title: miRNA-293T

value: HEK-293T cells


title: miRNA-HCT116

status: Public on Mar 24 2021

type: SRA

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA. For small RNA-seq, homemade PERL software was used to  remove adaptor sequences, and Bowtie sofeware was used to align sequencing reads to miRNA database
For polyA(+) RNA-seq,mouse Cdna database(UCSC, NCBI37)  was used for alignment. For small RNA-seq, 20-25nt small RNAs was aligned to known mature miRNA sequences(miRBase)
Both polyA(+) and small RNA-seq, Reads per Million was calculated for the normalization
Genome_build: mm9
Supplementary_files_format_and_content: csv

molecule: total RNA

organism: Homo sapiens

source_name: WT

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina)。Small RNA-seq libraries preparation using NEBNext® Small RNA Library Prep Set for Illumina kit。

tag: genotype

value: WT

tag: cell line


title: FKBP5 KD_sample_1

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR v2.7.7a with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM
Counts per Million (CPM) values were calculated using edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from control scramble and FKBP5 KD cells using TRIzol and purified according to manufacter's instructions.
A modified NEBNext RNA Ultra II directional protocol was used to prepare the libraries for total RNA.

tag: genotype/variation

value: FKBP5 knockdown


title: FKBP5 KD_sample_2


title: 111617p1_H2_S86

city: Boston

first: Lauren

last: Mifflin

state: MA

address: 260 Longwood Ave

department: Department of Cell Biology

country: USA

institute: Harvard Medical School

description: Optn KO-1

data_processing:
scumi pipeline, The samples which are not showing up in the processed data were filtered out during QC.
Genome_build: mm10
Supplementary_files_format_and_content: nextseq_180111_rsem.genes.tpm.matrix

organism: Mus musculus

source_name: Spinal cord

extract_protocol:
Spinal cords were digested in Accutase; myelin was removed using a 0.25% BSA spin, cells were stained for CD45, CD11b, and CX3CR1 and single cells were isolated into plates using FACS Aria II
Samples were prepared according to the SmartSeq2 protocol

value: Optn KO


title: 111617p2_A8_S104

description: Optn KO-1


title: 111617p1_H1_S85

description: Optn KO-1


title: 111617p1_H11_S95

description: Optn KO-1


title: H1_EPS_in_XF-LCDM

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

data_processing:
The raw data were preprocessed with cellranger-3.1.0.
The output gene expression matrix was loaded using R package DropletUtils.
Low quality cells with low log total UMI counts(<median - 3*MAD), low log total genes(<median - 3*MAD) or high mitochondrial gene proportions(> median +2*MAD) were filtered.
Normalization was performed using R package Seurat.
Genome_build: hg19
Supplementary_files_format_and_content: cellranger output files; normalized expression matrix in tsv format; metadata in tsv format

source_name: xeno-free human EPS cells

growth_protocol: Xeno-free human EPS  cells were cultured in chemically defined LCDM medium under 20% O2 and 5% CO2 at 37°C. Feeder-cultured human EPS cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. H1 PSCs were clutured in mTeSR1 medium under  20% O2 and 5% CO2 at 37°C.

extract_protocol:
Cells were harvested and resuspended at 1*10^6 cells per milliliter in 13PBS with 0.04% BSA. Then, cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V2 (10x Genomics, 120237). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Invitrogen, 37002D)
Single-cell RNA-seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction. Sequencing was performed on an Illumina HiSeq X Ten with pair end 150bp (PE150).

tag: cell type

value: Human extended pluripotent stem (EPS) cells

tag: culture condition

value: Xeno-free


title: 111617p1_H10_S94

description: Optn KO-1


title: H1_EPS_in_F-LCDM

source_name: feeder-cultured human EPS cells

value: Feeder-cultured


title: 111617p1_G9_S81

description: Optn KO-1


title: 111617p1_G8_S80

description: Optn KO-1


title: miRNA-H1299


title: 111617p1_H4_S88

description: Optn KO-1


title: 111617p1_G7_S79

description: Optn KO-1


title: 111617p1_H5_S89

description: Optn KO-1


title: miRNA-K562


title: 111617p2_A6_S102

description: Optn KO-1


title: 111617p1_G6_S78

description: Optn KO-1


title: 111617p1_G5_S77

description: Optn KO-1


title: miRNA-U2OS


title: 111617p1_G2_S74

description: Optn KO-1


title: 111617p1_G3_S75

description: Optn KO-1


title: 111617p1_H12_S96

description: Optn KO-1


title: 111617p1_G1_S73

description: Optn KO-1


title: H1_in_mTESR1

source_name: primed PSCs

value: Human pluripotent stem cells (PSCs)


title: 111617p1_G11_S83

description: Optn KO-1


title: 111617p1_F9_S69

description: Optn KO-1


title: B. burgdorferi B31-A3△bbq67 rep3 Sample 9

city: Hamilton

first: Jenny

last: Wachter

state: MT

address: 4th St

department: NIAID

institute: RML

data_processing:
RNA-seq reads were compiled and filtered to remove any reads with PHRED scores less than 10 and aligned to the B. burgdorferi B31 genome (RefSeq AE000783-AE000794 and AE001575-AE001584) using bowtie2
Reads for annotated genes were determined using featureCounts
Genome_build: RefSeq AE000783-AE000794 and AE001575-AE001584
Supplementary_files_format_and_content: featureCounts

organism: Borreliella burgdorferi

source_name: bacterial culture

growth_protocol: B. burgdorferi strains were cultured in Barbour-Stoener-Kelly (BSK II) medium supplement with 6% rabbit serum and appropriate antibiotics (streptomycin, 50 μg/mL; kanamycin, 200 μg/mL) at 35⁰C under 2.5% CO2

extract_protocol:
RNA was isolated using TRIzol reagent per the manufacturer’s instructions and treated with 1 unit of DNAse I for 1 hr at 37 C
cDNA libraries were synthesized using Ribo-Zero and ScriptSeq complete bacteria kit with indexing primers for synthesis of directional libraries per the manufacturer’s instructions. The quality and quantity of the resulting cDNA libraries were assessed with an Agilent DNA 1000 assay on an Agilent 2100 Bioanalyzer and with a KAPA Library Quantification Kit prior to RNA-seq.

tag: strain

tag: status of plasmid-encoded restriction-modification genes

value: Lacking bbq67, contains two R/M genes (bbe02 and bbh09)

tag: missing plasmids

value: lacking cp9


title: B. burgdorferi B31-A3△bbe02△bbq67 rep2 Sample 11

value: Lacking bbe02 and bbq67, contains one R/M gene (bbh09)


title: B. burgdorferi B31-A3△bbe02△bbq67 rep3 Sample 12


title: B. burgdorferi B31-A3△bbq67 rep2 Sample 8


title: 111617p1_G4_S76

description: Optn KO-1


title: peripheral nuclear cells blood Healthy-goat 1

type: RNA

city: Warszawa

first: Joanna

last: Pławińska-Czarnak

address: Nowoursynowska 159

country: Poland

institute: WULS-SGGW

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Capra hircus

source_name: peripheral nuclear cells blood (PNCB)

extract_protocol: isolation of total RNA from goat PNCB (peripheral nuclear cells blood) was conducted by using Total RNA mini Kit (A & A Biotechnology, POLAND)

treatment_protocol: Blood from vein was mixed with erythrocyte lysis buffer RBCL and protected with fenozol from Total RNA mini Kit (A & A Biotechnology,POLAND)

tag: tissue

value: blood

tag: disease state

value: healthy

source_name: common reference sample compsed of total RNAs isolated from peripheral nuclear cells blood 7 healthy goats in 4th lactation from both Polish breeds (PWI=4 & PFI=3) after the lactation cycle

value: pool of healthy goats


title: peripheral nuclear cells blood SRLV - goat 2

label_protocol: according to the manufacturer's protocol

value: SRLV infected


title: peripheral nuclear cells blood Healthy-goat 4


title: peripheral nuclear cells blood SRLV - goat 4


title: peripheral nuclear cells blood SRLV - goat 3


title: B. burgdorferi B31-A3△bbq67 rep1 Sample 7


title: 111617p1_F7_S67

description: Optn KO-1


title: B. burgdorferi B31-A3△bbe02 rep3 Sample 6

value: Lacking bbe02, contains two R/M genes (bbq67 and bbh09)


title: peripheral nuclear cells blood SRLV - goat 1


title: peripheral nuclear cells blood Healthy-goat 3


title: 111617p1_G10_S82

description: Optn KO-1


title: peripheral nuclear cells blood Healthy-goat 2


title: 111617p1_F5_S65

description: Optn KO-1


title: 111617p1_G12_S84

description: Optn KO-1


title: B. burgdorferi B31-A3△bbe02△bbq67 rep1 Sample 10


title: B. burgdorferi B31-A3△bbe02 rep1 Sample 4


title: 111617p1_F3_S63

description: Optn KO-1


title: B. burgdorferi B31-A3 rep3 Sample 3

value: Contains all three R/M genes (bbe02, bbq67, and bbh09)


title: 111617p1_F4_S64

description: Optn KO-1


title: B. burgdorferi B31-A3 rep2 Sample 2


title: 111617p1_F8_S68

description: Optn KO-1


title: B. burgdorferi B31-A3△bbe02 rep2 Sample 5


title: 111617p1_F12_S72

description: Optn KO-1


title: B. burgdorferi B31-A3 rep1 Sample 1


title: B. burgdorferi B31-A34 Tn::H09 rep2 Sample 26

description: featurecounts

value: Lacking all three R/M genes (bbe02, bbq67, and bbh09)


title: 111617p1_F2_S62

description: Optn KO-1


title: B. burgdorferi B31-A34 Tn::H09 rep1 Sample 25

description: featurecounts


title: 111617p1_F11_S71

description: Optn KO-1


title: 111617p1_F6_S66

description: Optn KO-1


title: B. burgdorferi B31-A3 lp28-3- rep2 Sample 22

description: featurecounts

value: Lacking bbh09, contains two R/M genes (bbe02 and bbq67)

value: lacks cp9 and lp28-3


title: 111617p1_E8_S56

description: Optn KO-1

value: Optn KO


title: 111617p1_F10_S70

description: Optn KO-1


title: B. burgdorferi B31-A34 rep1 Sample 23

description: featurecounts


title: B. burgdorferi B31-A3 lp28-3- rep1 Sample 21

description: featurecounts


title: 111617p1_E7_S55

description: Optn KO-1


title: 111617p1_E9_S57

description: Optn KO-1


title: B. burgdorferi B31-A34 rep2 Sample 24

description: featurecounts


title: B. burgdorferi B31-A3-68△bbe02 rep2 Sample 20

description: featurecounts

value: lacks cp9 and lp56


title: B. burgdorferi B31-A3-68△bbe02 rep1 Sample 19

description: featurecounts


title: 111617p1_E5_S53

description: Optn KO-1


title: 111617p1_E6_S54

description: Optn KO-1


title: B. burgdorferi B31-A3-68 rep2 Sample 18

description: featurecounts


title: 111617p1_E4_S52

description: Optn KO-1


title: 111617p1_E3_S51

description: Optn KO-1


title: 111617p1_E2_S50

description: Optn KO-1


title: B. burgdorferi B31-A3△bbe02 rep1 Sample 15

description: featurecounts


title: B. burgdorferi B31-A3-68 rep1 Sample 17

description: featurecounts


title: 111617p1_F1_S61

description: Optn KO-1


title: 111617p1_E1_S49

description: Optn KO-1


title: B. burgdorferi B31-A3△bbe02 rep2 Sample 16

description: featurecounts


title: B. burgdorferi B31-A3 rep1 Sample 13

description: featurecounts


title: B. burgdorferi B31-A3 rep2 Sample 14

description: featurecounts


title: 111617p1_D9_S45

description: Optn KO-1


title: 111617p1_E10_S58

description: Optn KO-1


title: 111617p1_E12_S60

description: Optn KO-1


title: 111617p1_E11_S59

description: Optn KO-1


title: m9+ABA-2

city: Shanghai

first: Xiaolei

last: Liu

address: Chenhua Road 3888

institute: Chinese Academy of Sciences

data_processing:
the raw data is preprocessed by trimmomatic (version 0.36).
The clean reads were aligned to the TAIR 10 reference genome using hisat2 (version 2.1.0) with parameters "--rna-strandness RF -p 30 --dta”.
Reads_count matrix was produced by htseq-count (version 0.9.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis

extract_protocol:
flash frozen on liquid, and RNA was harvested using Trizol reagent. 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 standard Illumina protocols

tag: Stage

value: 12- -day-old

value: seedling

tag: cultivar

tag: treatment

value: ABA


title: m9+ABA-1


title: Col+ABA-3

value: WT


title: Col+ABA-2


title: 111617p1_D8_S44

description: Optn KO-1


title: m9-3


title: m9-2


title: 111617p1_D3_S39

description: Optn KO-1


title: Col+ABA-1


title: 111617p1_D5_S41

description: Optn KO-1


title: 111617p1_D4_S40

description: Optn KO-1


title: 111617p1_D6_S42

description: Optn KO-1


title: 111617p1_D7_S43

description: Optn KO-1


title: m9-1


title: Col-3


title: 111617p1_D1_S37

description: Optn KO-1


title: Col-1


title: 111617p1_D12_S48

description: Optn KO-1


title: 111617p1_D11_S47

description: Optn KO-1


title: Col-2


title: 111617p1_D10_S46

description: Optn KO-1


title: P.H.41

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were mapped to the mouse genome (mm10) using HISAT2
Reads were counted using featureCounts against ENCODE annotations, release 90.
Differential gene expression between samples of different conditions was determined using the DESeq2 package (v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

extract_protocol:
Whole hippocampal mRNA was extracted from flash frozen tissue using the RNeasy Lipid Tissue Mini Kit (Qiagen; Catalog # 74804). RNA concentration and quality were determined using a Bioanalyzer (Agilent).
Samples with a RIN > 9 (RNA Integrity Number) were used for sequencing (WT-N, n = 6; WT-CIH, n = 6; P301S-N, n = 5; P301S-CIH, n = 6). Sequencing libraries were prepared using the TrueSeq Stranded mRNA Kit (Illumina) by the GENEWIZ (South Plainfield, NJ, USA). Libraries were barcoded to allow for multiplexing in a single flow cell. 100 bp paired- end reads were collected on a HiSeq 2500 (Illumina) at a sequencing depth of ~40 million reads per sample.

tag: strain background

value: mixed; C57Bl6 + Balbc

tag: condition

value: Hypoxia

value: Brain


title: m9+ABA-3


title: P.H.40


title: 111617p1_C9_S33

description: Optn KO-1


title: P.H.29


title: 111617p1_C8_S32

description: Optn KO-1


title: 111617p1_C7_S31

description: Optn KO-1


title: P.H.24


title: P.H.14


title: 111617p1_C6_S30

description: Optn KO-1


title: 111617p1_C4_S28

description: Optn KO-1


title: P.N.64

value: Normoxia


title: 111617p1_C2_S26

description: Optn KO-1


title: 111617p1_C5_S29

description: Optn KO-1


title: 111617p1_C1_S25

description: Optn KO-1


title: P.N.62


title: 111617p1_C12_S36

description: Optn KO-1


title: 111617p1_C11_S35

description: Optn KO-1


title: 111617p1_B9_S21

description: Optn KO-1


title: WT.H.32.L1


title: WT.H.31.L2


title: WT.H.32.N


title: 111617p1_C10_S34

description: Optn KO-1


title: WT.H.31.L1


title: P.N.43


title: 111617p1_B8_S20

description: Optn KO-1


title: WT.H.31.R1


title: 111617p1_B6_S18

description: Optn KO-1


title: WT.H.31.N


title: 111617p1_B5_S17

description: Optn KO-1


title: WT.N.66.L2


title: P.N.65


title: WT.N.66.L1


title: P.N.61


title: 111617p1_C3_S27

description: Optn KO-1


title: WT.N.66.R2


title: 111617p1_B2_S14

description: Optn KO-1


title: WT.N.66.R1


title: 111617p1_B1_S13

description: Optn KO-1


title: WT.N.66.N


title: 111617p1_B11_S23

description: Optn KO-1


title: miRNA-Neural-D5

source_name: mESC cultured in Nerual differentiation medium for 5 day

value: neural progenitor cells


title: 111617p1_B12_S24

description: Optn KO-1


title: 111617p1_B7_S19

description: Optn KO-1


title: miRNA-Neural-D0

source_name: mESC cultured in serum/lif medium

value: mESC


title: 111617p1_A9_S9

description: Optn KO-1


title: 111617p1_B10_S22

description: Optn KO-1


title: EpiLC-48H-ΔSL1-2

source_name: mESC cultured in Differentiation medium for EpiLC induction for 48 hours

value: EpiLC


title: EpiLC-24H-ΔSL1-2

source_name: mESC cultured in Differentiation medium for EpiLC induction for 24 hours


title: 111617p1_B4_S16

description: Optn KO-1


title: EpiLC-6H-ΔSL1-2

source_name: mESC cultured in Differentiation medium for EpiLC induction for 6 hours


title: 111617p1_A7_S7

description: Optn KO-1


title: 111617p1_A6_S6

description: Optn KO-1


title: EpiLC-48H-ΔSL1-1


title: WT.N.37.L1


title: 111617p1_B3_S15

description: Optn KO-1


title: 111617p1_A4_S4

description: Optn KO-1


title: EpiLC-24H-ΔSL1-1


title: P.H.12


title: EpiLC-6H-ΔSL1-1


title: 111617p1_A3_S3

description: Optn KO-1


title: 111617p1_A2_S2

description: Optn KO-1


title: mESC-ΔSL1-1(2i medium)-EpiLC-0h

source_name: ΔSL1 mESC cultured in 2i/lif medium


title: mESC-DGCR8-/- rep1 (serum/lif)

source_name: DGCR8-/- mESC cultured in serum/lif medium


title: 111617p1_A8_S8

description: Optn KO-1


title: mESC-ΔSL1-rep2 (serum/lif)


title: 111617p1_A11_S11

description: Optn KO-1


title: SOD1-Nec 2

data_processing:
DropSeq gene alignment tools (McCarroll lab)
Genome_build: mm9
Supplementary_files_format_and_content: UMI counts

extract_protocol:
Spinal cords were digested in Accutase; myelin was removed and live cells were isolated using a OptiPrep and Hibernate A gradient
Samples were prepared according to the DropSeq protocol

tag: sample no


title: 111617p1_A10_S10

description: Optn KO-1


title: 111617p1_A12_S12

description: Optn KO-1


title: mESC-ΔSL1-rep1  (serum/lif)


title: Optn

data_processing:
indrops.py pipeline
Genome_build: mm10
Supplementary_files_format_and_content: counts.mtx
Supplementary_files_format_and_content: counts.mtx.colnames
Supplementary_files_format_and_content: counts.mtx.rownames

extract_protocol:
Spinal cords were digested in Accutase; myelin was removed using a 0.25% BSA spin and resuspended in OptiPrep for live cell isolation
Samples were prepared according to the inDrop protocol

value: mixed sample (non-demultiplexed)


title: mESC-WT-rep1 (serum/lif)


title: Treg_SPF_2-2

city: Braunschweig

first: Carolin

last: Wiechers

state: Niedersachsen

address: Inhoffenstraße 7

department: Experimental Immunology

country: Germany

institute: Helmholtz Centre for Infection Research

library_source: genomic

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR and aligned reads to annotated genes were quantified with htseq-count
calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression. Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values.
Gene ontology analysis was performed using topGO
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values (.csv) file of DESeq2 results

molecule: genomic DNA

source_name: Adoptively transferred DO.11.10

growth_protocol: Single cell suspensions from spleen and LNs of Foxp3hCD2xRag2‑/‑xDO11.10 mice were generated. CD4+ T cells were enriched with CD4 (L3T4) MicroBeads and autoMACS separation (Miltenyi Biotec) after which CD4+ T cells were labelled with CPDviolet (Invitrogen) to track cell proliferation before being adoptively transferred. Approximately 3‑10x106 cells in 100µl PBS were injected i.v. per recipient mouse.

extract_protocol:
The following fluorochrom-conjugated antibodies were purchased from BD, Biolegend and eBioscience (human)-CD2 (RPA-2.10), CD4 (RM4-5), Ova‑TCR (KJ1.26), CD62L (MEL14). To prevent unspecific antibody binding, cell suspensions were incubated with 10µg/ml Chrom Pure rat IgG (Jackson ImmunoResearch Laboratories) and 10 µg/ml anti-mouse CD16/CD32 antibody (BioXcell). For surface staining cells were washed and then incubated with the corresponding antibodies dissolved in PBS containing 0.2% BSA for 15 min on ice. Cell sorting for RNA-seq and ATAC-seq analysis was performed at the cell sorting facility (Helmholtz Centre for Infection Research, Braunschweig, Germany) on FACSAria IIu (BD Bioscience) and FACS Aria-II SORP (BD Bioscience). Acquired data was analyzed utilizing FlowJo software (Tree Star).
Foxp3hCD2+CD4+OvaTCR+ Tregs and CD4+OvaTCR+CD62L+ naïve T cells were directly FACS sorted into RLT+ lysis buffer (Qiagen) containing 10 µl/ml β-Mercaptoethanol (Roth). Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufactures instructions. cDNA conversion was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.
Sequencing of libraries was carried out at the sequencing facility on Illumina HiSeq2500 using 50 bp single-end reads and quality of sequenced libraries was verified with FastQC.

treatment_protocol: Starting one day after adoptive transfer of CD4+ T cells of Foxp3hCD2xRag2‑/‑xDO11.10 mice, 20 µg Ova323‑339 peptide was injected i.v. on two consecutive days to study de novo Treg induction. Two days after the last dose of Ova immunization, recipient mice were sacrificed and cells were isolated from indicated endogenous LNs.

value: Treg

value: Specific-pathogen-free (SPF)


title: mESC-ΔSL1-2(2i medium)-EpiLC-0h


title: SOD1-Nec 1


title: 111617p1_A5_S5

description: Optn KO-1


title: Treg_SPF_2-1


title: SOD1-Veh 1

value: Vehicle


title: WT-Veh 2


title: Treg_SPF_1-2


title: Treg_SPF_1-1


title: WT-Veh 1


title: Treg_GF_2-1

value: germ-free (GF)


title: mESC-DGCR8-/- rep2  (serum/lif)


title: Treg_GF_1-1


title: 111617p1_A1_S1

description: Optn KO-1

value: Optn KO


title: mESC-WT-rep2 (serum/lif)


title: Treg_GF_1-2


title: Tnaive_T1

value: Tnaive

value: Unprimed


title: SOD1-Veh 2


title: ID2KO3

first: Liuhui

last: Fu

address: Zhongguancun North Street

department: Institute for Immunology

institute: Tsinghua university

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
FPKM were calculated using RSEM tool
Genome_build: mm10
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: ID2KO_CD8+ T cells

extract_protocol:
CD8+ T cells were sorted by FACS and total RNA was isolated with the RNeasy Micro Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iLN

value: CD8+ T cells


title: Tnaive_T2


title: ID2KO1


title: ID2KO2


title: WT2

source_name: WT_CD8+ T cells


title: WT3


title: SC156_CONup_23year_female

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

description: same patient as SC155

data_processing:
FASTQ files were generated by using CellRanger mkfastq, a wrapper for bcl2fastq
Aligned to the 10X Genomics human reference genome, refdata-cellranger-GRCh38-3.0.0, with Cell Ranger 3.0.2 using cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 was analyzed in R using the Seurat package
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data file is in hierarchical data format (HDF).  It contains a gene x cell matrix with mRNA counts per cell of each gene.  Genes are in rows and cells are designated by barcodes in each column with UMI (unique molecular identifier) counts for each gene provided.

molecule: polyA RNA

source_name: whole lung, upper lobe

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v1 and Single Cell 3’ Reagent Kits v2 User Guide
single cell RNA-seq

tag: chemistry

value: 10X Genomics 3Prime V2 chemistry

value: CONTROL

tag: protocol

value: digested into single cell suspension

value: whole lung, upper lobe


title: WT1


title: SC155_CONlow_23year_female

description: same patient as SC156

source_name: whole lung, lower lobe

value: whole lung, lower lobe


title: neurons culture_melatonin untreated_3

city: POZNAN

first: MONIKA

last: WEGLARZ

address: FREDRY 10

institute: POZNAN UNIVERSITY OF MEDICAL SCIENCES

description: Gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The slides were scanned using the SureScan Dx Microarray Scanner (Agilent, USA)

data_processing: The images obtained after scanning were analysed using Agilent Feature Extraction software v. 12.0.3.1.

source_name: primary cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: Primary cultures of dissociated hippocampal neurons (HN) were prepared faccording to the standard protocol (doi:10.3791/3634)

extract_protocol: RNA isolation and purification were performed according to Alternative Protocol for Extraction of RNA from PBMC captured on LeukoLOCK™ Filters. Total RNA was extracted from cell culture samples using the RNeasy® Mini Kit (QIAGEN).

treatment_protocol: Cultured neurons from two independent culture were stimulated for 24h by 10 µM MEL dissolved in ethanol at DIV19

tag: gender

value: not applicable

tag: age

value: FVB Mouse


title: SC59_CON_18year_male

source_name: whole lung

value: whole lung


title: Tnaive_T3

tag: cell type


title: neurons culture_melatonin treated_3

description: Gene expression


title: SC56_CON_57year_female


title: oocyte 74

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

data_processing:
Primary data analysis and QC assessment was carried out with the standard Illumina pipeline following the manufacturer's protocol
Smart-seq2 libraries were mapped as paired-end reads using STAR 2.5.4b and RSEM 1.3.0 for the quantification
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated values (TSV) files containing gene expression values as raw counts

extract_protocol:
Oocyte retrieval was performed 36h later by ultrasound-guided transvaginal follicular aspiration. Oocytes were denuded 30 minutes after pick-up by exposure to 80 IU/ml hyaluronidase (Hyase-10x, Vitrolife, Sweden) in G-MOPS medium (Vitrolife, Sweden), followed by gentle pipetting. Once denuded, oocytes were scored for polar body presence and immature GV were either processed immediately as GV or further cultured in vitro in 50 μl of G2-PLUS (Vitrolife, Sweden) medium in a humidified atmosphere of 6%CO2/94% at 37ºC for 30 hours, when they were checked again for polar body presence and processed.
Full-length single-cell RNA-seq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. Briefly, oocytes were dezoned with Pronase (Roche Diagnostics, Spain), and individually placed in 2.3 µl of a lysis buffer containing 0.2% Triton-X100 (T8787, Sigma) and 1 U/µl RNAse inhibitor (N8080119, Applied Biosystem), and stored at -80ºC until use. Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems) and IS PCR primer (IDT), with 20 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of >1 million reads per cell. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes (Unique dual indexing).

treatment_protocol: Women were stimulated with highly purified urinary hMG (Menopur®, Ferring, Spain) or follitropin alpha (Gonal®, Merck-Serono, Spain), with daily injections of 150-300 IU (Blazquez et al., 2014). A GnRH antagonist (0.25 mg of Cetrorelix acetate, Cetrotide®, Merck Serono, Spain) was administered daily from day 6 of stimulation (for donors) or from when a follicle of 14 mm  or estradiol ≥ 400 pg/ml was detected (for patients) (Olivennes et al., 1996). In the case of donors, when 3 or more follicles of >18 mm of diameter were observed, final oocyte maturation was triggered with 0.2 mg of triptorelin (Decapeptyl®, Ipsen Pharma, Spain). In the case of patients, when 3 follicles of >17 mm of diameter were observed, final oocyte maturation was triggered with 250 µg of alpha-choriogonadotropin (Ovitrelle®, MERCK) or 0.3 mg of triptorelin (Decapeptyl®, Ipsen Pharma, Spain).

value: oocyte

tag: ID

tag: maturation stage

value: MII


title: oocyte 75


title: SC45_CON_55year_male


title: SC31_CON_56year_male

value: 10X Genomics 3Prime V1 chemistry


title: SC31D_CON_56year_male

description: biological duplicate of SC31


title: neurons culture_melatonin treated_2

description: Gene expression

tag: strain


title: neurons culture_melatonin treated_1

description: Gene expression


title: neurons culture_melatonin untreated_1

description: Gene expression


title: PBMC_haelthy control_1

description: Gene expression

source_name: whole blood

value: female


title: PBMC_haelthy control_2

description: Gene expression


title: PBMC_agomelatine untreated_2

description: Gene expression


title: SC14_CON_76year_male


title: PBMC_agomelatine untreated_3

description: Gene expression


title: PBMC_agomelatine treated_2

description: Gene expression


title: SC161_IPAH_50year_female

value: IPAH


title: PBMC_haelthy control_3

description: Gene expression


title: neurons culture_melatonin untreated_2

description: Gene expression


title: PBMC_agomelatine untreated_1

description: Gene expression


title: PBMC_agomelatine treated_1

description: Gene expression


title: oocyte 70

value: GV


title: oocyte 72


title: oocyte 71


title: SC17_IPAH_21year_male


title: oocyte 69


title: oocyte 68


title: oocyte 67


title: oocyte 73


title: 111617p1_D2_S38

description: Optn KO-1

source_name: Spinal cord

tag: genotype

value: Optn KO


title: oocyte 66


title: Patient-derived GSC -ZH305 shCD109 D11-

city: Helsinki

first: Vadim

last: Le Joncour

state: Uusimaa

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

description:
GSCs_RNAseq_2.xlsx
ZH305shD11_S11

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCh38.p12 reference genome (for processed data file included in the GSCs_RNAseq_1.xlsx) and GRCh38.p13 from GENCODE human release v.33 (for processed data file included in the GSCs_RNAseq_2.xlsx) using STAR aligner (2.6.0c) with parameters --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.v28.chr_patch_hapl_scaff.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCh38.p12 reference genome (for processed data file included in the GSCs_RNAseq_1.xlsx) and GRCh38.p13 from GENCODE human release v.33 (for processed data file included in the GSCs_RNAseq_2.xlsx)
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

source_name: Patient-derived glioblastoma stem cell

extract_protocol:
Total RNA was extracted from lysed cells or gliospheres using the RNeasy Mini kit (#74104) (Qiagen) according to the manufacturer’s instructions. After DNase treatment, the quality of the RNA preparations (0.5 µg) was controlled using a Tapestation (Agilent). Total RNA 0.5 µg is treated with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) to remove the ribosomal RNA. First the samples are treated with rRNA removal solution after which the rRNA is removed combining probe-hybridized samples and magnetic beads. The Ribo-Zero treated RNA is purified with Qiagen RNeasy MinElute Cleanup Kit. The absence of rRNA is assessed by Bioanalyzer and the quantity of RNA by Bioanalyzer.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760, #E7765) is used to generate cDNA libraries for next generation sequencing. First, the ribosomal RNA depleted sample (10 ng) is fragmented to generate inserts around 200 bp, and then primed with random primers. The first strand cDNA synthesis utilizes Actinomycin D, which inhibits the DNA polymerase activity of the reverse transcriptase increasing strand specificity. In the second strand cDNA synthesis dUTP labelled oligo nucleotides are incorporated to mark the second strand with uracils (U). The cDNA synthesis product is purified with Agencourt AMPure XP beads. Next, the cDNA is end-repaired, and adapter ligated utilizing dA-tailing. The adaptor ligated DNA goes through a bead-based size selection after which the final PCR enrichment takes place. At this point, each sample is given a unique index to enable pooling of multiple samples (multiplexing) for sequencing. During the high-fidelity PCR, USER (Uracil-specific Excision Reagent) enzyme cuts away the uracil strand preserving only the first strand. In addition, the loop adaptor is cut open to enable the PCR. The amplified library is then purified using AMPure XP Beads. Library quality is assessed by Bioanalyzer (Agilent DNA High Sensitivity chip) and library quantity by Qubit (Invitrogen).
Illumina NextSeq 500 High Output 75 cycle kit for single-end 1x75bp reads (1 flow cell). Loading concentration 1,3 pM + 1% PhiX control. Starting amount of Total RNA: 500 ng, PCR cycles used in method: 9.

treatment_protocol: Following shRNA constructs from the RNAi Consortium (TRC) library (Broad Institute of MIT and Harvard) in pLKO.1 lentiviral vector were used to silence  CD109 expression: human shCD109#1 (TRCN0000073649). Complete targeting sequences were as follows (5’- 3’): shCD109; GCCGATCCTTACATAGATATT. Lentivirus was produced by transfecting shRNA constructs or non-targeting control vector (shControl) together with CMVg and CMV delta8.9 packaging plasmids (both from Addgene) and Fugene 6 transfection reagent (Promega) into 293FT cells. Silencing efficiencies of different shRNA constructs were confirmed using western blotting and/or qRT-PCR.

tag: molecular subtype/phenotypic state

value: Classical/Astrocyte-like cell

tag: cell culture condition

value: serum-free DMEM/F-12 medium supplemented with 1 x B27 (both from Gibco), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 15 mM HEPES (all from Lonza), 0.02 μg/ml human EGF, and 0.02 μg/ml human FGF-basic.

tag: cell transduction

value: short hairpin RNA targeting CD109, day 11 post silencing


title: Patient-derived GSC -BT13 shCD109 D11-

description:
GSCs_RNAseq_2.xlsx
BT13shD11_S6

value: serum-free DMEM/F-12 medium supplemented with 1 x B27 (both from Gibco), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 15 mM HEPES (all from Lonza), 0.02 μg/ml human EGF, and 0.01 μg/ml human FGF-basic.


title: oocyte 64


title: oocyte 65


title: Patient-derived GSC -BT13 shCTRL D11-

description:
GSCs_RNAseq_2.xlsx
BT13scrD11_S5

value: Mesenchymal/Mesenchymal

value: scrambled short hairpin RNA, day 11 post silencing


title: oocyte 63


title: oocyte 62


title: oocyte 60


title: Patient-derived GSC -BT3 CD133+ sorted cells-

description:
GSCs_RNAseq_2.xlsx
BT3CD133_pos_S2

value: BT3 cells sorted for high expression of PROM1/CD133.


title: Patient-derived GSC -ZH305 shCTRL D11-

description:
GSCs_RNAseq_2.xlsx
ZH305scrD11_S10

value: Proneural/Neuronal Precursor Cell


title: Patient-derived GSC -BT3-

description:
GSCs_RNAseq_2.xlsx
BT3_S1

value: Wild Type


title: oocyte 58


title: oocyte 59


title: oocyte 56


title: Patient-derived GSC -BT13 shCTRL D6-

description:
GSCs_RNAseq_1.xlsx
BT_13_SHCTRL_D5_S14

extract_protocol:
Total RNA was extracted from lysed cells or gliospheres using the RNeasy Mini kit (#74104) (Qiagen) according to the manufacturer’s instructions. After DNase treatment, the quality of the RNA preparations (1 µg) was controlled using a Tapestation (Agilent). Total RNA 1 ug is treated with Illumina's Ribo-Zero Complete Gold Kit to remove the ribosomal RNA. First the samples are treated with rRNA removal solution after which the rRNA is removed combining probe-hybridized samples and magnetic beads. The Ribo-Zero treated RNA is purified with Qiagen RNeasy MinElute Cleanup Kit. The absence of rRNA is assessed by Bioanalyzer and the quantity of RNA by Bioanalyzer.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420S/L Version 8.0 3/16) is used to generate cDNA libraries for next generation sequencing. First, the ribosomal RNA depleted sample (10 ng) is fragmented to generate inserts around 200 bp, and then primed with random primers. The first strand cDNA synthesis utilizes Actinomycin D, which inhibits the DNA polymerase activity of the reverse transcriptase increasing strand specificity. In the second strand cDNA synthesis dUTP labelled oligo nucleotides are incorporated to mark the second strand with uracils (U). The cDNA synthesis product is purified with Agencourt AMPure XP beads. Next, the cDNA is end-repaired, and adapter ligated utilizing dA-tailing. The adaptor ligated DNA goes through a bead-based size selection after which the final PCR enrichment takes place. At this point, each sample is given a unique index to enable pooling of multiple samples (multiplexing) for sequencing. During the high-fidelity PCR, USER (Uracil-specific Excision Reagent) enzyme cuts away the uracil strand preserving only the first strand. In addition, the loop adaptor is cut open to enable the PCR. The amplified library is then purified using AMPure XP Beads. Library quality is assessed by Bioanalyzer (Agilent DNA High Sensitivity chip) and library quantity by Qubit (Invitrogen).
Illumina NextSeq 500 High Output 75 cycle kit for single-end 1x75bp reads (2 flow cells). Loading concentration 1,5 pM + 1% PhiX control. Starting amount of Total RNA: 1000 ng, PCR cycles used in method: 15.

value: scrambled short hairpin RNA, day 5 post silencing


title: Patient-derived GSC -ZH305-

description:
GSCs_RNAseq_1.xlsx
ZH305_S7


title: Patient-derived GSC -BT18-

description:
GSCs_RNAseq_2.xlsx
BT18_S7


title: Patient-derived GSC -BT12 shCD109 D11-

description:
GSCs_RNAseq_2.xlsx
BT12shD11_S4


title: oocyte 55

value: oocyte


title: Patient-derived GSC -BT27-

description:
GSCs_RNAseq_2.xlsx
BT27_S8


title: oocyte 57


title: Patient-derived GSC -S24-

description:
GSCs_RNAseq_1.xlsx
S24_S6


title: Patient-derived GSC -BT13-

description:
GSCs_RNAseq_1.xlsx
BT_13_S3


title: oocyte 61

value: MII


title: Patient-derived GSC -BT12 shCTRL D6-

description:
GSCs_RNAseq_1.xlsx
BT_12_SHCTRL_D5_S12


title: oocyte 53


title: oocyte 52


title: oocyte 51


title: Patient-derived GSC -BT12 shCTRL D11-

description:
GSCs_RNAseq_2.xlsx
BT12scrD11_S3


title: oocyte 50


title: Patient-derived GSC -BT12 shCD109 D6-

description:
GSCs_RNAseq_1.xlsx
BT_12_SHCD109_1_D5_S13

value: short hairpin RNA targeting CD109, day 5 post silencing


title: Patient-derived GSC -BT12-

description:
GSCs_RNAseq_1.xlsx
BT_12_S2


title: oocyte 49


title: Patient-derived GSC -BT11-

description:
GSCs_RNAseq_1.xlsx
BT_11_S1


title: CircSPI1_Control

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

data_processing:
The adapter sequences were removed using Trim-Galore and clean reads were mapped to the hg38 genome (GRCh38) by STAR (v2.7). The gene expression levels were quantified by Htseq-count. The significant differentially expressed genes (DEGs) were called by DESeq2 by using p-value <0.05, fold change >=2 .
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample.

source_name: NB4 Cell

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from NB4 cells using the RNeasy Mini Kit (Qiagen, Valencia, CA) and then purified using the RNeasy kit (Quiagen).
RNA-seq libraries were preapared with the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were infected with shcircSPI1 or scramble lentivirus for 3days

tag: cell line

value: Control


title: oocyte 48


title: oocyte 47


title: CircSPI1_KD

tag: treatment

value: CircSPI1 knockdown


title: oocyte 46

value: GV


title: FT671 H3K27me3

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

data_processing:
Sequenced reads were trimmed for adapter sequence, after which they were aligned to the hg38 reference genome use BWA software.
SAMtools was used for processing of aligned reads.
Peak calling was performed using MACS2 with the estimated fragment size. H3K4me3 peaks were called using narrow settings (default) and H2AK119ub peaks were identified using broad settings.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using Bedtools and BedGraphToBigWig from UCSC.

source_name: human leukemia cell line

extract_protocol:
Chromatin was sonicated and histone DNA-complexes were isolated with antibody
Sequencing libraries were generated using the KAPA Hyper Prep Kit (Roche Sequencing and Life Sciences) according to manufacturer's protocol

tag: antibody

tag: agent


title: FT671 H3K36me3


title: FT671 H3K4me3


title: oocyte 45


title: FT671 H2AK119ub


title: DMSO H3K27me3

value: DMSO


title: DMSO H3K36me3


title: oocyte 41


title: oocyte 43


title: oocyte 42


title: DMSO H3K4me3


title: oocyte 39


title: oocyte 40


title: DMSO H2AK119ub


title: oocyte 38


title: oocyte 36


title: HepG2_c

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

country: United Kingdom

institute: AstraZeneca

description:
G4 ChIP-seq
HepG2_async_rep1-3.mult.6of9.bed
HepG2_async_rep1-3.mult.2of9.bed

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/sblab-bioinformatics/G4-vs-TFs
Genome_build: hg19
Supplementary_files_format_and_content: K562 data was processed jointly with two other K562 G4 ChIP-seq biological replicates available in GSE107690 (GSM2876090, GSM2876091, GSM2876092, GSM2876093, GSM2876094, GSM2876095, GSM2876096)
Supplementary_files_format_and_content: bed files

source_name: HepG2 cell line

growth_protocol: HepG2 (HB-805) cells were kindly provided by M. Narita (CRUK Cambridge Institute, University of Cambridge), grown in DMEM (high glucose without sodium pyruvate, Life Technologies) supplemented with 10% of fetal bovine serum (Life Technologies) at 37°C in 5% CO2. Cells were periodically tested for mycoplasma contamination and identity confirmed by STR typing.

extract_protocol:
Chromatin was isolated from HepG2 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). Final products were sequenced by Illumina Nextseq 500 platform.  For further details see methods section in the associated manuscript.


title: HepG2_b


title: HepG2_a


title: oocyte 35


title: FT671 Rep3

data_processing:
Sequenced reads were trimmed for adapter sequence, after which they were aligned and counted using the STAR software.
Read counts were normalized and filtered using the DESeq2 package, which we used to find differential gene expression as well.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include counts for each sample.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands) according to the manufacturer’s recommendations. Initial quality check and RNA quantification of the samples were performed by automated gel electrophoresis on the 2200 TapeStation System (Agilent Technologies).
Sequence libraries were generated using the KAPA RNA HyperPrep kit with riboErase (HMR) (Roche Sequencing and Life Sciences) according to manufacturer’s protocol (DMSO/FT671 samples).

treatment_protocol: Cells were treated with DMSO or the USP7 inhibitor FT671 (10 uM, 48h).

value: Leukemia cell line


title: FT671 Rep2


title: oocyte 34


title: oocyte 33


title: oocyte 44


title: FT671 Rep1


title: DMSO rep3


title: DMSO rep2


title: K562_IP

description:
input
20180108_K562_async_rep1-3.mult.5of8.bed
20180108_K562_async_rep1-3.mult.2of8.bed

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/sblab-bioinformatics/G4-vs-TFs
Genome_build: hg19
Supplementary_files_format_and_content: Data was processed jointly with two other G4 ChIP-seq biological replicates available in GSE107690

source_name: K562 cell line

growth_protocol: Mycoplasma-free human chronic myelogenous leukemia K562 cells (CCL-243) were purchased from ATCC, grown in RPMI1640 (Glutamine plus, Life Technologies) supplemented with 10% of fetal bovine serum (Life Technologies) at 37°C in 5% CO2. Cells were periodically tested for mycoplasma contamination and identity confirmed by STR typing.

extract_protocol:
Chromatin was isolated from K562 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). Final products were sequenced by Illumina Nextseq 500 platform.  For further details see methods section in the associated manuscript.


title: oocyte 31


title: oocyte 30


title: HepG2_IP

description:
input
HepG2_async_rep1-3.mult.6of9.bed
HepG2_async_rep1-3.mult.2of9.bed


title: K562_c

description:
G4 ChIP-seq
20180108_K562_async_rep1-3.mult.5of8.bed
20180108_K562_async_rep1-3.mult.2of8.bed


title: DMSO rep1


title: oocyte 28


title: oocyte 37


title: oocyte 26


title: K562_a


title: K562_b


title: oocyte 25


title: oocyte 24


title: oocyte 23


title: oocyte 22


title: oocyte 21


title: oocyte 32


title: oocyte 20


title: oocyte 27


title: oocyte 19


title: oocyte 18


title: ESC_A485_10uM_15min_H3K27ac_ChIP_rep2

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description: processed data file: ChIP.ESC_A485_10uM_H3K27ac_TC15.n2.smooth.bw

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools.  The DAC Blacklisted Regions  were also omitted from the bam file using bedtools. Peaks were called using epic with the following parameters: --fragment-size 200 --gaps-allowed 5.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: mouse ES cells

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments 11932748. ESCs were cultured in a custom-made N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, without L-arginine and L-lysine (C.C.Pro GmbH, Oberdorla). The media was supplemented with L-arginine, L-lysine, 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1µM PD0325901, 3µM CT-99021 (custom-made by ABCR), 100µM 2-mercaptoethanol, 150µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), as well as with 0.5x N2 supplement (made in house; or from Thermo Fisher Scientific).

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or JQ1(0.5mM) were treated for 60 min if not indicated. For control samples, 0.1 % DMSO was added.

value: ES cells

value: H3K27ac ( Abcam, ab4729)

value: 10uM A-485 for 15 min.


title: ESC_A485_10uM_15min_H3K4me1_ChIP_rep1

description: processed data file: ChIP.ESC_A485_10uM_H3K4me1_TC15.n2.smooth.bw

value: H3K4me1 (Cell Signaling, 5326)


title: ESC_Ctrl_H3K4me1_ChIP_rep1

description: processed data file: ChIP.ESC_Ctrl_H3K4me1_TC0.n2.smooth.bw


title: ESC_Ctrl_H3K4me1_ChIP_rep2


title: ESC_A485_10uM_5min_H3K4me1_ChIP_rep1

description: processed data file: ChIP.ESC_A485_10uM_H3K4me1_TC5.n2.smooth.bw

value: 10uM A-485 for 5 min.


title: oocyte 17


title: oocyte 29


title: ESC_A485_10uM_15min_H3K4me1_ChIP_rep2


title: ESC_A485_10uM_5min_H3K4me1_ChIP_rep2


title: ESC_Ctrl_H3K27ac_ChIP_rep1

description: processed data file: ChIP.ESC_Ctrl_H3K27ac_TC0.n2.smooth.bw


title: ESC_Ctrl_H3K27ac_ChIP_rep2


title: ESC_A485_10uM_15min_H3K27ac_ChIP_rep1


title: ESC_A485_10uM_5min_H3K27ac_ChIP_rep2

description: processed data file: ChIP.ESC_A485_10uM_H3K27ac_TC5.n2.smooth.bw


title: oocyte 14


title: oocyte 15


title: ESC_A485_10uM_30min_Nanog_ChIP_rep1

description: processed data file: ChIP.ESC_A485_10uM_Nanog_TC30.n2.smooth.bw

value: NANOG (CST, 8785S)

value: 10uM A-485 for 30 min.


title: oocyte 13


title: oocyte 12


title: oocyte 10


title: ESC_A485_10uM_30min_Oct4_ChIP_rep2

description: processed data file: ChIP.ESC_A485_10uM_Oct4_TC30.n2.smooth.bw

value: OCT4 (abcam, ab181557)


title: ESC_A485_10uM_30min_Oct4_ChIP_rep1


title: ESC_A485_10uM_30min_Oct4_ChIP_rep3


title: ESC_A485_10uM_5min_H3K27ac_ChIP_rep1


title: oocyte 9


title: oocyte 16


title: oocyte 4


title: ESC_A485_10uM_15min_TBP_ChIP_rep3

description: processed data file: ChIP.ESC_A485_10uM_TBP_TC15.n2.smooth.bw


title: oocyte 3


title: oocyte 7


title: ESC_A485_10uM_15min_TBP_ChIP_rep2


title: oocyte 1


title: ESC_A485_10uM_15min_TBP_ChIP_rep1


title: ESC_A485_10uM_30min_Nanog_ChIP_rep2


title: oocyte 5


title: oocyte 2


title: oocyte 6


title: oocyte 8


title: ESC_A485_10uM_30min_TBP_ChIP_rep1

description: processed data file: ChIP.ESC_A485_10uM_TBP_TC30.n2.smooth.bw


title: oocyte 11


title: NOA_Cell_385_480

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg38 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg38
Supplementary_files_format_and_content: text file

source_name: Human Testicular Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

tag: tissue

value: testis

value: male


title: NOA_Cell_289_384

description: polyA RNA


title: ESC_A485_10uM_30min_TBP_ChIP_rep2


title: ESC_A485_10uM_5min_TBP_ChIP_rep1

description: processed data file: ChIP.ESC_A485_10uM_TBP_TC5.n2.smooth.bw


title: ESC_A485_10uM_5min_TBP_ChIP_rep3


title: NOA_Cell_193_288

description: polyA RNA


title: NOA_Cell_97_192

description: polyA RNA


title: NOA_Cell_1_96

description: polyA RNA


title: ESC_Ctrl_Med1_ChIP_rep2

description: processed data file: ChIP.ESC_Ctrl_Med1_TC0.n2.rpkm.smooth.bw

value: MED1 (Sigma-Aldrich 17-10530)


title: ARID00_16

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

data_processing:
Reads from RNA-seq were aligned to the mouse genome (mm9) using STAR (version XXX). Aligned reads mapping to genes were counted at the gene level using subreads featureCounts. The mm9 knownGene annotation track and aligned reads were used to generate quality control information using the full RSeQC tool suite. Unaligned reads were quality checked using FastQC.
Raw count data for all samples were used for differential expression analysis using edgeR. Genes with at least 20 reads per million in at least one sample were included for analysis, resulting in a final set of 8942 genes for differential testing.
Tagwise dispersion estimates were generated and differential expression analysis was performed using a generalized linear model with genotype as the variable for testing. Normalized expression levels were generated using the edgeR rpkm function. Normalized log2(RPKM) values were used for plotting of expression data for Arid1b. Pseudo-count values were used for plotting the summary heatmap.
Mouse gene ontology (GO) data was downloaded from Bioconductor (org.Mm.eg.db). We used the goseq package to test for enrichment of GO terms indicating parent:child relationships. For GO analysis, we examined down- and up-regulated genes separately for genes meeting an FDR < 0.2.
For the enrichment analysis, the test set of differentially expressed genes was compared against the background set of genes expressed in our study based on minimum read-count cutoffs described above.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix file of gene counts

source_name: Adult Cerebellum

extract_protocol:
Cerebellum tissue was micro-dissected from adult heterozygous Arid1b mice and wild-type littermates (postnatal day 140-150).
Stranded mRNA sequencing libraries were prepared using a TruSeq Stranded mRNA kit with all four samples pooled and sequenced in one lane on the Illumina HiSeq platform using a single-end 100bp strategy. Each library was quantified and pooled before sequencing at the UC Davis DNA Technologies Core.

value: Cerebellum

tag: genotype/variation

value: WT

tag: Sex

value: F


title: ESC_Ctrl_Nanog_ChIP_rep2

description: processed data file: ChIP.ESC_Ctrl_Nanog_TC0.n2.smooth.bw

value: Control


title: ARID00_14

value: M


title: ARID00_15

value: HT


title: ESC_Ctrl_TBP_ChIP_rep1

description: processed data file: ChIP.ESC_Ctrl_TBP_TC0.n2.smooth.bw

value: ES cells


title: ESC_Ctrl_Oct4_ChIP_rep3

description: processed data file: ChIP.ESC_Ctrl_Oct4_TC0.n2.smooth.bw


title: ARID00_13


title: ESC_Ctrl_Oct4_ChIP_rep2


title: Control_Scaff_B

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: Michigan

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

data_processing:
Samples OT_Tumor_1, Control_Scaff_B and iKras_p53_Scaff were run on HiSeq 4000. All other samples were run on the NovaSeq 6000 (Illumina). All samples were run using paired end 50 cycle reads to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 2.2.0, 3.0.0, or 3.1.0 with default settings was used, with an initial expected cell count of 10,000.
Genome_build: Mouse samples were aligned to the mouse genome mm10-3.0.0 using Cell Ranger. Human samples were aligned to the human genome hg19-3.0.0.
Supplementary_files_format_and_content: Zipped GZ archive file containing barcodes.tsv, genes.tsv/features.tsv, and matrix.mtx files, and .h5 files for reading into R using the Seurat Pipeline.

source_name: Biomaterial scaffold

growth_protocol: 7940b cells were grown in DMEM supplemented with 10% FBS and 1% Pen-Strep. Mouse tumors were harvested after three weeks. Biomaterial scaffolds were harvested three weeks after tumor cell implantation.

extract_protocol:
Samples were mechanically and enzymatically (Collagenase P; 1mg/mL in DMEM) digested under constant agitation. Single cell suspension was obtained by filtering through a 40 µm mesh. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were prepared and sequenced using the 10x Genomics Platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: iKras* and iKras* p53*mice were administered doxycycline chow (BioServ, F3949) to induce expression of KrasG12D for 72 hours, followed by two days of 8 intraperitoneal injections of caerulein (Sigma, 75 ?g/kg) to induce pancreatitis. Doxycycline chow was continuously administered until experiment endpoint.

tag: doxycycline treatment duration

value: 18 weeks

tag: condition

value: Healthy control

value: p48Cre; R26rtTa/rtTa


title: ESC_Ctrl_Oct4_ChIP_rep4

tag: cell type


title: ESC_Ctrl_Oct4_ChIP_rep1


title: OT_Tumor_1

source_name: Orthotopic pancreas tumor

value: pancreatic cancer (PDA)

value: KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre (7940b)

value: mouse orthotopic pancreatic tumors


title: ESC_Ctrl_TBP_ChIP_rep3


title: E4-19m-MU20-Br-N

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCm38 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated by featurecounts from Rsubread_1.24.0 with minFeatureOverlap 10
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counst for each sample

source_name: brain

extract_protocol:
Total RNA from muscle samples was isolated using Trizol reagent (Life technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MRPS5 V338Y

tag: age

value: 19 months

value: brain


title: ESC_Ctrl_TBP_ChIP_rep2


title: E4-19m-MU19-Br-N


title: Flag.Taf1.ESC cells. A485_10uM_15min_Taf1_ChIP_rep2

description: processed data file: ChIP.Flag.Taf1.ESC_A485_10uM_Taf1_TC15.n2.smooth.bw

value: Flag (Sigma-Aldrich, 3165)

value: 10uM A-485 for 15 min.


title: Flag.Taf1.ESC cells. A485_10uM_15min_Taf1_ChIP_rep1


title: ESC_Ctrl_Nanog_ChIP_rep1

value: NANOG (CST, 8785S)


title: Flag.Taf1.ESC cells. A485_10uM_15min_Taf1_ChIP_rep3


title: E4-19m-MU18-Br-N


title: oocyte 54

value: oocyte

tag: ID

tag: maturation stage

value: GV


title: E4-19m-MU17-Br-N

tag: genotype


title: iKras_p53_Scaff

value: PDA


title: E4-19m-WT15-Br-N

value: MRPS5 WT


title: Flag.Taf1.ESC cells. A485_10uM_30min_Taf1_ChIP_rep2

description: processed data file: ChIP.Flag.Taf1.ESC_A485_10uM_Taf1_TC30.n2.smooth.bw

value: ES cells

value: 10uM A-485 for 30 min.


title: Flag.Taf1.ESC cells. A485_10uM_30min_Taf1_ChIP_rep3


title: Flag.Taf1.ESC cells. A485_10uM_30min_Taf1_ChIP_rep4

value: Pol2Ser2 (Abcam, ab5095)


title: Flag.Taf1.ESC cells. A485_10uM_5min_Taf1_ChIP_rep2

description: processed data file: ChIP.Flag.Taf1.ESC_A485_10uM_Taf1_TC5.n2.smooth.bw

value: 10uM A-485 for 5 min.


title: Flag.Taf1.ESC cells. A485_10uM_5min_Taf1_ChIP_rep1


title: E4-3m-MUT16-Br

value: 3 months


title: E4-3m-MUT14-Br


title: Flag.Taf1.ESC cells. A485_10uM_5min_Taf1_ChIP_rep3


title: Flag.Taf1.ESC cells. Ctrl_Input

description: processed data file: ChIP.Flag.Taf1.ESC_Ctrl_Taf1_TC0.n2.smooth.bw

value: Control


title: E4-3m-WT12-Br


title: E4-19m-WT12-Br-N


title: E4-19m-WT13-Br-N


title: E4-3m-MUT15-Br


title: Patient-derived cell line -H2-

description:
GSCs_RNAseq_1.xlsx
H2_S5

tag: molecular subtype/phenotypic state

value: Mesenchymal/Mesenchymal

value: Wild Type


title: Flag.Taf1.ESC cells. Ctrl_Taf1_ChIP_rep1


title: E4-3m-WT11-Br


title: Flag.Taf1.ESC cells. Ctrl_Taf1_ChIP_rep3


title: Flag.Taf1.ESC cells. Ctrl_Taf1_ChIP_rep4


title: Flag.Taf1.ESC cells. Ctrl_Taf1_ChIP_rep2


title: E4-19m-WT14-Br-N

value: 19 months


title: E4-3m-WT10-Br

value: brain


title: E4-3m-WT9-Br


title: Flag.Taf1.ESC cells. Ctrl_Taf1_ChIP_rep5

value: Flag (Sigma-Aldrich, 3165)


title: Flag.Taf1.ESC cells. A485_10uM_30min_Taf1_ChIP_rep1


title: dTAG.BRD4.ESC cells Ctrl_Input.


title: E4-3m-MUT13-Br

value: MRPS5 V338Y


title: Patient-derived GSC -BT13 shCD109 D6-

description:
GSCs_RNAseq_1.xlsx
BT_13_SHCD109_1_D5_S15

value: Classical/Astrocyte-like cell

tag: cell culture condition

value: serum-free DMEM/F-12 medium supplemented with 1 x B27 (both from Gibco), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 15 mM HEPES (all from Lonza), 0.02 μg/ml human EGF, and 0.01 μg/ml human FGF-basic.

value: short hairpin RNA targeting CD109, day 5 post silencing


title: dTAG.BRD4.ESC cells. Ctrl.Pol2 ChIP.

description: processed data file: ChIP.GFP.BRD4.ESC_Ctrl_TC0_Pol2.n2.rpkm.smooth.bw

value: Pol2 (BioLegend, 664912)


title: Upf1_S-phase_2_22032011

type: genomic

city: Edgebaston

first: Saverio

last: Brogna

state: West midlands

address: School of Biosciences, University of Birmingham

department: School of Biosciences

institute: University of Birmingham

description: ChIP-DNA

hyb_protocol: Fragmented and labelled DNA samples were hybridized according to the protocol described by the GeneChip® Hybridization, Wash, and Stain Kit according to Affymetrix specifications.

scan_protocol: Hybridization signal produced from tiling arrays was detected with a GeneChip® Scanner 3000 7G and .CEL files (The CEL file stores the results of the intensity calculations on the pixel values of the DAT file.

data_processing:
Data processed using custom scripts, initially a matlab script using the "Bioinformatics Toolbox" to process raw data, then R scripts to carry out noise correction, gene expression value calculation, normalisation and finally correlations with downloaded datasets.
Table with values corresopnding to correlation plots in figure 2A and 2B. Each row corresponds to a different gene and each column to different datasets (log(FPKM+1) values from downloaded processed RNA-seq data (GSM2803075 and GSM2803077), gene expression values from downloaded Pol2 ChIP-chip data (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-18/), assynchronous and S-phase Upf1 gene expression values from raw data described here, normalised using control files).

label: biotin

organism: Schizosaccharomyces pombe

label_protocol: amplified ChIP DNA was fragmented and labelled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (P/N 900812).

growth_protocol: 2 ml pre-culture of tested strain was grown over night. Next day, appropriate amount of over night grown pre-culture was added to 100 ml of YES media, the volume of cells inoculated should be such that the culture reaches the desired cell density next morning

extract_protocol: Phenol chloroform

treatment_protocol: First in small start-up culture, 1-2 ml culture of cdc25-22 was grown overnight at 25°C in shaking air incubator.   Next day two cdc25-22 culture (biological replicates) were grown in 50 ml YES media in a 500 ml flask at 25°C to 2 x 106 cells/ml.  3. The cultures were transferred to a 37°C shaking air incubator for 3.5 hr to arrest.   4. 2 μl of the cultures were examined under the microscope for cell cycle arrest at 3 and 3.5 hr, more than 80% cells should be elongated and stuck in G2 phase after 3.5 hr.   5. Cell number was counted with a hemocytometer to 2 x 106 cells/ ml.   6. Cultures were removed from 25°C incubator at 60 min after release and fixed with formaldehyde for ChIP at S phase. Cell cycle synchrony was monitored every time by visualization under microscope before fixing the cells. Typically more than 80% of the cells should be in a specific cell cycle.

value: S phase syncronisation


title: CONTROL

description: Input DNA

source_name: CONTROL


title: SB_Pombe_Control_04082008

description: Input DNA


title: dTAG.BRD4.ESC cells. Cells were tereated with dTAG13 for 120min . Pol2 ChIP.

description: processed data file: ChIP.GFP.BRD4.ESC_dTAG13_TC120_Pol2.n2.rpkm.smooth.bw

value: ES cells

value: Brd4-dTAG cells were treated with dTAG13 for 120min


title: ChIP_input

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

description: Immunoprecipitated DNA

data_processing:
Demultiplexing was performed with bcl2fastq2-2.18.2, adaptater trimming with Cutadapt 1.15.
Qualities of fastq were checked with FastQC v0.11.5.
A specific trimming was performed with perl (for R1 : prinseq-lite.pl -fastq fileR1.fastq -trim_left 5 ; for R2 : perl prinseq-lite.pl -fastq fileR2.fastq -trim_ns_left 1 and then perl prinseq-lite.pl -fastq fileR2.fastq -trim_tail_left 4 ).
To associate the pairs before the mapping, python was used fastqCombinePairedEnd.py fileR1.fastq fileR2.fastq.
Map Bowtie bwa-0.6.2
peaks were called using MACS2 tool (Galaxy tool version version 2.1.1.20160309.4) with the following setting: Set lower mfold bound  5, Set upper mfold bound  50, Band width for picking regions to compute fragment size  340
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig

source_name: ovarian granulosa cells

growth_protocol: Cells were transiently transfected in 2 150-mm plates with 450 pmoles of a pool of 3 different siRNAs against Esr2 (Dharmacon, ON-TARGETplus siRNAs, pool KD1: J-040709-06-0005, J-040709-07-0005, J-040709-08-0005 and KD2: J-040709-06-0005, J-040709-08-0005, J-040709-09-0005) or an equal amount of the non-targeting/scrambled siRNA (Dharmacon, D-001810-10-05) using Lipofectamine RNAiMax (Thermo Fisher Scientific). Cells are pooled before ChIP experiment.

extract_protocol:
ChIP-IT High Sensitivity kit (Active Motif, Carlsbad, CA, USA) according to manufacturer recommendation
DNA SMART ChIPseq Kit (Takara Bio, USA) according to manufacturer recommendation with 18 PCR cycles amplification

treatment_protocol: Lipofectamine RNAiMax

tag: cells

value: primary ovarian granulosa cells

tag: strain

tag: gender

value: female

tag: chip antibody


title: ChIP_FOXL2_siESR2

description: Immunoprecipitated DNA

tag: treatment

value: anti-FOXL2 (home-made, directed against C-terminal hexadecapeptides WDHDSKTGALHSRLDL corresponding to human FOXL2 protein)


title: WT2

city: Montreal

first: David

last: Hipfner

state: QC

address: 110, ave des Pins O

country: Canada

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.8
The quality of the raw reads was assessed with FASTQC v0.11.8
The reads were aligned to the dm6 reference genome with STAR v2.7.6a
Raw counts were computed using FeatureCounts v1.6.0 based on Flybase Drosophila melanogaster reference genome r6.38
Raw counts were normalized using FPKM method implemented in DESeq2 R package.
Genome_build: dm6
Supplementary_files_format_and_content: FPKM normalized count

organism: Drosophila melanogaster

source_name: w;apGAL4/+ wing discs

growth_protocol: larvae were raised under uncrowded conditions at 25 degrees C on standard medium until wandering third instar stage, approximately 5 days after egg laying

extract_protocol:
Wing discs were dissected for 20 min, snap-frozen in liquid nitrogen, and stored at -70°C. Total RNA was isolated from 100-120 imaginal discs per sample using TRIzol reagent.
Illumina TruSeq RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

value: wild type


title: dTAG.BRD4.ESC cells. Cells were tereated with dTAG13 for 90min_followed by 10uM A485 treatment for 30min. Pol2 ChIP.

description: processed data file: ChIP.GFP.BRD4.ESC_dTAG13_TC90_A485_10uM_TC30_Pol2.n2.rpkm.smooth.bw

tag: cell line

tag: antibody

value: Brd4-dTAG cells were treated with dTAG13 for 90min, followed by 10uM A485 treatment for 30min.


title: WT3

tag: genotype/variation


title: gbpl3-5_rep2

city: West Haven

first: John

middle: David

last: MacMicking

state: CT

address: 850 West Campus Dr.

department: Microbial pathogenesis and immunobiology

institute: Yale University

description: harvest time: 10:00am

data_processing:
Illumina bcl2fastq2 version 2.17.1.14 and the RTA module version 2.7.7 were used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality reads using Flexbar, then mapped to Arabidopsis TAIR10 whole genome using HISAT2 v2.1.0 with default settings
SAMtools version 1.5 was used to convert SAM files, sort and index BAM files
Read counts were generated for each gene using HTseq-count version 0.9.1 with parameters: order = position, mode = union, stranded = no
R package DESeq2 version 3.9 was used to determine differentially expressed genes
Genome_build: TAIR10
Supplementary_files_format_and_content: CSV files include counts per gene for each Sample

source_name: Rosette Leaf

growth_protocol: Short-day grown (12 h light/12 h night)

extract_protocol:
Leaves were collected, flash frozen in liquid nitrogen, ground into fine power and RNA was extracted using Trizol reagent with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: developmental stage

value: three week old

tag: tissue

value: Leaf


title: ChIP_FOXL2_scr_30h

description: Immunoprecipitated DNA


title: gbpl3-5_rep1

description: harvest time: 10:00am


title: gbpl1-1_rep1

description: harvest time: 10:00am


title: wt_rep2

description: harvest time: 10:00am


title: siFOXL2_3_30h

data_processing:
Demultiplexing using bcl2fastq2 V2.15.0
adapters were removed with Cutadapt1.9.1.
Only reads longer than 10pb were kept for analysis (about 10,000,000 reads per sample). Reads mapped on the mouse genome (mm10) with TopHat2.
Mapped reads were assigned to features with features count (1.5.0-p2)
differential analysis  performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

extract_protocol:
RNA extraction was performed 30h after transfection, following the TRI-reagent supplier’s instructions (MRC). 1.3 µg of total RNAs underwent high throughput sequencing
Directional RNA-Seq Libraries were constructed using the TruSeq mRNA Stranded library prep kit (Illumina), following the manufacturer’s instructions. Final library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were pooled in equimolar proportions and sequenced on Single Read 75pb runs, on an Illumina NextSeq500 instrument, using NextSeq 500 High Output 75 cycles kits.

value: 8-week-old female


title: siFOXL2_2_54h


title: siFOXL2_3_54h


title: siFOXL2_2_30h


title: gbpl1-1_rep2

description: harvest time: 10:00am


title: wt_rep1

description: harvest time: 10:00am


title: ESC_A485_10uM_30min_Oct4_ChIP_rep4

tag: cell type

value: OCT4 (abcam, ab181557)

value: 10uM A-485 for 30 min.


title: Assynchronous_Upf1_1_04082008

description: ChIP-DNA


title: siFOXL2_1_30h

tag: age


title: TRAPCORARCONSLX

first: Siobhan

last: Brady

address: 451 Health Sciences Dr

department: Genome Center and Plant Biology

institute: University of California Davis

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z15
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1

data_processing:
Library strategy: TRAP-seq
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

organism: Solanum lycopersicum

source_name: Adventitious roots of 1-month-old plants.

growth_protocol:
growth protocol 1: Transgenic Solanum lycopersicum seeds from transgenic lines were surface sterilized in 50% (v/v) bleach solution for 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Seven seeds were plated on 10 cm x 10 cm plates containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose and germination was scored daily after plating. Seedlings were grown for 3-5 days after germination in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 ?Em-2s-1) and 1cm primary root tips were harvested and flash frozen into liquid nitrogen.
growth protocol 2: 1-month-old control plants: Transgenic Solanum lycopersicum seeds were germinated on 1xMS media with 1% sucrose and 200ug/ml Kanamycin. After 7d, seedlings were transplanted into pots with Turface Athletic Profile Field & Fairway clay substrate (Turface Athletics, 2017) that was pre-wetted with a nutrient water solution containing 4% nitrogen, 18% phosphoric acid, and 38% soluble potash. Plants were grown in a randomized design for 31 d in a Conviron Growth Chamber at 22°C, 70% RH, 16/8 h light/dark cycle, light intensity of 150-200 µmol/m2/s.
growth protocol 3: Field: Transgenic Solanum lycopersicum seeds were germinated on 1xMS plate (0-7d), screened for correct GFP pattern from root tip, transplanted on soil and grown in a growth chamber for one week (7-14d) ,  grown in a screenhouse for two weeks (14-28d), and finally transplanted into the field and grown for one month (29-60d)  with drip watering and weekly removal of flower buds.
growth protocol 4: Rice seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. Seedlings were grown on plates (10 cm x 10 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 ?Em-2s-1). The whole root system was placed immediately into liquid nitrogen upon harvesting.

extract_protocol:
extract protocol 1: Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al, 2019).
extract protocol 2: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al, 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of  streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet  to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
extract protocol 3: For Rice: TRAP was performed as previously described (Reynoso et al, 2019)
library construction protocol 1: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.
library construction protocol 2: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.

tag: cultivar

tag: line

value: 1 month

value: Adventitious roots


title: siFOXL2_1_54h


title: GBPL3-OX_rep1

description: harvest time: 10:00am

tag: genotype


title: TRAPCORARCONSLP

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z14
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: GBPL3-OX_rep2

description: harvest time: 10:00am


title: siESR2_2_30h


title: ChIP_FOXL2_scr_54h

description: Immunoprecipitated DNA


title: siESR2_3_30h


title: WT1


title: TRAPCORLRCONSLX

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z05
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1

source_name: Lateral roots at the depth of 6-12 cm of 1-month-old plants.

value: Lateral roots


title: TRAPCORLRCONSLP

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z04
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: TRAPCORLRCONSLO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z01
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: TRAPCORARCONSLZ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z16
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: TRAPMCOARCONSLL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
X25
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: TRAPMCOLRCONSLL

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
X19
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: scr3_54h


title: siESR2_1_30h


title: TRAPMCOLRCONSLE

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
X09
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: MCO-TR-Rep6

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
X3
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1

source_name: Whole root system of 2-month-old tomato plants.

value: 2 months

value: Whole root system


title: S07_01_B1 Adaptive trNK

city: Stockholm

first: Jakob

last: Michaelsson

address: Alfred Nobels allé 8, ANA Futura, level 7

country: Sweden

institute: Karolinska Institutet

description:
210210__GEO_counts.csv
S07_01_B1

data_processing:
Read pairs were trimmed from Illumina adapters using cutadapt (version 1.14), and UrQt was used to trim all bases with a phred quality score below 20
Read pairs were aligned to the protein coding sequences of the human transcriptome (gencode.v26.pc_transcripts.fa) using Salmon (version 0.8.2) and gene annotation using gencode.v26.annotation.gtf
Genome_build: Homo sapiens, GRCh38
Supplementary_files_format_and_content: Comma-separated text file include counts for each sample

source_name: Lung

extract_protocol:
Cells were sorted directly into lysis buffer (0.2% Triton X-100, 2.5uM oligo-dT (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), 2.5mM dNTP, RNAse Inhibitor (Takara), and ERCC RNA spike in controls (Ambion)) in a 96-well V-bottom PCR plate.
Standard SMART-Seq2 protocol with 22 cycles of cDNA amplification. Sample quality was determined using a bioanalyzer (Agilent, High Sensitivity DNA chip). 5ng of amplified cDNA was taken for tagmentation using a customized in-house protocol) and Nextera XT primers.

treatment_protocol: Fresh human lung tissue was digested using collagenase II and DNAse and enriched for lymphocytes by density gradient centrifugation using Ficoll. Peripheral blood mononuclear cells from healthy donors were isolated from buffy coats by density gradient centrifugation using Ficoll. All cells were cryopreserved in FCS with 10% DMSO in liquid nitogen until sorting of NK cell subsets by FACS.

value: Adaptive trNK

tag: donor

value: B

tag: replicate


title: scr3_30h

value: primary ovarian granulosa cells


title: S05_01_A1 Adaptive trNK

description:
210210__GEO_counts.csv
S05_01_A1

value: A


title: S25_02_D2 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_D2

source_name: Blood

value: CD49a+NKG2C+ CD56bright

value: D


title: S05_01_A2 Adaptive trNK

description:
210210__GEO_counts.csv
S05_01_A2


title: MCO-TR-Rep5

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
W2
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: scr2_54h


title: TRAPCORLRCONSLZ

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z06
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: S25_02_D1 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_D1


title: MCO-TR-Rep2

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
T2
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: S07_01_B2 Adaptive trNK

description:
210210__GEO_counts.csv
S07_01_B2


title: TRAPCORARCONSLO

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Z13
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: MCO-TR-Rep4

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
V1
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: MCO-TR-Rep1

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
S1
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: S15_02_D2 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_D2

value: CD49a-NKG2C- CD56bright


title: scr2_30h


title: MZ-TR-Rep6

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
R
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: scr1_54h


title: TRAPMCOLRCONSLAA

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
X01
processed data file: Tomato_DWL_raw_counts.csv
protocols used: growth protocol 2, extract protocol 1 and library construction protocol 1


title: MZ-TR-Rep5

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
Q
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: S15_02_D1 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_D1


title: S15_02_G02 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_G02

value: G


title: S15_02_G01 CD49a-NKG2C- CD56bright

description:
210210__GEO_counts.csv
S15_02_G01


title: S25_02_G01 CD49a+NKG2C+ CD56bright

description:
210210__GEO_counts.csv
S25_02_G01


title: MZ-TR-Rep3

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
O
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: MZ-TR-Rep2

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
N
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: MZ-TR-Rep4

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
P
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: X35S-TR-Rep5

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
E
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: EN-TR-Rep6

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
L
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: EN-TR-Rep5

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
K
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: EN-TR-Rep2

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
H
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: EN-TR-Rep1

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
G
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: X35S-TR-Rep6

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
F
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: X35S-TR-Rep3

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
C
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1


title: X35S-TR-Rep4

description:
Solanum lycopersicum cv. M82
Random primed libraries
TRAP RNA
D
processed data file: Tomato_Field_raw_counts.csv
protocols used: growth protocol 3, extract protocol 1 and library construction protocol 1