catalogue # 17250) and quality of the samples examined using Nanodrop.
A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in first strand synthesis reaction buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Neurospheres were dissociated to single cell suspension (Stemcell Technologies) and transfected with the oligonucleotides using Neuromag 500 (OZ Biosciences) for 72 hours.

value: low-passage glioma-initiating stem-like cells (GBM4)

value: U6 inhibitor

tag: time

value: treated with oligonucleotides for 72 hours


title: Colonic LP macrophages sample 9


title: Colonic LP macrophages sample 8

value: Cdcs1, Il10ra -/-


title: DU145_Dox_pos_ve_2


title: 48_S9_L003

description:
HEALTHY TWIN IN PAIR 6
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

tag: disease

tag: zygosity

value: MZ


title: Colonic LP macrophages sample 7

value: lamina propria from colon and cecum tissue


title: 30A_S24_L006

description:
AFFECTED TWIN IN PAIR 11
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt

tag: diffuse/limited

value: diffuse

tag: twins


title: Colonic LP macrophages sample 6

value: Cdcs1, Ccr2 -/-


title: Parental H295R cells rep2

description: WT 3001


title: Parental H295R cells rep1

description: WT 1801


title: 24_S15_L004

description:
HEALTHY TWIN IN PAIR 8
Disease_vs_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: eight


title: RNAseq_GBM4_ASO_U6_inhibitor_rep2

tag: treatment


title: RNAseq_GBM4_Scr_for_U6_rep3

value: Scr


title: RNAseq_GBM4_ASO_U6_inhibitor_rep1


title: Colonic LP macrophages sample 5

tag: genotype


title: 22_S11_L003

description:
HEALTHY TWIN IN PAIR 9
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: HEALTHY CONTROL


title: Triple Negative Breast Cancer Cell line BT-549_DOX+_rep2

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing:
A customized analysis pipeline was applied to process the sequencing data of ATAC-seq libraries (https://github.com/macs3-project/genomics-analysis-pipelines).
The data from each replicate was aligned to the human genome (version GRCh38) with bwa-mem (https://arxiv.org/abs/1303.3997v2), evaluated by customized quality control scripts, and cleaned by Picard (https://broadinstitute.github.io/picard/) tools to mark and remove the duplicated reads.
Detection of the accessible regions for each replicate was performed using MACS2 (v2.2.7.1) with q-value cutoff 0.05 in Paired-end mode.
To combine all replicates, all peaks from replicates were first merged, then only the consensus genomic regions detected as accessible region in at least three replicates regardless the condition were kept, and the regions were split into non-overlapping 100bps bins. The UCSC toolkit bigWigAverageOverBed was used to extract the count of fragments in each bin for each replicate and to made a count-table for the differential analysis.
Genome_build: hg38

growth_protocol: DU-145 cells were grown in RPMI 1640 media  with 10% FBS and BT-549 cells were grown in RPMI 1640 media with 10% FBS supplemented with 10ug/ml insulin

extract_protocol:
Nuclei were extraxted from cells and subjected to tagmentation using Illumina Tagment DNA Enzyme and Buffer kit (20034210) and purified by Qiagen PCR purification kit
Libraries were prepared according to Buenrostro et al. 2015 protocol using reagents from Illumina

treatment_protocol: DOX- cells were treated with 0.1% DMSO) as vehicle control and  DOX+ cells were treated with Doxycycline

value: Treated

value: Triple Negative Breast Cancer

tag: disease state

value: TNBC


title: Triple Negative Breast Cancer Cell line BT-549_DOX+_rep3


title: RNAseq_GBM4_Scr_for_U6_rep2


title: Colonic LP macrophages sample 4

tag: strain


title: Triple Negative Breast Cancer Cell line BT-549_DOX+_rep1


title: 20A_S16_L004

description:
AFFECTED TWIN IN PAIR 8
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_All_vs_Limited_All_Control.txt

value: SSc AFFECTED

value: DZ

value: limited


title: RNAseq_GBM4_Scr_for_U6_rep1

value: low-passage glioma-initiating stem-like cells (GBM4)


title: Colonic LP macrophages sample 3


title: Triple Negative Breast Cancer Cell line BT-549_DOX-_rep3

value: Untreated


title: RNAseq_GBM4_ASO_miR10b_inhibitor_rep3

description: ASO_miR10b_inhibitor vs Scr_for_miR10b.Alternative splicing_summary.txt

value: miR-10b inhibitor

value: treated with oligonucleotides for 72 hours


title: 2A_S4_L001

description:
AFFECTED TWIN IN PAIR 16
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

value: sixteen


title: RNAseq_GBM4_ASO_miR10b_inhibitor_rep2


title: Colonic LP macrophages sample 2

value: Cdcs1, Il10ra -/-

value: lamina propria from colon and cecum tissue


title: 14_S5_L002

description:
HEALTHY TWIN IN PAIR 10
Disease_vs_Control.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: MZ

value: ten


title: Colonic LP macrophages sample 1


title: RNAseq_GBM4_ASO_miR10b_inhibitor_rep1


title: Triple Negative Breast Cancer Cell line BT-549_DOX-_rep1


title: Triple Negative Breast Cancer Cell line BT-549_DOX-_rep2


title: 12_S17_L005

description:
HEALTHY TWIN IN PAIR 13
Disease_vs_Control.txt
Limited_All_vs_Limited_All_Control.txt
Diffuse_vs_Limited_All.txt

value: thirteen


title: TestesWT521

city: College Park

first: Iqbal

last: Hamza

state: MD

address: 8127 Regents Drive, 1109 Animal Sciences

institute: University of Maryland

data_processing:
STAR, 2.7.0f
RSEM, 1.2.31
DESeq2, 1.12.3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was extracted from frozen tissues following standard Trizol chloroform protocol (Invitrogen, cat. number 15596026) and aqueous fractions were then taken directly into Qiagen RNA plus extraction kit (Qiagen, cat. number 74136) for maximum purity. Total RNA quality and quantity were tested on an Agilent Bioanalyzer 2100 System (Agilent cat. number G2939BA) using RNA Nano Chip On-Chip Electrophoresis trays for samples with RIN scores greater than 8 prior to processing for library prep/construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wildtype

value: testes


title: RNAseq_GBM4_Scr_for_miR10b_rep3

value: Scr


title: TestesWT520


title: 13_S27_L007

description:
HEALTHY TWIN IN PAIR 5
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt

value: HEALTHY CONTROL

value: five


title: RNAseq_GBM4_Scr_for_miR10b_rep2


title: 10A_S8_L002

description:
AFFECTED TWIN IN PAIR 7
Disease_vs_Control.txt
Diffuse_vs_Diffuse_Control.txt
Diffuse_vs_Limited_All.txt
DZ_Diffuse_vs_MZ_Diffuse.txt

value: SSc AFFECTED

value: DIFFUSE

value: seven


title: Prostate Cancer Cell line DU145_DOX+_rep2

value: Treated

value: Castration resistant Prostate Cancer

value: CRPC


title: Prostate Cancer Cell line DU145_DOX+_rep3


title: Prostate Cancer Cell line DU145_DOX+_rep1


title: RNAseq_GBM4_Scr_for_miR10b_rep1

value: low-passage glioma-initiating stem-like cells (GBM4)

value: treated with oligonucleotides for 72 hours


title: 21A_S18_L005

description:
AFFECTED TWIN IN PAIR 13
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_All_vs_Limited_All_Control.txt

value: DZ

value: limited


title: TestesWT519


title: TestesDKO514

source_name: MRP5-/- and MRP9-/-_testis

value: MRP5-/- and MRP9-/-


title: Prostate Cancer Cell line DU145_DOX-_rep3

value: Untreated


title: TestesDKO513


title: Prostate Cancer Cell line DU145_DOX-_rep2


title: 19A_S6_L002

description:
AFFECTED TWIN IN PAIR 10
Disease_vs_Control.txt
Diffuse_vs_Limited_All.txt
Limited_vs_Limited_Control.txt
Limited_All_vs_Limited_All_Control.txt

value: MZ

value: ten


title: TestesDKO512

value: testes


title: Prostate Cancer Cell line DU145_DOX-_rep1


title: RNAseq of NK-92 cell line, rep2

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Illumina Casava2.20 software used for basecalling.
Paired-end reads were mapped to hg19 whole genome using bowtie STAR
Read counts were generated using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

growth_protocol: The NK-92 cell line was cultured in Minimum Essential Medium Eagle - alpha modification (STEMCELL TECHNOLOGIES, #36463) supplemented with 12.5% heat-inactivated FBS, 12.5% heat-inactivated horse serum (Gibco, #16050122), and 100 U/mL penicillin-streptomycin in the presence of 100 U/ml recombinant human IL-2 (Protech, #200-2) at 37°C and 5% carbon dioxide.

extract_protocol:
RNA was extracted from isolated human engrafted cells by AllPrep DNA/RNA Mini kit (Qiagen, #80204) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using total-standard Illumina protocols

treatment_protocol: The NK-92 cells were infected on RetroNectin (Takara, #T100B)-coated plates preloaded with viral supernatants of empty vector, wild-type CCL22, and Pro79Arg-CCL22 cloned CL20-MSCV-IRES-GFP vector and cultured in the presence of cytokines for 48 hours.

value: NK

tag: age

value: wild type


title: RNAseq of NK-92 cell line, rep3


title: RNAseq of NK-92 cell line, rep1


title: MSCs derived exosome replicate 1

first: Tian

last: Zhou

state: Guangdong

address: NO.7 Jinsui Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center

data_processing:
illumina instrument for small RNA sequencing
Clean reads were trimmed by removing the sequences smaller than 15 nt or longer than 35 nt.
Reads were alligned to mm10 by Bowtie v0.12.2 and compared with databases including Silva,GtRNAdb,Rfam and Repbase databases. The following RNAs were filtered including ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase.
Differential expression analysis was performed using the DESeq2 R package (1.10.1)
Genome_build: mm10
Supplementary_files_format_and_content: All-counts.csv

source_name: Exosome of Primary bone marrow MSCs

growth_protocol: Primary murine bone marrow MSCs and L9292 cells were cultured in medium containing 10% exosome-free FBS for 48 hours before the supernatants were collected

extract_protocol:
Exosomes were derived by ultracentrifuge from the supernant of primary murine bone marrow MSCs and L929 cells
Library preparation and miRNA sequencing were performed by Biomarker Technologies Corporation (Beijing, China). Standard PAGE gel electrophoresis was used to examine RNA integrity. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and single-end reads and paired-end reads were generated.

value: MSCs


title: MSCs derived exosome replicate 2


title: DMSO_HUVEC_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (nt) (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads between 30 and 150 nt were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
For mLECs, Ensembl mouse genome version mm10 (GRCm38.p5) and STAR 2.6.0c was used.
The number of reads aligning to genes was counted with featureCounts tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes in HUVEC were identified using DESeq2 version 1.30.0 (for mLEC version 1.18.1 was used).
The Ensembl annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt))
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: library size normalized counts

source_name: human umbilical vein endothelial cells

growth_protocol: Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. Murine lung endothelial cells (mLEC) were isolated as described previously (DOI: 10.1242/jcs.02541). Briefly, the tissue was minced and digested with dispase at 37°C for 60 min. After washing and filtering, mLEC separation was done with CD144 coated Dynabeads. mLECs were cultured in DMEM/F12 supplemented with 20% FCS, penicillin (50 U/ml) and streptomycin (50 µg/ml) and ECGF Bovine + Heparin (PeloBiotech) at 37°C with 5% CO2.

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
). 1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Acriflavine (10µM) or DMSO for 16h.

value: HUVEC


title: MSCs derived exosome replicate 3


title: DMSO_HUVEC_3


title: DMSO_HUVEC_1


title: RNAseq of NK-92 cell line infected with empty vector, rep2

value: empty vector

value: infected with empty vector


title: kd_vivo_sgScr_RNAseq_3

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

description:
vivo_sgKdm5d_counts.csv
vivo_sgKdm5d_deseq_normalize.csv

data_processing:
Sequenced reads were mapped to GRCm38 reference using STAR
Counts were normalized by deseq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files with gene counts
Supplementary_files_format_and_content: csv files with gene deseq2 normalized

source_name: Bone Marrow

growth_protocol: The AML was developed on recipient mice after transplantation through tail vein injection.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mLOY(sgSsty1/sgSsty2) or control(sgScr) with AE in Trp53-/- ckit+ cells or BM harvested from AML mice. sgKdm5d or control(sgScr) in Trp53-/- cas9 ckit+ cells or BM harvested from AML mice.

tag: sample type

value: sgKdm5d/sgScramble;Trp53-/- Bone marrow in vivo

tag: replicates


title: RNAseq of NK-92 cell line infected with empty vector, rep1


title: Acriflavine_HUVEC_2


title: kd_vivo_sgScr_RNAseq_2


title: RNAseq of NK-92 cell line with P75R mutation, rep2

value: CCL22 P79R

value: infected with CCL22 P79R


title: Acriflavine_HUVEC_1


title: RNAseq of NK-92 cell line with P75R mutation, rep1


title: kd_vivo_sgKdm5d_RNAseq_3


title: DMSO_HUVEC_ATAC

data_processing:
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nt.
Only reads above 15 nt were cleared for further analyses. These were mapped versus the hg19 version of the human genome with STAR 2.5.2b using only unique alignments to exclude reads with uncertain arrangement.
Reads were further deduplicated using Picard 2.6.0 to avoid PCR artefacts leading to multiple copies of the same original fragment.
The MUSIC peakcaller (version from Dec. 2015) was employed in punctate mode to accommodate for the range of peak widths typically expected for ATAC-seq. The maximum qvalue was set to 0.2 and the p-value normalization window length was changed to 1500.
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded. Peaks were annotated with the promoter (TSS +- 5000 nt) of the gene most closely located to the centre of the peak based on reference data from GENCODE v19.
In order to be able to compare peaks in different samples, the resulting lists of significant peaks were overlapped and unified to represent identical regions. The counts per unified peak per sample were computed with BigWigAverageOverBed (UCSC Genome Browser Utilities, http://hgdownload.cse.ucsc.edu/downloads.html). Raw counts for unified peaks were submitted to DESeq2 (version 1.20.0) for normalization.
For converting the data to the updated genome version hg38, bwtool was used.
Genome_build: hg19
Supplementary_files_format_and_content: library and background normalized counts in unified peaks

extract_protocol:
50.000 HUVEC were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina). The cell pellet was resuspended in 50 µL PBS and mixed with 25 µL TD-Buffer, 2.5 µL Tn5, 0.5 µL 10% NP-40 and 22 µL H2O and incubated at 37°C for 30 min followed by 30 min at 50°C together with 500 mM EDTA pH8.0. 100 µL of 50 mM MgCl2 was added for neutralization. Purification of DNA fragments was done with the MinElute PCR Purification Kit (Qiagen).
50.000 HUVEC were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina). The cell pellet was resuspended in 50 µL PBS and mixed with 25 µL TD-Buffer, 2.5 µL Tn5, 0.5 µL 10% NP-40 and 22 µL H2O and incub
The cell pellet was resuspended in 50 µL PBS and mixed with 25 µL TD-Buffer, 2.5 µL Tn5, 0.5 µL 10% NP-40 and 22 µL H2O and incubated at 37°C for 30 min followed by 30 min at 50°C together with 500 mM EDTA pH8.0.
100 µL of 50 mM MgCl2 was added for neutralization. Purification of DNA fragments was done with the MinElute PCR Purification Kit (Qiagen).
Amplification of Library and Indexing was performed as descried elsewhere (Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015).


title: kd_vivo_sgKdm5d_RNAseq_2


title: Acriflavine_HUVEC_ATAC


title: HLE-B3 Atg7KO_12h_rep2

city: Hangzhou

first: Wei

last: Han

state: Zhejiang

address: 88 Jiefang Road

department: Eye Center

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in all samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in all samples

source_name: human lens epithelial cells,HLE-B3

growth_protocol: HLE-B3 cells were cultured in DMEM/F12 supplemented with 10% FBS. All cells were incubated at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were treated with or without 200 μM H2O2 for 12 hrs.

value: human lens epithelial cells

value: 200 μM H2O2 for 12 hrs


title: HLE-B3 Atg7KO_12h_rep3


title: kd_vitro_sgScr_RNAseq_3

description:
vitro_sgKdm5d_counts.csv
vitro_sgkdm5d_deseq_normalize.csv

source_name: ckit

value: Trp53-/- c-kit+ HSPCs in vitro

value: control(sgScr)


title: HLE-B3 Atg7KO_12h_rep1


title: Lung adenocarcinoma sample5

city: Shenyang

first: Le-Tian

last: Huang

state: Liaoning

address: NO.39 Huaxiang Road, Tiexi District

department: Department of Oncology

institute: Shengjing Hospital of China Medical University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality were examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5,3-adaptor bases by cutadapt) were aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that did not map were aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads were aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The abundance of tRF and tiRNA were evaluated using their sequencing counts and was normalized as counts per million of total aligned reads (CPM).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: The samples were frozen freshly in liquid nitrogen and stored in -80 degrees Celsius until the specimens were used.

extract_protocol:
Total RNA was first pretreated to remove some RNA modifications that interfere with small RNA-seq library construction by Agilent DNA 1000 chip kit (Agilent, part # 5067-1504).
Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-4042005, Illumina), according to the manufacturer’s instructions.

value: lung

tag: pathology

value: adenocarcinoma

tag: state of organism

value: Initial diagnosis with no treatment


title: Adjacent normal sample5

tag: tissue

value: normal


title: kd_vivo_sgKdm5d_RNAseq_1


title: Adjacent normal sample4