title: WT_3h_IP_rep1


title: Subject_06_PolyIC_Cord

status: Public on Aug 24 2022

type: SRA

city: Perth

first: James

last: Read

state: WA

address: 15 Hospital Ave.

country: Australia

institute: Telethon Kids Institute

library_source: transcriptomic

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: CBMC_genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data), with transcripts as rows and samples as columns. Transcript information (e.g. EnsembleID, gene symbol) are supplied in the final columns. CBMC_corrected_counts.txt contains a matrix of VST transformed and batch/RUV corrected gene counts, formatted as the raw gene count file.

molecule: total RNA

organism: Homo sapiens

source_name: CBMC

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cryopreserved cord blood mononuclear cells were thawed and stimulated with LPS, Imiquimod or Poly(I:C), of left untreated, and cultured at 37oC (5% CO2) for 18 hrs.

tag: stimuli

value: PolyIC

value: Cord

tag: Sex

value: Female

value: Yes

value: No


title: CD-mock

city: Daejeon

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Using cellranger 'mkfastq' module to demultiplexes raw base call files generated by Illumina sequencers into FASTQ files
Using cellranger 'count' to perform alignment, filtering, barcode counting and UMI counting
Assembly: Mm10
Supplementary files format and content: h5 file including matrix, barcodes, and features

organism: Mus musculus

source_name: brain

extract_protocol:
Isolate single cells from mouse brain tissues by using percoll gradient and sort CD45-positive immune cells by FACS
Chromiun Single Cell 3' RNA library v3

treatment_protocol: 4 week-aged mice were fed with control diet or high-salt diet and brain tissues were harvested after 4 weeks.

tag: tissue

value: brain

tag: strain

tag: treatment

value: control diet


title: HSD-mock

value: high-salt diet


title: 12-T

city: Taipei

first: Yen-Chen

last: Chang

address: No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (R.O.C.)

country: Taiwan

institute: Graduate institute of molecular and comparative pathobiology, School of veterinary medicine, National Taiwan University

library_source: genomic

data_processing:
The raw sequencing reads were merged, filtered, and generated to obtain effective reads. Assembled reads were assigned to the corresponding samples using the default parameters. Thereafter, reads shorter than 293 bp or longer than 455 bp were removed, and 95% of the reads were retained. All reads were then aligned using NAST-based sequence alignment based on SILVA alignment. Reads that did not align with the anticipated region of the reference alignment and chimeric sequences identified using the UCHIME algorithm were removed. All reads were classified using a Bayesian classifier in the Silva database.
Library strategy: DNA-Seq

molecule: genomic DNA

organism: Bacteria

source_name: feline fecal sample

extract_protocol:
For each sample, 200 mg of the homogenized fecal samples were used for DNA extraction using a commercial stool extraction kit (QIAamp Fast DNA Stool Mini Kit, QIAGEN, Hilden, Germany), following the manufacturer’s instructions.
The Celero DNA Seq Library Preparation Kit (NuGEN) was used for DNA sequencing and library construction, followed by 2 x 301bp paired-end sequencing using the MiSeq system.

value: feline fecal sample

value: collected feces after oral BLFP administration


title: 12-C

department: Graduate institute of molecular and comparative pathobiology

value: collected feces before oral BLFP administration


title: IL6_hep_rep2

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm.
Htseq-count algorithm was used to count reads mapped to each gene uniquely.
DESeq2 R package was used to detect differentially expressed genes (DEGs) between groups.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver hepatocyte

extract_protocol:
Liver was perfused using three-steps methods. Cells in liver were sorted by BD FACSAriaIII. 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

treatment_protocol: Mice was fed with normal and DDC diet for 1 week for isolation of immune cells. And, for discovering IL-6/STAT3 signaling in hepatocyte, mice was treated with DDC diet or IL-6 via HTVi of IL6 plasmids in physiological saline (5ug/mL). To deplete STAT3 in hepatocyte, mice was tail-vein injected AAV-TBG-Cre with the titer of 2.5x10^11, while control mice was injected AAV-TBG-GFP.

tag: genotype

value: WT

value: HTVi of IL6 plasmids for 1 week

value: liver

tag: cell type

value: hepatocyte


title: 11-T


title: IL6_hep_rep1


title: Subject_06_LPS_Cord

value: LPS


title: GFP_hep_rep2

value: HTVi of GFP plasmids for 1 week


title: Subject_06_IMIQ_Cord

value: IMIQ


title: GFP_hep_rep1


title: Subject_05_PolyIC_Cord

value: PolyIC

value: Cord


title: 11-C


title: Subject_07_CTRL_Cord

value: CTRL

value: Male

value: Yes


title: Subject_06_CTRL_Cord

value: Female

value: No


title: DDC1w_liver_Ly6Chigh_monocyte_rep1

source_name: liver monocyte

value: DDC diet for 1 week

value: monocyte


title: DDC1w_liver_Ly6Clow_monocyte_rep2


title: 9-T

value: feline fecal sample

value: collected feces after oral BLFP administration


title: Subject_05_IMIQ_Cord


title: 10-T


title: 3mmPi-2

city: Suita

first: Takuo

last: Kubota

state: Osaka

address: 2-2, Yamadaoka

department: Pediatrics

country: Japan

institute: Osaka University Graduate School of Medicine

description:
hBM-MSCs, 3mM Pi, Day7
3mmPi-2

data_processing:
The constructed library was then sequenced using 2×101-bp paired end reads on the HiSeqX platform (Illumina, USA).
The adapter trimming was conducted using trimmomatic (version 0.36).
Trimmed sequence reads were mapped to GRCh38 with only protein coding by adopting quasi-mapping method by salmon (0.14.1) with gcBias option.
The outputs were converted to count date using tximport (version 1.16.1) with scaled TPM option.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include scaled TPM values for each Sample

source_name: hBM-MSCs

growth_protocol: hBMMSCs were maintained in αMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (74106, Qiagen, USA) on day 7 and RNA samples were subjected to an RNA-seq analysis.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA following manufacture's protocols.

treatment_protocol:
osteogenic differentiation was induced by treatment of 100 nM dexamethasone (Wako), 50 μM L-ascorbic acid (Sigma-Aldrich, USA) and a phosphate source,
Osteogenic induction medium which contains α-MEM supplemented with 10% FCS, 1% P/S, 100 nM dexamethasone (Wako), 50 μM L-ascorbic acid (Sigma-Aldrich, USA) and a phosphate source,10mM β-glycerophosphate (GP) (Sigma-Aldrich, USA or 3 mM Pi sodium phosphate (Na2HPO4; Sigma-Aldrich) was used as the phosphate source.

tag: cell line

value: hBM-MSCs

value: mesenchymal stem cells

value: WT

value: osteogenic differentiation(3mM Pi)

tag: time

value: Day 7


title: 3mmPi-3

description:
hBM-MSCs, 3mM Pi, Day7
3mmPi-3

value: osteogenic differentiation (3mM Pi)


title: 9-C

value: collected feces before oral BLFP administration


title: Subject_05_LPS_Cord

value: LPS

value: Cord


title: DDC1w_liver_Ly6Clow_monocyte_rep1

value: liver


title: Subject_05_CTRL_Cord

value: CTRL


title: 8-T


title: DDC1w_liver_Ly6Chigh_monocyte_rep2


title: DDC1w_liver_Neutrophil_rep2

source_name: liver neutrophil

value: neutrophil


title: 10-C


title: Subject_04_IMIQ_Cord

value: IMIQ

value: Male

value: No


title: D-3

description:
hBM-MSCs, GP, Day7
D-3


title: 3mmPi-1

description:
hBM-MSCs, 3mM Pi, Day7
3mmPi-1


title: 8-C

value: feline fecal sample


title: D-2

description:
hBM-MSCs, GP, Day7
D-2


title: D-1

description:
hBM-MSCs, GP, Day7
D-1


title: DDC1w_liver_T_rep2

source_name: liver T cell

value: DDC diet for 1 week

value: T cell


title: Subject_04_LPS_Cord


title: DDC1w_liver_T_rep1


title: DDC1w_liver_Neutrophil_rep1


title: Subject_04_PolyIC_Cord

value: PolyIC


title: 6-T

value: collected feces after oral BLFP administration


title: Normal_liver_Macrophage_rep2

source_name: liver macrophage

value: WT

value: Normal diet

value: macrophage


title: M-1

description:
hBM-MSCs, MM, Day7
M-1

value: hBM-MSCs

value: mesenchymal stem cells

value: maintenance culture

value: Day 7


title: Subject_04_CTRL_Cord

value: CTRL

value: Cord


title: 7-T


title: M-3

description:
hBM-MSCs, MM, Day7
M-3


title: Tub01: Fly Hemocyte Control Replicate1

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

country: USA

institute: University of Maryland School of Medicine

description: Fly Hemocyte Control Replicate1

data_processing:
RNA-Seq mapping and gene level quantification were performed by Novogene (Beijing, China).
HISAT2 2.0.5 (PMID: 31375807) was used for mapping the short reads with the --dta and --phred33 options.
The mapped reads were counted using featureCounts 1.5.0-p3 with its default parameters (PMID: 24227677).
For mapping and counting the reads, the Drosophila gene annotation from Ensembl (Release 100, corresponding to Flybase 6.28) was used.
Genome_build: Berkeley Drosophila Genome Project (BDGP) reference genome release 6
Supplementary_files_format_and_content: Tab-delimited text files include Flybase gene IDs and read counts for each sample.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Hemocyte

growth_protocol: All flies were raised at 25°C on standard Drosophila medium (Meidi Laboratories).  We used the y[1] M{RFP[3xP3.PB] GFP[E.3xP3]=vas-int.Dm}ZH-2A w[*]; M{3xP3-RFP.attP}ZH-86Fb flies (Bloomington Drosophila Stock Center ID BL-24749) to generate the transgenic flies.

extract_protocol:
For each heart sample, one-week old adult fly hearts (total 50) were dissected and collected into ice-cold TRIzol LS reagent. For blood samples, hemocytes were collected into artificial hemolymph from ~15 third instar larvae and lysised by TRIzol LS reagent. Total RNAs were extracted according to the manufacturer's instructions (Direct-zol RNA Microprep, Zymo Research). RNA quality and concentration were checked by agarose gel electrophoresis, NanoDrop 8000 Spectrophotometer and Agilent 2100.
RNA libraries were prepared by Novogene (Beijing, China) using standard Illumina protocols.

tag: developmental stage

value: Third instar larvae


title: Subject_03_CTRL_Cord

value: Female

value: Yes


title: Subject_03_PolyIC_Cord

value: No


title: Normal_liver_Macrophage_rep1

value: liver


title: 5-T

value: feline fecal sample


title: Subject_03_LPS_Cord

value: LPS


title: 6-C

value: collected feces before oral BLFP administration


title: 4-T

value: collected feces after oral BLFP administration


title: Tub02: Fly Hemocyte Control Replicate2

description: Fly Hemocyte Control Replicate2


title: Subject_03_IMIQ_Cord

value: IMIQ


title: DDC1w_liver_Macrophage_rep2

value: WT

value: DDC diet for 1 week

value: macrophage


title: DDC1w_liver_Macrophage_rep1


title: Subject_02_PolyIC_Cord

value: PolyIC

value: Male


title: 7-C


title: 5-C


title: 4-C


title: LPLC_H3K27ac

data_processing:
Basecalls performed using CASAVA version 1.4
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations,Duplicate reads were removed using DeepTools v2.1.0
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5 and peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to chrX, chrY, chrM.
Raw signals from individual samples were converted to signal files (bigWig) using DeepTools v2.1.0
signals were quantile-normalized using Haystack, with 25-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Liver were perfused and hepatocytes were isolated and lysed. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified ChIP DNA was used to prepare sequencing libraries via NEBNext Ultra DNA Library Prep Kit for the Illumina (E7370).

value: Sox9-CreERT2; Rosa-LSL-tdTomato

value: DDC diet feeding

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

value: hepatocyte


title: Subject_02_IMIQ_Cord

value: Cord

value: Yes


title: Orf7a03: Fly Hemocyte Orf7a Replicate3

description: Fly Hemocyte Orf7a Replicate3

value: Third instar larvae

value: Tub-Gal4 > UAS-Orf7a


title: Orf7a02: Fly Hemocyte Orf7a Replicate2

description: Fly Hemocyte Orf7a Replicate2


title: M-2

description:
hBM-MSCs, MM, Day7
M-2

value: hBM-MSCs

value: mesenchymal stem cells

value: maintenance culture

value: Day 7


title: Hepatocyte_H3K27ac

value: WT

value: normal diet feeding

value: liver


title: 3-T

value: feline fecal sample

value: collected feces after oral BLFP administration


title: 3-C

value: collected feces before oral BLFP administration


title: Hepatoblast_H3K27ac


title: Subject_02_LPS_Cord

value: LPS

value: Male


title: Subject_02_CTRL_Cord

value: CTRL


title: Non-SMC#2

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
ATAC-seq reads were aligned to the mouse reference genome mm10 using bowtie2 version 2.3.4 with default parameters.
Peaks calling were performed using macs2 version  2.1.1 with parameters -g hs -f BAMPE --shift -100 --extsize 200 -q 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: small cell lung cancer

growth_protocol: All cell lines were incubated at 37℃ in 5% CO2 with RPMI1640 plus 10% FBS, and 10% Penicillin-Streptomycin

extract_protocol:
DNA of SMC and Non-SMC were extracted according to Illumina's instructions
Libraries were prepared according to Illumina's instructions

value: mixed genetic background (C57Bl/6, Balb-c, and S129)

value: lung

value: untreated


title: 2-T


title: Subject_01_IMIQ_Cord

value: IMIQ

value: Cord

value: Female

value: No


title: Hand_rep2: Fly Heart Control Replicate 2

description: Fly Heart Control Replicate 2

source_name: Heart

value: One week old adult fly

value: 4xHand-Gal4 > w1118


title: Nsp6_rep2: Fly Heart Nsp6 Replicate 2

description: Fly Heart Nsp6 Replicate 2

value: 4xHand-Gal4 > UAS-Nsp6


title: 1-T


title: Hand_rep1: Fly Heart Control Replicate 1

description: Fly Heart Control Replicate 1


title: Subject_01_PolyIC_Cord

value: PolyIC


title: Subject_01_CTRL_Cord


title: 2-C

value: feline fecal sample


title: SMC#2


title: Non-SMC#1


title: 1-C


title: SMC#1


title: Nsp6_rep1: Fly Heart Nsp6 Replicate 1

description: Fly Heart Nsp6 Replicate 1


title: Orf7a01: Fly Hemocyte Orf7a Replicate1

description: Fly Hemocyte Orf7a Replicate1

value: Third instar larvae

value: Tub-Gal4 > UAS-Orf7a


title: spatial transcriptomics data of biopsy tissue from PCNSL patient 7

status: Public on Aug 23 2022

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

data_processing:
Raw bcl files were de-multiplexed using the cellranger or spaceranger mkfastq pipeline (cellranger v6.1, spaceranger v1.3)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count or spaceranger count pipeline with default parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger/spaceranger output format

source_name: biopsy

extract_protocol:
Biopsy samples were obtained using a frame-based (Leksell Stereotactic System, Elekta Instrument AB, Stockholm, Sweden) or a frameless image-guided (VarioGuide, Brainlab AG, Munich, Germany) stereotactic system. In all cases, the target point was defined within the contrast-enhancing, non-necrotic lymphoma-suspicious lesion.
The samples were loaded onto the 10x Genomics Chromium Single Cell Controller, using the Chromium Single Cell 3' Library & Gel Bead Kit v2-3. B cells were positively selected from blood-derived cells, using CD20-microbeads according to the manufacturer's protocol (Miltenyi). Biopsy-derived cells and B cell enriched blood cells in patient 1 were processed using CITE-seq supported scRNA-seq, all other samples were processed with standard scRNA-seq.  5µm FFPE sections of human PCNSL samples were placed on a Visium Gene Expression (GEX) slide (10x Genomics), which incorporates about 5000 molecularly barcoded and spatially encoded capture spots. Deparaffinization, hematoxylin and eosin (H&E) staining, and decrosslinking were performed according to the protocol of Visium Spatial Gene Expression for FFPE (10x Genomics).

value: biopsy tissue

tag: diagnosis

value: PCNSL

tag: type of library

value: spatial

tag: subject id


title: spatial transcriptomics data of biopsy tissue from PCNSL patient 2


title: C. briggsae PRG-1 input replicate 1

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

description: C. briggsae PRG-1 input replicate 1

data_processing:
Base calling and fastq file was done using Illumina Software.
Reads were trimmed of adapters and filtered of poorly sequenced reads was doen with TrimGalore.
Reads passing adapter trimming and quality control were collapsed using custrom shell scripts.
Processed reads were aligned using Bowtie1 Software.
Alignments were further processed using custom python scripts
Assembly: WS279
Supplementary files format and content: fasta file. Header is the sequence and count separated by a colon.

organism: Caenorhabditis briggsae

source_name: Whole Animal

growth_protocol: Synchronised L1 plated on 135 mm NGM plates seeded with OP50 and at 20°C.

extract_protocol:
Approximately 100,000 synchronized L1 animals were plated on 135 mm NGM plates seeded with OP50 and grown at 20 °C until the animals reached gravid adult stage. Gravid adult populations were harvested using M9, and subsequently suspended in Trizol. Worms were lysed using the Fisherbrand Bead Mill 24 homogenizer, bromochloropropane was added to the lysis to perform RNA extraction. Isopropanol was then used to precipitate RNA from the aqueous phase. Small RNAs were isolated from total RNAs using the miRVana miRNA isolation kit (Thermo Fisher Scientific) according to the manufacturers protocol.
Small RNA samples from wild-type and mutants were first incubated with a recombinant 5’ polyphosphatase PIR-1 which removes the γ and β phosphates from 5´-triphosphorylated RNAs (Li et al. 2020; Pastore et al. 2021). The resulting monophosphorylated RNAs were ligated to the 3’ adaptor (5’rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/3’, IDT) using T4 RNA ligase 2 in the presence of 25% PEG8000 (NEB) at 15 °C overnight. The 5’ adaptor (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to the product using T4 RNA ligase 1 (NEB) at 15 °C for 4 hours. The ligated products were converted to cDNA using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). The cDNAs were amplified by PCR using Q5 High-Fidelity DNA polymerase (NEB), and the libraries were sequenced on an Illumina Novaseq platform (SP 2 X 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: Whole Animal


title: C. briggsae PRG-1 input replicate 2

description: C. briggsae PRG-1 input replicate 2


title: C. briggsae PRG-1 IP replicate 2

description: C. briggsae PRG-1 IP replicate 2


title: single-cell BCR seq data of biopsy material from PCNSL patient 2

value: biopsy-derived cells

value: BCR


title: single-cell BCR seq data of blood from PCNSL patient 2

source_name: blood

value: B cell-enriched blood cells


title: spatial transcriptomics data of biopsy tissue from PCNSL patient 1


title: C. briggsae PRG-1 IP replicate 1

description: C. briggsae PRG-1 IP replicate 1


title: Subject_01_LPS_Cord

value: LPS

value: Cord


title: spatial transcriptomics data of biopsy tissue from PCNSL patient 3


title: C. briggsae smRNA sequencing prg-1 replicate 1

value: prg-1 mutant


title: C. briggsae smRNA sequencing wild type replicate 2

value: wild type


title: C. briggsae smRNA sequencing wild type replicate 1


title: 2D_12h_glucose

type: RNA

city: Córdoba

first: Muñoz Marin

last: Maria del Carmen

state: Córdoba

address: Campus Rabanales

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

hyb_protocol: The hybridization of cDNA samples (2.0 mg of ds-cDNA) to the microarray was done with Gene Expression Hybriditation kit (Cat#5188-5242) at “Centro de Investigación Principe. Slides were scanned immediately after washing (Gene Expression wash buffer Cat#5188-5377) on the Agilent DNA Microarray Scanner using one color scan setting for two 8x60k array slides and one color scan setting for 4x180k array slide. It was done at the facility “Centro de Investigación Principe Felipe” (Valencia, Spain). Felipe” (Valencia, Spain) according to the protocol in Agilent Technology for arrays.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 060208_G2_D_F_20130916) to obtain background subtracted and spatially detrended Processed Signal intensities. It was done at “Centro de Investigación Principe

data_processing: Transcription values for each gene were obtained using median polish summarization and values were normalized using quantile normalization. The transcription values of 4h control, 4h glucose, 12h control, 12h glucose, 24 h control and 24h glucose of both diel cycles are the median transcription of two different technical replicates, except some of  the samples where there were not sufficient RNA in the second technical replicate.

organism: Prochlorococcus

source_name: seawater, Second diel cycle, 12h incubation with glucose, replicate 1

label_protocol: The labeling of cDNA samples (2.0 mg of ds-cDNA) to the microarray was done with SureTag DNA labeling kit (Cat#5190-3400) at the facility “Centro de Investigación Principe Felipe” (Valencia, Spain) according to the protocol in Agilent Technology for arrays.

growth_protocol: For molecular approaches seawater was collected into 2 L PC-bottles in triplicate control and glucose amended samples. The glucose treatments were spiked with 0.1 µM of non-radiolabeled glucose and incubated alongside the controls (unamended) in the on-deck incubators.

extract_protocol: RNA for Prochlorococcus was extracted using the Ambion RiboPure kit (Life Technologies, Grand Island, NY, USA) with modifications that included mechanical lysis using glass beads as described in Shilova et al. (2014). Extracted RNA was cleaned and concentrated with Zymo Research RNA Clean & Concentrator TM-5 (Irvine, CA, USA) and treated with DNase (Ambion Turbo-DNA-freeTM Kit, (Life Technologies, Grand Island, NY, USA) to remove genomic DNA. cDNA was synthesized from 400 ng RNA from each sample, which was then amplified using the TransPlex Whole Transcriptome Amplification kit (WTA-2, Sigma-Aldrich, St Louis, MO, USA) and antibody-inactivated hot-start Taq DNA Polymerase (Sigma-Aldrich). The amplified cDNA was purified with the GenElute PCR cleanup kit (Sigma-Aldrich).

treatment_protocol: For the first experiment (October 6th), surface seawater was sampled at noon, while for the second experiment (October 7th) surface seawater was collected at 16:00. In both experiments, the two treatments (glucose addition and controls in triplicate) were incubated for 4 h, 12 h and 24 h, with two replicate subsamples taken at each time point.   At each sampling time point, RNA and DNA samples were collected by filtering 4 L and 1 L of seawater, respectively onto 0.22 µm pore-size Sterivex cartridges (Millipore Corp., Billerica, MA, USA) using a peristaltic pump set at low rate to maintain low pressure. Filters were opened and carefully placed in sterile 2 ml bead-beating tubes with sterile glass beads and stored at -80 ºC until extraction.

tag: sample type

value: Environmental samples


title: 12h_2glucose

source_name: seawater, First diel cycle, 12h incubation with glucose, replicate 2


title: section D very small oocyte rep 2 [X. laevis]

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE (v. 0.36) . Ribosomal RNA sequences were removed using sortmerna (v. 2.1b) and the SILVA rRNA database (version 119). The X. laevis reads were then aligned to the X. laevis v9.1 genome Xenbase (http://www.xenbase.org/, RRID:SCR_003280; Fortriede et al., 2020) using STAR v2.5.2b (Dobin et al., 2013) and counted using htseq-count.
Normalized number of reads was generated using DESeq2.
Transcripts were removed that had zero counts in all samples.
Assembly: X. laevis v9.1 genome
Supplementary files format and content: Excel files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column. "xlaevis_non_normalized.xlsx" contains the non-normalized reads while "xlaevis_altered_magnitudes_per_section_and_stage_normalized.xlsx" contains the normalized reads for all samples (all oocyte sections). "xlaevis_total_altered_counts_per_stage_non_normalized.xlsx" contains the non-normalized reads while "xlaevis_total_altered_counts_per_stage_normalized.xlsx" the normalized reads for the total transcripts within the whole oocyte. "xlaevis_alteration_between_the_sections_at_big_stage_normalized.xlsx", "xlaevis_alteration_between_the_sections_at_medium_stage_normalized.xlsx", "xlaevis_alteration_between_the_sections_at_small_stage_normalized.xlsx", and "xlaevis_alteration_between_the_sections_at_very_small_stage_normalized.xlsx" contain the normalized reads at a given oocyte stage.

organism: Xenopus laevis

source_name: oocyte

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Minikit according to the manufacturer’s instructions. The concentration of total RNA was measured using a spectrophotometer (Nanodrop 2000, Thermo Scientific), and the quality of RNA was assessed using a Fragment Analyzer (AATI, Standard Sensitivity RNA analysis kit, DNF-471).
Samples were depleted using RiboCop rRNA Depletion kit (Lexogen) and libraries were prepared using SureSelect XT (Agilent). Library qualities were assessed using the Fragment Analyzer (AATI, NGS High Sensitivity kit (DNF-474) and the concentrations were determined by the Qubit 4 Fluorometer (ThermoFisher Scientific). Equimolar library pools were prepared and sequenced using two 2x80bp, NextSeq 500 runs.

value: oocyte

value: female

tag: source female

tag: oocyte stage

tag: oocyte size

tag: section

value: D

tag: biological replicate


title: section E very small oocyte rep 3 [X. laevis]

tag: Sex

value: E


title: 12h_1glucose

source_name: seawater, First diel cycle, 12h incubation with glucose, replicate 1

tag: treatment


title: section E very small oocyte rep 2 [X. laevis]


title: 2D_4h_1glucose

source_name: seawater, Second diel cycle, 4h incubation with glucose, replicate 1


title: 2D_4h_control

source_name: seawater, Second diel cycle, 4h incubation without glucose, replicate 1


title: C. briggsae smRNA sequencing prg-1 replicate 2

tag: tissue

tag: genotype


title: 4h_1glucose

source_name: seawater, First diel cycle, 4h incubation with glucose, replicate 1


title: 2D_4h_2glucose

source_name: seawater, Second diel cycle, 4h incubation with glucose, replicate 2


title: 4h_2glucose

source_name: seawater, First diel cycle, 4h incubation with glucose, replicate 2


title: 24h_1control

source_name: seawater, First diel cycle, 24h incubation without glucose, replicate 1


title: 24h_1glucose

source_name: seawater, First diel cycle, 24h incubation with glucose, replicate 1


title: 4h_1control

source_name: seawater, First diel cycle, 4h incubation without glucose, replicate 1


title: section D very small oocyte rep 3 [X. laevis]

tag: cell type


title: 4h_2control

source_name: seawater, First diel cycle, 4h incubation without glucose, replicate 2


title: 2D_12h_control

source_name: seawater, Second diel cycle, 12h incubation without glucose, replicate 1


title: 2D_24h_glucose

source_name: seawater, Second diel cycle, 24h incubation with glucose, replicate 1


title: section C very small oocyte rep 3 [X. laevis]

value: C


title: section A very small oocyte rep 3 [X. laevis]

value: A


title: section B very small oocyte rep 2 [X. laevis]

value: B


title: section A very small oocyte rep 2 [X. laevis]


title: section E very small oocyte rep 1 [X. laevis]


title: section B very small oocyte rep 3 [X. laevis]


title: section D very small oocyte rep 1 [X. laevis]


title: section C very small oocyte rep 2 [X. laevis]


title: 12h_control

source_name: seawater, First diel cycle, 12h incubation without glucose, replicate 1


title: section C small oocyte rep 5 [X. laevis]

value: small


title: section A small oocyte rep 5 [X. laevis]


title: section B very small oocyte rep 1 [X. laevis]


title: section B small oocyte rep 4 [X. laevis]


title: section D small oocyte rep 5 [X. laevis]


title: section E small oocyte rep 3 [X. laevis]


title: section E small oocyte rep 5 [X. laevis]


title: section E small oocyte rep 4 [X. laevis]


title: section A small oocyte rep 4 [X. laevis]


title: Caco2 cells 72h B.1.617.2 -1

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

description:
HHK-52
Cellular RNA

data_processing:
MGI adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the human genome GRCh38 using hisat2 with default parameters. Uniquely aligned reads were counted using featureCounts of Subread package. There were 60683 genes in the gtf file, downloaded from ensembl, for which we had count information. Genes with total read count 10 across all the samples were removed resulting in 35906 genes for further analysis. Differential gene expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: countMatrix_unstranded_upload.count.txt: Tab-delimited counts file.

source_name: Caco2 cells

growth_protocol: Caco2 cells were cultured in cDMEM supplemented with 20% FBS and 1× penicillin-streptomycin cocktail (Gibco) at 37°C and 5% CO2.

extract_protocol:
Cellular RNA prepared using MN nucleospin RNA isolation kit (Takara).
Library preparation was done using the MGIEasy RNA Library Prep Set (MGI) according to the manufacturer’s instructions. In brief, 500 ng total RNA was used as starting material and ribosomal RNA was removed using Ribo-Zero Plus rRNA Depletion Kit (Illumina). The rRNA depleted samples were fragmented, reverse transcribed and second strand was synthesised. DNA was then purified using DNA Clean Beads provide in the kit followed by end repair and A-tailing. Barcoding and adaptor ligation was performed and the samples were purified. Samples were amplified using adaptor specific primers and quantified using Qubit dsDNA high sensitivity kit (ThermoScientific). Sample fragment size was determined using 4200 TapeStation (Agilent). The samples were denatured and single stranded circular DNA strands were created. Rolling cycle amplification was performed and DNA nanoballs were created. The samples were loaded onto FCL and sequenced at PE100.

treatment_protocol: 1 MOI infection for three time points 24, 48, and 72 Hours.

tag: cell line

value: Colorectal adenocarcinoma cells

tag: infection

value: Infected

tag: cov-2 variant

tag: time point


title: Caco2 cells 72h B.1.617.2 -2

description:
HHK-53
Cellular RNA


title: section C small oocyte rep 4 [X. laevis]


title: section D small oocyte rep 3 [X. laevis]


title: section A small oocyte rep 3 [X. laevis]


title: section D small oocyte rep 2 [X. laevis]


title: section C very small oocyte rep 1 [X. laevis]


title: Caco2 cells 72h B.1.617.2 -3

description:
HHK-54
Cellular RNA


title: section B small oocyte rep 3 [X. laevis]


title: Caco2 cells 48h B.1.617.2 -3

description:
HHK-51
Cellular RNA


title: Caco2 cells 48h B.1.617.2 -2

description:
HHK-50
Cellular RNA


title: section C small oocyte rep 2 [X. laevis]


title: Caco2 cells 24h B.1.617.2 -2

description:
HHK-47
Cellular RNA


title: section D small oocyte rep 4 [X. laevis]


title: section E small oocyte rep 2 [X. laevis]


title: section B small oocyte rep 2 [X. laevis]


title: Caco2 cells 72h B.6 -3

description:
HHK-45
Cellular RNA


title: Caco2 cells 48h B.1.617.2 -1

description:
HHK-49
Cellular RNA


title: section E small oocyte rep 1 [X. laevis]


title: Caco2 cells 72h B.6 -2

description:
HHK-44
Cellular RNA


title: Caco2 cells 72h B.6 -1

description:
HHK-43
Cellular RNA


title: section D small oocyte rep 1 [X. laevis]


title: section B small oocyte rep 5 [X. laevis]


title: Caco2 cells 24h B.1.617.2 -3

description:
HHK-48
Cellular RNA


title: section C small oocyte rep 1 [X. laevis]


title: Caco2 cells 24h B.1.617.2 -1

description:
HHK-46
Cellular RNA


title: section C small oocyte rep 3 [X. laevis]


title: section C medium oocyte rep 2 [X. laevis]

value: medium


title: section A medium oocyte rep 2 [X. laevis]


title: section A small oocyte rep 2 [X. laevis]


title: Caco2 cells 72h B.1.1.7 -2

description:
HHK-35
Cellular RNA


title: Caco2 cells 72h B.1.1.7 -3

description:
HHK-36
Cellular RNA


title: section E medium oocyte rep 1 [X. laevis]


title: section B small oocyte rep 1 [X. laevis]


title: section A small oocyte rep 1 [X. laevis]


title: Caco2 cells 72h B.1.1.7 -1

description:
HHK-34
Cellular RNA


title: section B medium oocyte rep 1 [X. laevis]


title: Caco2 cells 48h B.6 -3

description:
HHK-42
Cellular RNA


title: Caco2 cells 48h B.6 -2

description:
HHK-41
Cellular RNA


title: Caco2 cells 72h B.1.1.8 -1

description:
HHK-28
Cellular RNA


title: Caco2 cells 24h B.6 -2

description:
HHK-38
Cellular RNA


title: section D medium oocyte rep 2 [X. laevis]


title: Caco2 cells 48h B.6 -1

description:
HHK-40
Cellular RNA


title: section E medium oocyte rep 2 [X. laevis]


title: Caco2 cells 24h B.6 -1

description:
HHK-37
Cellular RNA


title: section D big oocyte rep 2 [X. laevis]

value: big


title: Caco2 cells 24h B.6 -3

description:
HHK-39
Cellular RNA


title: section B medium oocyte rep 2 [X. laevis]


title: section C medium oocyte rep 1 [X. laevis]


title: section D medium oocyte rep 1 [X. laevis]


title: Caco2 cells 72h B.1.1.8 -3

description:
HHK-30
Cellular RNA


title: Caco2 cells 72h B.1.1.8 -2

description:
HHK-29
Cellular RNA


title: section E big oocyte rep 1 [X. laevis]


title: section A medium oocyte rep 1 [X. laevis]


title: section E big oocyte rep 2 [X. laevis]


title: Caco2 cells 72h Mock-3

description:
HHK-27
Cellular RNA

value: Uninfected


title: Caco2 cells 48h B.1.1.8 -1

description:
HHK-16
Cellular RNA


title: section C big oocyte rep 2 [X. laevis]


title: Caco2 cells 72h Mock-2

description:
HHK-26
Cellular RNA


title: section A big oocyte rep 1 [X. laevis]


title: Caco2 cells 72h Mock-1

description:
HHK-25
Cellular RNA


title: Caco2 cells 48h B.1.1.7 -2

description:
HHK-23
Cellular RNA


title: Caco2 cells 48h B.1.1.7 -3

description:
HHK-24
Cellular RNA


title: Caco2 cells 24h B.1.1.7 -3

description:
HHK-12
Cellular RNA


title: section A big oocyte rep 2 [X. laevis]


title: Caco2 cells 24h B.1.1.7 -2

description:
HHK-11
Cellular RNA


title: Caco2 cells 48h B.1.1.7 -1

description:
HHK-22
Cellular RNA


title: section B big oocyte rep 2 [X. laevis]


title: Tumor infiltrated immune cells,IgG

city: Houston

first: Xin

last: Li

state: Texas

address: 6670 Bertner ave

institute: Houston methodist hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Goblet cells

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Goblet cells

value: 6-8 weeks old


title: Tumor infiltrated immune cells,aC+C

description: 10x Genomics


title: Caco2 cells 48h B.1.1.8 -3

description:
HHK-18
Cellular RNA


title: section C big oocyte rep 1 [X. laevis]


title: MERTK 23

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

data_processing:
Raw sequencing reads were checked for overall quality and adapter contamination using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) prior to downstream analysis. Reads were then used to quantifying transcript abundances with Salmon
The resulting transcript abundances were summarized to gene level counts using functions in the Bioconductor package tximport
Significantly differentially expressed genes were identified using the Bioconductor package DESeq2 with a significance threshold of FDR < 0.1.
Assembly: GENCODE version M25 mouse reference
Supplementary files format and content: comma-separated counts values (TPM)

source_name: FPC 0.05% chol - Regression

extract_protocol:
Cell isolation protocol: Non-parenchymal cells were isolated from mice livers using perfusion with calcium/magnesium-free HBSS containing 3mg/mL of Liberase TM (Roche), and mechanically dissociated in calcium/magnesium-free HBSS containing 0.5% BSA and 2mM EDTA. NPCs were isolated by density gradient centrifugation with 20% Optiprep (StemCell Technologies).
Sorting staining protocol : NPCs were stained with the anti-mouse antibodies CD45 (BD Horizon; 30-F11), MertK (eBio; DS5MMER), CD64 (BioLegend; X54-5/7.1), F4/80 (eBio; BM8), and CD11b (eBio; M1/70) antibodies. Cell incubation took place on ice and at dark for 25 minutes. Mertk+ macrophages sorting was performed at the BD FACSAria™ Fusion Flow Cytometer, with 100µm nozzle, into 90% FBS media at 4˚C.
Cells were then harvested in Buffer RLT (Qiagen) + 1% 2-Mercaptoethanol (Sigma-Aldrich) and RNA was extracted using Rneasy Mini kit (Qiagen) following manufacture's instructions.
libraries were simultaneously prepared using Kapa mRNA Hyper kit (cat#08098123702) following manufacturer's protocol. Prepared RNAseq libraries were sequenced on the Illumina Nextseq 500 platform at a read length of 2x75 at 25 million reads per sample.

tag: strain

tag: diet

value: FPC 0.05% chol - for 20 weeks / FPC 0.05% chol - for 10 weeks

value: hepatic non-parenchymal cells

tag: sorted cell type

value: Mertk+ macrophages


title: section D big oocyte rep 1 [X. laevis]

source_name: oocyte

value: oocyte

value: female

tag: source female


title: Caco2 cells 48h Mock-1

description:
HHK-13
Cellular RNA


title: Caco2 cells 48h Mock-2

description:
HHK-14
Cellular RNA


title: section B big oocyte rep 1 [X. laevis]

tag: oocyte stage


title: MERTK 20

source_name: FPC 0.2% chol - Regression

value: FPC 0.2% chol - for 20 weeks / FPC 0.05% chol - for 10 weeks


title: Caco2 cells 48h B.1.1.8 -2

description:
HHK-17
Cellular RNA


title: Caco2 cells 48h Mock-3

description:
HHK-15
Cellular RNA


title: PL-15 dehydrated camel supraoptic nucleus

city: Bristol

first: Panjiao

last: Lin

address: Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

data_processing:
The paired end sequencing files (.fastq) were merged and trimmed for adaptor sequences using BBDuk tool.
All samples passed the FastQC check and were aligned to the reference dromedary camel genome Camdro2 (GCA_000803125.2) using STAR aligner.
The mapped reads aligned to each gene were counted using FeatureCounts.
Differential expression analysis were performed using DESeq2.
Assembly: Camdro2 (GCA_000803125.2)
Supplementary files format and content: Matrix table with raw read counts for each gene and every sample
Supplementary files format and content: Matrix table with DESeq2-normalized (median of ratios method) read counts for each gene and every sample

organism: Camelus dromedarius

source_name: Supraoptic nucleus

extract_protocol: Unilateral supraoptic nucleus samples were isolated from hypothalamus of male dromedary camels under control (water ad libitum) and dehydrated (water deprivation for 20 days) conditions (n=5 per group). Total RNA was extracted using a Direct-zol™ RNA MiniPrep kit (Zymo research, R2052) following the manufacturer’s instructions. Average RNA Integrity Number (RIN) of samples processed for sequecing (n=10) was 6.27. Ribosomal depleted sequencing libraries were produced using TruSeq® Stranded Total RNA library preparation kit (illumina). Libraries were sequenced on Illumina NextSeq500 platform using NextSeq 500 High Output v2.5 (2 x 75 bp run) Kit (Illumina; 20367064).

value: Supraoptic nucleus

tag: gender

value: Male

value: free access to food and no access to water


title: Caco2 cells 24h Mock-1

description:
HHK-1
Cellular RNA


title: Tumor infiltrated immune cells,Ac

description: 10x Genomics


title: PL-9 dehydrated camel supraoptic nucleus


title: MERTK 24


title: Caco2 cells 24h B.1.1.7 -1

description:
HHK-10
Cellular RNA


title: PL-7 dehydrated camel supraoptic nucleus


title: MERTK 14

source_name: FPC 1.2% chol - Regression

value: FPC 1.2% chol - for 20 weeks / FPC 0.05% chol - for 10 weeks


title: Tumor infiltrated immune cells,C

description: 10x Genomics


title: MERTK 21


title: Caco2 cells 24h B.1.1.8 -2

description:
HHK-5
Cellular RNA

value: Colorectal adenocarcinoma cells


title: PL-4 control camel supraoptic nucleus

value: free access to food and water


title: PL-5 control camel supraoptic nucleus


title: Caco2 cells 24h B.1.1.8 -1

description:
HHK-4
Cellular RNA

value: Infected


title: Caco2 cells 24h Mock-3

description:
HHK-3
Cellular RNA


title: MERTK 8

source_name: FPC 0.2% chol - Progression

value: FPC 0.2% chol - for 20 weeks


title: PL-3 control camel supraoptic nucleus


title: MERTK 7


title: MERTK 19


title: PL-2 control camel supraoptic nucleus


title: Caco2 cells 24h Mock-2

description:
HHK-2
Cellular RNA

value: Uninfected


title: MERTK 5


title: MERTK 17


title: MERTK 18


title: Caco2 cells 24h B.1.1.8 -3

description:
HHK-6
Cellular RNA


title: MERTK 15


title: MERTK 13


title: MERTK 12

source_name: FPC 0.05% chol - Progression

value: FPC 0.05% chol - for 20 weeks


title: PL-8 dehydrated camel supraoptic nucleus


title: Pabpn1-ZP3CKO-GO-3

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

institute: Life Sciences Institute

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the 1Cell-stage embryo sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: GO (growing oocytes)

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

value: oocytes

tag: Stage

value: GO (growing oocytes)

tag: genotype/variation


title: Pabpn1-ZP3CKO-GO-2


title: Pabpn1-ZP3CKO-GO-1


title: MERTK 9

value: hepatic non-parenchymal cells


title: MERTK 11

value: Mertk+ macrophages


title: PL-13 control camel supraoptic nucleus


title: Pabpn1-ZP3CKO-FGO-3

source_name: FGO (fully grown oocytes)

value: FGO (fully grown oocytes)


title: Pabpn1-WT-FGO-1

value: WT


title: Pabpn1-WT-FGO-2


title: Pabpn1-WT-MI-2

source_name: MI (metaphase I)

value: MI (metaphase I)


title: MERTK 3

source_name: FPC 1.2% chol - Progression

value: FPC 1.2% chol - for 20 weeks


title: Pabpn1-ZP3CKO-MI-3


title: Pabpn1-ZP3CKO-MI-1


title: MERTK 2


title: Pabpn1-ZP3CKO-MI-2


title: PL-6 dehydrated camel supraoptic nucleus

value: Supraoptic nucleus

value: Male


title: MERTK 1


title: PABPN1-WT-GO-3


title: Pabpn1-ZP3CKO-FGO-2


title: Pabpn1-WT-MI-3


title: MERTK 10


title: Pabpn1-ZP3CKO-FGO-1


title: Pabpn1-WT-FGO-3


title: PABPN1-WT-GO-2


title: Input, E17.5, cerebral cortex

first: Yaqiong

last: Wang

address: 399 Wanyuan Rd

institute: Children's hospital of Fudan University

data_processing:
Actve Motif provided Illumina chastity-filtered reads with phred+33 quality scores in fastq format
Reads were aligned to the mouse genome (mm10) by BWA (v 0.7.17)
normalised bigWig files scaled to 1 million mapped reads by BEDTools(v2.29.2)
MACS2 (v2.2.7) (Zhang et al., 2008) was used to call narrow peaks with FDR < 0.001
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: cerebral cortex

growth_protocol: All C57BL/6J mice were experimental model and were fed in a specific pathogen-free room with automatically controlled temperature (16℃), humidity (40%), ventilation and light conditions (light, 6:00 to 18:00; dark, 18:00 to 6:00)

extract_protocol:
ChIP reactions were carried out using 22 ug of chromatin and anti-SATB2 antibody (Novus, cat# NBP176912, Lot# 4627-0904)
ChIP-seq is performed by Active Motif according to their procedures

value: cerebral cortex

tag: age

tag: chip antibody


title: PABPN1-WT-GO-1


title: section E small oocyte rep 7 [A. ruthenus]

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE (v. 0.36). Ribosomal RNA sequences were removed using sortmerna (v. 2.1b) and the SILVA rRNA database (version 119). Using Kallisto (v. 0.43.1), the reads were then pseudo-aligned to the de novo transcriptome (sterlet_transcriptome_merged.fasta).
Normalized number of reads was generated using DESeq2.
Transcripts were removed that had zero counts in all samples.
Assembly: Attached de novo transcriptome file “sterlet_transcriptome_merged.fasta”. This transcriptome file is similar to the one submitted to the Gene Expression Omnibus (GEO: GSE125819) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125819). It represents the original transcriptome from trinity while the previously deposited GEO one represents the one after an additional processing with evidential gene.
Supplementary files format and content: Excel files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column. "aruthenus_non_normalized.xlsx" contains the non-normalized reads while "aruthenus_altered_magnitudes_per_section_and_stage_normalized.xlsx" contains the normalized reads for all samples (all oocyte sections). "aruthenus_total_altered_counts_per_stage_non_normalized.xlsx" contains the non-normalized reads while "aruthenus_total_altered_counts_per_stage_normalized.xlsx" the normalized reads for the total transcripts within the whole oocyte. "aruthenus_alteration_between_the_sections_at_small_stage_normalized.xlsx" and "aruthenus_alteration_between_the_sections_at_big_stage_normalized.xlsx" contain the normalized reads at a given oocyte stage.

organism: Acipenser ruthenus

value: oocyte

tag: treatment

tag: Sex

value: female

value: small

tag: oocyte size

tag: section

value: E

tag: biological replicate


title: KP230 + DMSO replicate 3

city: Cambridge

first: Anne

middle: E

last: Carpenter

state: MA

address: 415 Main Street

institute: The BROAD Institute of MIT and Harvard

data_processing:
FASTQ files were generated with the bcl2fastq command line program (Illumina). Transcript alignment was performed with Salmon. Differential expression analysis (NB4A- vs. DMSO-treated cells) was performed with the DESeq2 R package. DESeq2 “stat” values for each gene were used as inputs to pre-ranked GSEA, where enrichment was tested against the Hallmark gene sets from the Molecular Signatures Database (MSigDB).
Assembly: GRCm38; gencodeM23

source_name: Undifferentiated pleomorphic sarcoma cells

growth_protocol: KP230 cells were grown in DMEM with 10% FBS, 1% L-glutamine, and 1% penicillin/streptomycin. Routine passage was performed when cells reached 50% confluency.

extract_protocol:
Total RNA from cultured cells was isolated with the QIAGEN RNeasy Mini Kit with on-column DNase digestion. RNA quality checks were performed with an Agilent 2100 Bioanalyzer (Eukaryotic Total RNA Nano kit).
Library preparation (500 ng input RNA) was performed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490) with SPRIselect Beads (Beckman Coulter), the NEBNext Ultra II Single-End RNA Library Prep kit (#7775S), and the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) according to the manufacturer’s instructions. Library size was confirmed with an Agilent 2100 Bioanalyzer (DNA1000 chip). Pooled libraries were diluted to 1.8 pM (concentrations checked with the Qubit Fluorometer high-sensitivity assay, Thermo Fisher), and sequenced on an Illumina NexSeq 500 instrument with the NexSeq 500 75-cycle high-output kit.

treatment_protocol: Cells were treated with 10 µM NB4A (diluted in DMSO) every 24 hours for 3 days.

tag: cell type

tag: cell line

value: DMSO


title: section D small oocyte rep 7 [A. ruthenus]

value: D


title: Pabpn1-WT-MI-1

value: oocytes

tag: strain


title: KP230 + NB4A replicate 2

value: Undifferentiated pleomorphic sarcoma cells


title: section A small oocyte rep 8 [A. ruthenus]

value: A


title: section E small oocyte rep 6 [A. ruthenus]


title: section E small oocyte rep 8 [A. ruthenus]


title: section B small oocyte rep 8 [A. ruthenus]

value: B


title: section C small oocyte rep 7 [A. ruthenus]

value: C


title: section C small oocyte rep 8 [A. ruthenus]


title: section B small oocyte rep 6 [A. ruthenus]


title: KP230 + NB4A replicate 1


title: Satb2, E17.5, cerebral cortex

tag: tissue

tag: genotype

value: WT

value: SATB2(Novus, # NBP176912)


title: KO_3

city: Dallas

first: Weibo

last: Luo

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to mm10 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Genome_build: mm10
Supplementary_files_format_and_content: TXT

source_name: neuron

growth_protocol: Mouse cortexes were isolated from embryos at E18, kept separately in cold HBSS (Gibco, 14175) and incubated for 15 min with 20 units/mL of papain (Worthington, LK003178) at 37 °C. Dissociated cells were suspended in plating media (DMEM supplemented with 10% horse serum) and plated at a density of 6 × 104 per well onto poly-L-lysine–coated 18-mm coverslips (Fisherbrand, 12-545-100) in a 12-well plate (Thermo Scientific, 150628) or 6 × 105 per well on a 6-well plate (Thermo Scientific, 140675). Neurons  were incubated for 4 h before replacing with maintaining media containing Neurobasal A medium (ThermoFisher Scientific, 10888022) supplemented with 2% N21-MAX supplement (R&D Systems, AR008), 1% GlutaMax (ThermoFisher Scientific, 35050061), and 1% penicillin/streptomycin (ThermoFisher Scientific, 15140122), and cultured at 37 °C in 5% CO2, by changing half of media every 2–3 days with fresh maintaining media.

extract_protocol:
Total RNA was isolated using Trizon and treated with DNase I (Invitrogen).
mRNA-seq libraries were prepared with a KAPA mRNA HyperPrep kit (Roche).

tag: strain background

value: KDM6B KO

value: neuron


title: section D small oocyte rep 6 [A. ruthenus]

tag: source female

tag: oocyte stage


title: KO_2


title: KO_1


title: section E small oocyte rep 5 [A. ruthenus]


title: section D small oocyte rep 5 [A. ruthenus]


title: section C small oocyte rep 6 [A. ruthenus]


title: section A small oocyte rep 6 [A. ruthenus]


title: section D small oocyte rep 8 [A. ruthenus]


title: KP230 + DMSO replicate 2


title: section C small oocyte rep 5 [A. ruthenus]


title: section B small oocyte rep 5 [A. ruthenus]


title: KP230 + NB4A replicate 3


title: WT_3

value: wild type


title: scRNA_Stag2f/y_rep2

first: Hongtao

last: Yu

address: 6001 Forest Park Rd

institute: University of Texas Southwestern Medical Center

data_processing:
Data demultiplexing and alignment was performed using the Cell Ranger pipeline (10x Genomics) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq).
The raw features, barcodes, and matrixes were used as input for further analysis using R package Seurat3 (https://satijalab.org/seurat/).  Cells were filtered as follows: nFeature_RNA (200-9500) & percent.mt < 10
All datasets were then integrated together using identified anchors (dims = 1:30).
Standard scaling and PCA were performed on the integrated dataset before clustering (resolution = 0.5) and tSNE reduction (dims = 1:30).
Clusters were manually assigned to distinct cell type identities with identified biomarkers and top features, along with knowledge from previous research (http://www.brainrnaseq.org/) (http://dropviz.org/).
Genome_build: mm10
Supplementary_files_format_and_content: R object that contains the clusters from all samples and scaled data for each sample
Supplementary_files_format_and_content: Comma-separated table including cluster features

source_name: forebrain

extract_protocol:
The single-cell suspension was prepared from mouse forebrains using the Papain dissociation system (Worthington Biochemical, cat#LK003150) according to the manufacturer’s instructions
The single-cell RNA-seq libraries were generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics) according to the manufacturer’s guidelines.

value: brain

value: post natal day 13


title: WT_1


title: Input_H3K27ac_Stag2f/y; Cre

data_processing:
Reads were mapped to mouse genome with bowtie2(v2.2.3) with parameter “--sensitive”,
Alignments with mapping quality less than 10 were first removed
Duplicate reads identified by Picard MarkDuplicates (v1.127) were then filtered out.
For STAG2 ChIP-seq, Picard MarkDuplicate was used to remove duplicates along with options to use molecular identifiers (MIDs) information in the reads.
Enriched regions (peaks) were identified using MACS2 (v2.0.10) with a q-value cut-off of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file showing the abundance measurements of target protein across the genome

source_name: Oligodendrocytes

extract_protocol:
Lysates were clarified from sonicated cells and targeted protein-DNA  complexes were isolated with antibody.
Libraries were generated by Next Gen DNA Library Kit (Active Motif, cat#53216) with the Next Gen Indexing Kit (Active Motif, cat#53264) for STAG2 ChIP-seq or KAPA HyperPrep Kits (KAPA Systems, cat#KK8501) for histone ChIP-seq according to the manufacturer's protocol

tag: cell types

value: isolated primary oligodendrocytes

value: post natal day 12

value: Stag2f/y; Cre


title: section A small oocyte rep 5 [A. ruthenus]

value: oocyte

value: female

value: small


title: scRNA_Stag2f/y; Cre_rep2


title: WT_2

tag: genotype/variation


title: section B big oocyte rep 11 [A. ruthenus]

value: big


title: scRNA_Stag2f/y; Cre_rep1

tag: age


title: KP230 + DMSO replicate 1

value: Undifferentiated pleomorphic sarcoma cells

value: DMSO


title: ChIPseq_H3K27ac_Stag2f/y; Cre

tag: chip antibody


title: section A big oocyte rep 11 [A. ruthenus]

tag: treatment

value: A


title: section D big oocyte rep 3 [A. ruthenus]

tag: Sex

value: D


title: scRNA_Stag2f/y_rep1


title: Input_STAG2

value: post natal day 14


title: section D big oocyte rep 2 [A. ruthenus]

tag: oocyte size


title: section E big oocyte rep 3 [A. ruthenus]

tag: section

value: E


title: section A big oocyte rep 3 [A. ruthenus]

tag: biological replicate


title: section C big oocyte rep 3 [A. ruthenus]

tag: cell type

value: C


title: Input_H3K27ac_Stag2f/y


title: section B big oocyte rep 3 [A. ruthenus]

value: B


title: ChIPseq_H3K27ac_Stag2f/y


title: ChIPseq_STAG2

value: STAG2 (Homemade)


title: section B big oocyte rep 1 [A. ruthenus]


title: section E big oocyte rep 2 [A. ruthenus]


title: RNA_Stag2f/y; Cre_L'2

data_processing:
Raw data from machine were de-multiplexed and converted to fastq files using bcl2fastq (v2.17, Illumina).
The fastq files were checked for quality using fastqc (v0.11.2)42 and fastq_screen (v0.4.4).
Fastq files were mapped to mm10 mouse reference genome (from igenomes) using STAR
Read counts were then generated using featureCounts.
TMM normalization and differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample

source_name: brain hemisphere

extract_protocol:
RNA was harvested from freshedly dissected brain hemispheres using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq stranded mRNA library Prep Kit (Cat#20020594) was used for the construction of sequencing libraries.

value: brain

value: post natal day 21


title: section C big oocyte rep 2 [A. ruthenus]


title: RNA_Stag2f/y; Cre_R'1


title: RNA_Stag2f/y; Cre_rep2

description: The dissected brain cortex was triturated in papain dissociation solution with B-27 supplement, and the single-cell suspension was incubated with anti-O4 magnetic beads and pass through a magnetic column to allow for oligodendrocytes enrichment.

value: isolated primary oligodendrocytes

value: post natal day 12


title: section A big oocyte rep 1 [A. ruthenus]

value: oocyte


title: RNA_Stag2f/y_R2


title: section B big oocyte rep 2 [A. ruthenus]

value: female


title: RNA_Stag2f/y_L2


title: 3236124-PrefrontalCortex

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: rheMac10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

organism: Macaca mulatta

extract_protocol:
Automated. Promega Maxwell RSC ccfDNA Plasma Kit for cffDNA and Tecan workflow for Zymo Quick-DNA Miniprep Plus Kit for brain.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit

tag: group

value: Pravastatin

tag: timepoint

tag: infantid

tag: birthgd

value: No

tag: foster

tag: cohort

tag: sample type

value: PrefrontalCortex


title: section A big oocyte rep 2 [A. ruthenus]

tag: source female

tag: oocyte stage

value: big


title: 3216119-Hypothalamus

source_name: Hypothalamus

value: Obese

value: Hypothalamus


title: RNA_Stag2f/y; Cre_rep1

tag: strain

tag: cell types

tag: age

tag: genotype

value: Stag2f/y; Cre


title: RNA_Stag2f/y_rep1


title: RNA_Stag2f/y_rep2


title: RNA_Stag2f/y_L1

tag: tissue


title: section E big oocyte rep 1 [A. ruthenus]

source_name: oocyte

tag: treatment

tag: Sex

tag: oocyte size

tag: section

value: E


title: RNA_Stag2f/y; Cre_L'1


title: section D big oocyte rep 1 [A. ruthenus]

tag: cell type

value: D

tag: biological replicate


title: RNA_Stag2f/y; Cre_R'2


title: section C big oocyte rep 1 [A. ruthenus]

value: C


title: 3216119-Hippocampus

source_name: Hippocampus

tag: group

tag: timepoint

tag: infantid

tag: birthgd

value: Hippocampus


title: iPSC-OP9-T_3 bulk RNA-Seq

city: Boston

first: Mohamad Ali

last: Najia

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
For 10X scRNA-Seq, libraries were computationally demultiplexed and the data were aligned to the GRCh38 reference genome using cellranger v2.1 (10X Genomics). CellRouter was used for quality control and downstream analysis (Lummertz da Rocha et al., 2018). Cell by gene count matrices of all samples were combined to a single gene expression matrix. Cells with 500–3000 detected genes and expressing <10% mitochondrial genes as well as genes expressed in > 25 cells were retained for downstream analysis. The final dataset after quality control was composed of 10907 cells, with a median of 1,456 genes detected per cell. Variation caused by mitochondrial gene expression and sample replicates were regressed out. All genes passing QC metrics were used for principal component analysis. Clustering analysis was performed using parameters k=150 and 30 principal components.  UMAP analysis was performed using 10 principal components. Cluster annotation was performed using differential expression and marker genes. Gene signatures, as well as ranked gene lists ordered by log fold change for GSEA analysis, were generated by testing for differential expression of a cluster/cell type against all other cells using a Wilcox test, as implemented in CellRouter. Trajectory analysis and calculation of GRN scores was performed with CellRouter. SCENIC analysis was used to identify regulons enriched in each annotated cell type (Aibar et al., 2017).
For bulk RNA-Seq, adaptor-trimmed RNA-seq reads were aligned to the hg19 transcriptome using Tophat. Reads per gene were counted with HTSeq and normalized as CPM (counts per million) values with the edgeR package in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cells by genes count matrices produced from the cellranger pipeline

source_name: T cells

growth_protocol: Human 1157.2 iPSCs were maintained on Matrigel-coated plates using Stemflex media (Gibco, A3349401) and transferred to mouse embryonic fibroblast  (MEF) feeder cells (Gibico, A34181) prior to differentiation. After one week of culture of on MEFs, iPSCs were collected for the generation CD34+ HE cells using a previous described protocol (Ditadi et al., 2015). Briefly, iPSC colonies were scraped and transferred to ultra-low attachment plates and cultured with aggregation media contains BMP4 (10ng/ml, day 0-2), bFGF (5ng/ml, day 1-2), CHIR99021 (3μM, day 2), and SB431542 (6μM, day2) to allow EB formation. From day 4, EBs were cultured with StemPro-34 media (Gibco, 10639011) supplemented with VEGF (15ng/ml, day3-8), bFGF (5ng/ml, day3-8), SCF (50ng/ml, day 6-8), EPO (day6-8), IL-6 (day6-8), IL-11 (day6-8), and IGF-1 (day6-8). After 8 days of culture, EBs were dissociated using EB Dissociation Kit (Miltenyi, 130096348), and HE cells were isolated by magnetic-activated cell sorting (MSCS) using the human CD34 Microbead Kit (Miltenyi, 130046702). 24 well non-tissue culture treated plates were coated with 10μg/ml recombinant human DL4-Fc protein (Life Technologies, A42510) and 2 μg/ml VCAM-1 (R&D, 862VC100) in PBS for 2 hours at 4°C. CD34+ HE cells (1X105 cells/well) were then seeded on DL4-coated plates and cultured in SFEMII (StemCell Tech, 09605) media supplemented with 10% BIT serum substitute (StemCell Tech, 09500), 2mM L-Glutamine (Gibco, 35050061), 1mM sodium pyruvate (Gibco, 11360070), 50μg/ml 2-phospho-L-ascorbic acid (Huijskens et al., 2014) (sigma, 49752),  55μM 2-Mercaptoethanol (Gibco, 21985023), 1mM None-essential amino acids (Gibco, 11140050), 1% penicillin-streptomycin (Corning, 30002CI), 30ng/ml SCF, 20ng/ml Flt3, 30ng/ml IL-7, 5ng/ml IL-3 (first week only), and 5ng/ml TPO for 2 weeks to induced the differentiation into proT cells. For the production of EZ-T cells, EZH1 knockdown was performed via lentiviral transduction (MOI=5) after 24 hours of HE seeding. After 2 weeks of differentiation, SCF and TPO were withdrawn from the media, and the proT cells were replated into new DL4-coated plates and cultured in the presence of 20ng/ml Flt3 and 15ng/ml IL-7 till week 5, followed by 1 week of treatment with CD3/CD28 T activator (StemCell Tech, 10971) and 5ng/ml IL-15 to induced SP T cells. During T cell differentiation, half media changes were conducted every 2-3 days. T cell differentiation using the OP9-DL1 co-culture system was conducted following previous reports (Holmes and Zúñiga-Pflücker, 2009) (Themeli et al., 2013). Briefly, day 8 CD34+ HE cells were seeded on OP-DL1 stromal cells and co-cultured with OP9 media (α-MEME, 20% FBS, 1% penicillin-streptomycin, 1mM None-essential amino acids, 2mM L-Glutamine, 10μM 2-Mercaptoethanol, 50μg/ml 2-phospho-L-ascorbic acid) supplemented with 10ng/ml SCF, 5ng/ml Flt3, and 10ng/ml IL-7. Cells were mechanically dissociated and filtered through 40μm strainers to be seeded on new stromal cells every five days.

extract_protocol: Total RNA was isolated using a column assay with the DNase treatment (Direct-zol MicroPrep, ZYMO). Quantity and quality of the RNA were evaluated using the nanodrop machine and RNA screen tape. High quality RNA (Both 280/260 and 230/260 over 1.7 with RNA integrity number >7) were underwent ribosomal RNA depletion and following library construction.

value: iPS-derived T cells

value: 1157-2 iPS cell line


title: iPSC-OP9-T_2 bulk RNA-Seq


title: WM989 A6-G3 cells, 1µM vemurafenib, Resistant Colony 4

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Blvd

department: Bioengineering

institute: University of Pennsylvania

data_processing:
We aligned RNA-seq reads to the human genome (hg19) with STAR v2.5.2a and counted uniquely mapping reads with HTSeq v0.6.1 (Dobin et al. 2013; Mellis et al. 2021; Shaffer et al. 2017) and outputs count matrix. The counts matrix was used to obtain tpm and other normalized values for each gene using scripts provided at: https://github.com/arjunrajlaboratory/RajLabSeqTools/tree/master/LocalComputerScripts
Because each sample was split between 4 lanes of a flow cell (L001, L002, L003, L004) with paired-end reads (R1, R2) there are 8 raw data files per sample.
Assembly: hg19
Supplementary files format and content: Comma-separated values text files which include multiple quantification measures (FPKM, TPM, etc.)

source_name: WM989 A6-G3 RC4_1uM_PLX

growth_protocol: The WM989 A6-G3 human melanoma cell line, first described in (Shaffer et al. 2017) was derived from WM989 cells (a gift from the lab of Dr. Meenhard Herlyn) that were twice isolated from a single cell and expanded. Cells were cultured in Tu2% media (80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4mM CaCl2, 50 U/mL penicillin, and 50 μg/mL streptomycin) in a 10cm dish. WM989 A6-G3 RC4 cells were derived by treating WM989 A6-G3 cells with 1µM vemurafenib in Tu2%, isolating a single drug-resistant colony, and culturing these cells in 1µM vemurafenib in Tu2% (Goyal et al. 2021) for several months.

extract_protocol:
We used RNeasy Micro (Qiagen 74004) for extraction.
We used NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S), and an Illumina NextSeq 550 75 cycle high-output kit (Illumina 20024906). Described in Goyal et al. (https://doi.org/10.1101/2021.12.08.471833).

tag: cell line

value: melanoma cells

value: 1µM vemurafenib


title: 3216119-PrefrontalCortex

tag: foster

tag: cohort

tag: sample type


title: 3215218-Hippocampus

value: Yes


title: 3235224-PrefrontalCortex


title: PBMC-NK_2 bulk RNA-Seq

source_name: Natural killer cells

value: PBMC derived natural killer cells

tag: strain

value: PBMCs


title: 3215218-Hypothalamus


title: RNA_Stag2f/y_R1

value: brain

tag: age

value: post natal day 21

tag: genotype


title: 3236124-Hippocampus

value: Pravastatin

value: No


title: iPSC-OP9-T_1 bulk RNA-Seq


title: WM989 A6-G3 cells, drug-naive

tag: treatment

value: control


title: 3236124-Hypothalamus

value: Hypothalamus


title: 3235224-Hippocampus


title: iPSC-EZ-T_1 bulk RNA-Seq


title: 3235224-Hypothalamus


title: PBMC-NK_3 bulk RNA-Seq


title: 3215218-PrefrontalCortex

value: Obese

value: PrefrontalCortex


title: iPSC-SF-T_3 bulk RNA-Seq


title: PBMC-NK_1 bulk RNA-Seq


title: 3243225-Hippocampus

value: Control


title: 3233113-PrefrontalCortex


title: iPSC-EZ-T_3 bulk RNA-Seq


title: 3233113-Hippocampus

value: Hippocampus


title: iPSC-EZ-T_2 bulk RNA-Seq

value: iPS-derived T cells


title: iPSC-SF-T_1 bulk RNA-Seq

value: 1157-2 iPS cell line


title: 3214217-Hippocampus


title: HSPC_1 bulk RNA-Seq

source_name: Hematopoietic progenitors

value: Cord blood HSPCs

value: Umbilical cord blood


title: 3242201-PrefrontalCortex

value: Yes


title: 3243225-PrefrontalCortex


title: PBMC-gdT_2 bulk RNA-Seq

value: PBMC derived T cells


title: iPSC-SF-T_2 bulk RNA-Seq


title: 3214217-PrefrontalCortex


title: 3242201-Hypothalamus


title: 3233113-Hypothalamus


title: 3243225-Hypothalamus


title: PBMC-gdT_1 bulk RNA-Seq

value: PBMCs


title: PBMC-gdT_3 bulk RNA-Seq


title: HSPC_2 bulk RNA-Seq


title: 3242201-Hippocampus


title: 3212115-PrefrontalCortex


title: CB-T_2 bulk RNA-Seq

value: Cord blood derived T cells


title: CB-T_1 bulk RNA-Seq


title: 3212115-Hypothalamus


title: PBMC-abT_3 bulk RNA-Seq


title: PBMC-abT_1 bulk RNA-Seq


title: 3241217-Hippocampus


title: 3241217-Hypothalamus


title: PBMC-abT_2 bulk RNA-Seq


title: shEZH1_iPS_T_activated_rep2 10X scRNA-Seq

extract_protocol:
T cells were FACS-isolated for DAPI-CD45+ expression following in vitro differentiation and/or activation.
Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10X Genomics) according to the manufacturer’s instructions for a target recovery of ~6000 cells per lane. Each sample was loaded into two lanes to serve as technical replicates for scRNA-Seq library preparation. Libraries were then prepared per the 10X scRNA-Seq v2 protocol in parallel for all conditions. Final 10X scRNA-Seq libraries were assayed via an Agilent High Sensitivity dsDNA Bioanalyzer, normalized, pooled and shallow sequenced on a MiniSeq to quantify the number of high confidence cell barcodes. The libraries were then renormalized per the distribution of reads/library from the MiniSeq run and deep sequenced on a NextSeq to a depth of 50,000 reads per cell barcode.


title: 3214217-Hypothalamus


title: CB-T_3 bulk RNA-Seq


title: 3212115-Hippocampus


title: 3221116-Hippocampus

value: Restriction


title: 3231122-PrefrontalCortex

value: Pravastatin


title: shEZH1_iPS_T_rep2 10X scRNA-Seq


title: 3221116-Hypothalamus

value: No


title: Control_iPS_T_rep1 10X scRNA-Seq


title: 3231122-Hypothalamus


title: 3211112-Hippocampus


title: shEZH1_iPS_T_rep1 10X scRNA-Seq


title: Control_iPS_T_rep2 10X scRNA-Seq


title: 3241217-PrefrontalCortex


title: 3145122-PrefrontalCortex


title: 3211112-PrefrontalCortex


title: condCKO_rep2_RPF

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

data_processing:
Library strategy: Ribo-Seq
Adapters were removed with the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and the four random nucleotides at the beginning and the end of the reads were trimmed.
Alignment was performed with Bowtie v1.2.2 (Langmead et al., 2009). Reads that did not map to tRNA or rRNA were aligned to a human transcriptome (Gencode V27 as downloaded from the UCSC Genome Browser wgEncodeGencodeBasic27 table).
To summarize reads at the gene level, only 25-35 nt long reads that map to the annotated ORF of isoforms of one specific gene (as defined by a common gene symbol) were counted with an in-house-developed perl script. Respective to the 5’-end of the read, an offset of 12 nts upstream of the start codon and 15 nts upstream of the stop codon was assumed.
To identify individually regulated mRNAs with DESeq2 v1.16.1, read counts were normalized with the median ratio method. Only genes with > 10 reads were considered for all subsequent analyses.
Genome_build: Gencode V27
Supplementary_files_format_and_content: csv file containing raw read counts per gene, DESeq2-normalized read counts and ribosome densities.

source_name: CPEB4 KO HeLa

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in a humidified atmosphere with 5% CO2. Every two to three days, cells were carefully detached by scraping in warm 1x PBS and diluted 1:10.

extract_protocol:
Cell lysates were rotated end-over-end for 10 min at 4 °C and cleared by centrifugation at 10,000 x g for 10 min at 4 °C. All samples were adjusted to the same A260. 10% of the lysates were saved as input. The lysates were subsequently digested with RNase I (240 U per A260; Thermo Scientific) for 5 min at 4 °C. Samples were resolved on a linear 17.5–50% (w/v) sucrose density gradient by ultracentrifugation for 2.5 hours at 35,000 rpm. Fractions were eluted from the top of the gradient using a density gradient fractionation system (Brandel) coupled to a UA-6 UV/VIS detector (Teledyne Isco). During elution, 300 μl fractions were collected every 14 sec and immediately mixed with solution II (10 mM Tris-HCl pH 7.5, 350 mM NaCl, 10 mM EDTA, 1% (w/v) SDS, 7 M urea). RNA was purified from the cytoplasmic lysate (input) and from pooled monosomal fractions using phenol:chloroform:isamylalcohol (25:24:1; AppliChem) by phase separation.
RNA from both input and ribosome protected fragments (RPFs) was subjected to rRNA depletion using the Ribo-Zero Gold Kit (Illumina). Input RNA was randomly fragmented by alkaline hydrolysis at pH 10.0 for 12 min at 95 °C. Fragmented RNA and RPFs were size-selected (25–35 nts) on a 15% polyacrylamide TBE-urea gel. After end-repair with T4 PNK (NEB), 3 ng per sample was used for library preparation using the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer). Libraries were sequenced on a NextSeq550 device (Illumina) with 75 bases single end.

treatment_protocol: Cells were seeded at a density of 0.14 x 10^5 cells/cm2. The following day, cells were washed once with ice-cold 1x PBS supplemented with 100 μg/ml cycloheximide (CHX) and harvested by scraping in ice-cold polysome lysis buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 200 mM KCl, 1% (v/v) NP-40, 100 μg/ml CHX, 2 mM DTT, 5 U/ml RNasin) supplemented with 1x complete EDTA-free Protease Inhibitor Cocktail (Roche).

value: HeLa

value: CPEB4 KO

tag: fraction

value: small RNA


title: 3211112-Hypothalamus

value: Obese

value: Hypothalamus


title: condHeLa_rep2_IN

source_name: parental HeLa

value: wild-type

value: input


title: condCKO_rep1_IN


title: condCKO_rep2_IN


title: condCKO_rep1_RPF


title: 3145122-Hypothalamus

value: Control


title: 3145122-Hippocampus

value: Hippocampus


title: 3221116-PrefrontalCortex

value: PrefrontalCortex


title: 3124107-PrefrontalCortex


title: shEZH1_iPS_T_activated_rep1 10X scRNA-Seq

value: iPS-derived T cells

value: 1157-2 iPS cell line


title: 3124107-Hippocampus


title: condHeLa_rep1_IN


title: condHeLa_rep2_RPF


title: condHeLa_S181_RMD_time4

data_processing:
Reads were mapped with STAR v2.5.3a (Dobin et al., Bioinformatics 2012) to a reference of the human genome (Gencode V27 as downloaded from  UCSC Genome browser wgEncodeGencodeBasic27 table) and the ERCC92 RNA Spike-In Mix, allowing up to 2 mismatches and chimeric read detection with a minimum of 10 nt per segment  (--chimSegmentMin 10).
Read counts were summarized at the gene level with the featureCounts function of the subread package v1.6.3 (Liao et al., Bioinformatics 2014), requiring that a read is completely contained within an exon to be counted.
For normalization, read counts were divided by the sum of all reads assigned to ERCC92 spike-in sequences in the corresponding sample.
Linear regression was performed on log-transformed read counts. Half-lives were calculated from the slope of the regression line with the equation: ln(2) / -slope. Only genes with a positive half-life and a coefficient of determination  R2 of >0.5 in all conditions were used for subsequent analyses.
Genome_build: Gencode V27
Supplementary_files_format_and_content: csv file containing raw read counts per gene, expression values after normalization to spike-in RNA reads, half-lives in hours and the coefficient of determination (R2) of the linear regression used for determination of half-lives

source_name: HeLa

extract_protocol:
RNA was extracted with the GeneMatrix universal RNA purification kit (Roboklon). 2 µl of 1:100 diluted ERCC RNA Spike-In Mix (Thermo Scientific) was added per µg total RNA.
After depletion of rRNA using the Ribo-Zero Gold Kit (Illumina), sequencing libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) and sequenced on a NextSeq550 system (Illumina) with 75 bases single end.

treatment_protocol: Knock-down experiments were performed for 48 hours with Lipofectamine RNAiMAX transfection reagent (Thermo Scientific) and reverse transfection. siRNAs were used at a final concentration of 100 nM and diluted in Opti-MEM (Thermo Scientific) reduced serum medium. Cells were seeded at a density of 0.14 x 105 cells/cm2 in antibiotic-free DMEM (Gibco) supplemented with 5% (v/v) FBS and 2 mM L-Glutamine (all PAN Biotech). The following day, medium was changed to regular growth medium (DMEM supplemented with 10% (v/v) FBS, 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin). Cells were treated with 20 nM Romidepsin (Abcam, ab143287) or an equal volume of solvent (DMSO) for 16 hours. Transcription was inhibited by adding 5 µg/ml Actinomycin D (ApplicChem, A1489,0005) for 0, 2, 4 and 6 hours.

value: S181 transfected, RMD, 16h, ActD, 4h


title: condHeLa_rep1_RPF


title: 3231122-Hippocampus


title: 3124107-Hypothalamus


title: condHeLa_S181_RMD_time6

value: S181 transfected, RMD, 16h, ActD, 6h


title: condHeLa_S181_RMD_time2

value: S181 transfected, RMD, 16h, ActD, 2h


title: 3114102-Hippocampus


title: condHeLa_S181_DMSO_time4

value: S181 transfected, DMSO, 16h, ActD, 4h


title: 3114102-Hypothalamus

value: No


title: condHeLa_S181_DMSO_time6

value: HeLa

value: S181 transfected, DMSO, 16h, ActD, 6h


title: FGSC_control group_ChIP-seq

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
All RNA-Seq and ChIP-Seq data were trimmed and aligned to the mm9 reference genome using  bowtie2 .
Gene expression as FPKM was calculated by Cufflinks (version 2.2.1)(Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the number of reads relative RPKM values, and P-values for control and experimental group Sample.

source_name: FGSC_control group

extract_protocol:
For RNA-Seq,Total RNA was extracted from FGSCs using Trizol reagent (Life Technologies, CA). Next, 1000 ng of the digested RNA was used for the VAHTSTM mRNA-seqv2 Library Prep kit for Illumina1, and sequencing libraries were created according to the manufacturer's protocol.For ChIP-Seq, The  FGSCs were sheared with the Bioruptor water bath sonicator (Diagenode). The sequencing libraries were created according to the manufacturer's protocol.
For RNA-Seq, The extracted further treated with DNase to remove genomic DNA contamination. Isolation of mRNA was performed using the Oligotex mRNA Mini Kit (Qiagen GmbH, Hilden, Germany) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.For ChIP-Seq, the chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-H3K27ac (ab4729, Abcam). After reverse crosslinking, immunoprecipitated DNA and input DNA were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB).

tag: strain background

value: control group

value: Female germline stem cell (FGSC)

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: FGSC_028 treated group_ChIP-seq

source_name: FGSC_028 treated group

value: 028 treated group

tag: cell type


title: condHeLa_S181_DMSO_time0

value: S181 transfected, DMSO, 16h


title: condHeLa_S140_RMD_time6

value: S140 transfected, RMD, 16h, ActD, 6h


title: 3147111-PrefrontalCortex

value: Control


title: FGSC_028_treated_RNA-seq 3


title: condHeLa_S140_RMD_time4

value: S140 transfected, RMD, 16h, ActD, 4h


title: FGSC_028_treated_RNA-seq 2


title: condHeLa_S140_RMD_time2

value: S140 transfected, RMD, 16h, ActD, 2h


title: 3147111-Hippocampus

value: Hippocampus


title: condHeLa_S140_RMD_time0

value: S140 transfected, RMD, 16h


title: condHeLa_S140_DMSO_time4

value: S140 transfected, DMSO, 16h, ActD, 4h


title: FGSC_DMSO_RNA-seq 3


title: FGSC_028_treated_RNA-seq 1


title: 3147111-Hypothalamus

value: Hypothalamus


title: 3114102-PrefrontalCortex

value: Obese

value: PrefrontalCortex


title: 3144110-PrefrontalCortex

value: No


title: condHeLa_S140_DMSO_time6

value: HeLa

value: S140 transfected, DMSO, 16h, ActD, 6h


title: condHeLa_S140_DMSO_time0

value: S140 transfected, DMSO, 16h


title: 3144110-Hypothalamus


title: FGSC_DMSO_RNA-seq 2

value: control group

value: Female germline stem cell (FGSC)


title: condHeLa_S181_DMSO_time2

value: S181 transfected, DMSO, 16h, ActD, 2h


title: 3144110-Hippocampus


title: condHeLa_C2_RMD_time6

value: C2 transfected, RMD, 16h, ActD, 6h


title: condHeLa_S181_RMD_time0

value: S181 transfected, RMD, 16h


title: FGSC_DMSO_RNA-seq 1


title: condHeLa_C2_RMD_time4

value: C2 transfected, RMD, 16h, ActD, 4h


title: 3133108-PrefrontalCortex

value: Pravastatin


title: LAL-0058-A (MethylationEPIC)

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Minfi R package standard protocol
Minfi preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

source_name: Saliva

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: look-alike couple

tag: tissue

value: Normal human saliva sample


title: condHeLa_C2_DMSO_time2

value: C2 transfected, DMSO, 16h, ActD, 2h


title: condHeLa_C2_RMD_time0

value: C2 transfected, RMD, 16h


title: 3123107-PrefrontalCortex

tag: group

value: Restriction

tag: timepoint


title: LAL-0058-B (MethylationEPIC)


title: condHeLa_RMD_time6

value: RMD, 16h, ActD, 6h


title: condHeLa_RMD_time4

value: RMD, 16h, ActD, 4h


title: 3133108-Hypothalamus

tag: infantid

tag: birthgd

value: No

value: Hypothalamus


title: condHeLa_C2_DMSO_time4

tag: cell line

value: HeLa

value: C2 transfected, DMSO, 16h, ActD, 4h


title: condHeLa_S140_DMSO_time2

value: S140 transfected, DMSO, 16h, ActD, 2h


title: LAL-0047-B (MethylationEPIC)


title: LAL-0049-A (MethylationEPIC)


title: condHeLa_RMD_time2

value: RMD, 16h, ActD, 2h


title: 3123107-Hippocampus

tag: foster

tag: cohort

value: Hippocampus


title: condHeLa_C2_DMSO_time0

value: C2 transfected, DMSO, 16h


title: condHeLa_C2_RMD_time2

value: C2 transfected, RMD, 16h, ActD, 2h


title: condHeLa_DMSO_time2

value: DMSO 16h, ActD, 2h


title: 3132103-PrefrontalCortex

value: Pravastatin

tag: sample type

value: PrefrontalCortex


title: condHeLa_DMSO_time0

value: DMSO, 16h


title: LAL-0049-B (MethylationEPIC)

value: Normal human saliva sample


title: condHeLa_C2_DMSO_time6

value: C2 transfected, DMSO, 16h, ActD, 6h


title: 3133108-Hippocampus


title: CSU5-3_rep3

city: Beijing

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
Sequenced reads were preprocessed using Trimmomatic to remove reads in low quality and adaptor contamination (Bolger et al., 2014). The high-quality reads were aligned to Arabidopsis genome (TAIR 10) using Hisat2 (version 2.05; Kim et al., 2015) software using default parameters. Then, raw reads for each gene were calculated by HTseq (Anders et al., 2015) before calculating differential gene expression. Genes with a fold change >1.5 (FDR < 0.01) were defined as differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Col, csu5-1 and csu5-3 seedlings grown in constant W (14.59 μmol·m-2·s-1) light conditions for 5 days

extract_protocol:
Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
Quality control of DNase I treated mRNA was performed with an Agilent 2100 Bioanalyzer. cDNA libraries were generated, and sequencing was performed using the Illumina HiSeq 2500 platform according to the manufacturer's instruction (HiSequation 2500 user guide) by Novogene.

tag: ecotype

tag: genotype/variation

value: seedlings


title: condHeLa_DMSO_time6

tag: treatment

value: DMSO 16h, ActD, 6h


title: LAL-0046-B (MethylationEPIC)


title: CSU5-3_rep2

description: polyA RNA isolated


title: LAL-0046-A (MethylationEPIC)


title: CSU5-3_rep1

description: polyA RNA isolated


title: LAL-0047-A (MethylationEPIC)


title: LAL-0045-B (MethylationEPIC)


title: 3132103-Hypothalamus

value: No


title: CSU5-1_rep1

description: polyA RNA isolated


title: CSU5-1_rep2

description: polyA RNA isolated


title: Col-0 wildtype_rep2

description: polyA RNA isolated

value: wildtype


title: 3122106-Hippocampus

value: Restriction


title: condHeLa_DMSO_time4

value: HeLa

value: DMSO 16h, ActD, 4h


title: 3122106-Hypothalamus

value: Hypothalamus


title: CD8+ T cells, Treatment

data_processing:
The raw fastq sequences were trimmed with Cutadapt (version 2.5) before aligned to the mm10 using Bowtie (version 2.3). The bam files were then deduplicated using Picard (version 2.20) prior to being converted to tag files and then used MACS 2 (version 2.2.4) to call peaks. The differentially enriched peaks were identified using the MACS2 bdgdiff module. FDR of less or equal to 0.05 was used to correct for the multiple tests. Peaks were visualized by Deeptools2.0 (plotHeatmap)
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Transposed DNA was purified with MinElute PCR purification kit (Qiagen). Purified DNA was used for the construction of sequencing libraries.
DNA libraries for ATAC-seq were prepared using ATAC-Seq Library Prep Kit following manufacturer's protocols.

value: T cells

tag: genotype

value: global chromatin accessibility

value: Combined treatment


title: CD8+ T cells, Control

value: Treatment


title: condHeLa_RMD_time0

value: RMD, 16h


title: LAL-0029-B (MethylationEPIC)


title: LAL-0045-A (MethylationEPIC)


title: 3123107-Hypothalamus


title: CSU5-1_rep3

description: polyA RNA isolated


title: LAL-0033-B (MethylationEPIC)


title: 3132103-Hippocampus

value: Pravastatin

value: Hippocampus


title: 3112102-Hypothalamus

value: Obese


title: Org30 EYQ 0hr rep1

city: Salt Lake City

first: Yueqi

state: Utah

address: 20 South 2030 East

institute: University of Utah

description: no stimulation

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 100 and a reference database was created using STAR version 2.7.3a
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.28.1
Assembly: GRCh38
Supplementary files format and content: FeatureCounts output files combined into a single tab-delimited text file

source_name: EYQ

growth_protocol: The protocols used for generating organoids is described in the papers

extract_protocol:
Organoids were homogenized in Trizol (Invitrogen), and total RNA was purified using the RNeasy Micro Kit (Qiagen) with DNase I digestion. Ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina and verified using the Bioanalyzer RNA Nano Assay (Agilent).
After DNase treatment and rRNA depletion, strand-specific and single-end cDNA libraries were generated using the PE RNA-seq library kit (Illumina)

treatment_protocol:
Orhanoids produced from control and SHANK3+/- stem cell lines where treated
Organoids were silenced overnight with culture medium containing 1 uM TTX and100 uM APV.  The next day, KCl (or NCl as control) was added to the cultures (55 mM final conc) and organoids were incubated for 6h in KCl (or NCl) before harvesting. 3X KCl (or NaCl) stock solution contained: 170 mM KCl, 10 mM HEPES, 2 mM CaCl2, 1 mM MgCl2, pH 7.4. After stimulation (or no stimulation), organoids were placed into RNAlater solution (Thermo) overnight at +4C.

value: EYQ

value: telencephalic organoid

tag: Sex

value: female

value: vehicle

tag: age


title: Org28 H9 stim 6hr rep1

description: stimulate with 55 mM final concentration KCl for 6 hours

tag: cell type

value: WT


title: Org29 H9 stim 6hr rep2

value: stimulate with 55 mM final concentration KCl for 6 hours


title: LAL-0033-A (MethylationEPIC)

tag: look-alike couple

value: Normal human saliva sample


title: Org26 H9 0hr rep1

description: no stimulation


title: 3131106-PrefrontalCortex

value: No

value: PrefrontalCortex


title: Org31 EYQ 0hr rep2

description: no stimulation


title: Col-0 wildtype_rep3

description: polyA RNA isolated

value: wildtype

tag: tissue

value: seedlings


title: 3121105-PrefrontalCortex

tag: group

value: Restriction


title: Org32 EYQ stim 6hr rep1


title: Org33 EYQ stim 6hr rep2