title: K562-1.Nova

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

description: K562 cells, sequenced on Illumina NovaSeq 6000 platform, replica1

data_processing:
Only paired-end raw reads, where read 1 started with 9-11 Gs, read 2 started with 11-13 Ts and each base of each read had Phred quality score >20 were selected.
These reads were then aligned to the chrM of GRCh37/hg19, GRCm38/mm10, and GRCg6a/galGal6 assemblies of human, mouse, and chicken genomes from UCSC Genome Browser (PMID: 12045153) respectively using BWA-MEM (v0.7.12) with default settings.
Only pairs of reads where both reads 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
The 5’-end was defined as the first base after 9-11 Gs in read 1.
Read count of each position was obtained and normalized depth was calculated with read count of each position being normalized to total number of aligned reads.
Assembly: GRCh37/hg19, GRCm38/mm10, and GRCg6a/galGal6
Supplementary files format and content: Processed data are in BED files containing coordinates of mitochondrial genome positions with free DNA 5'-end signals. The 4th and 5th columns show the raw and normalized count of each position.

growth_protocol: Human breast cancer cell line BT549, human cervical carcinoma cell line HeLa, human liver cancer cell line HepG2, and human chronic myeloid leukemia cell line K562 were maintained in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco). Mouse neuroblastoma cell line N2a was cultured in MEM/EBSS (HyClone) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco). All cell lines were cultured at 37℃ in 5% CO2. Adult male mice (three-month-old) of C57BL/6J strain were used to extract heart and liver. The tissues were frozen in liquid nitrogen immediately after isolation. Chicken heart and liver samples were bought from the fresh market and frozen in liquid nitrogen within 30 min. The animal tissues were cut into pieces and ground with mortar in liquid nitrogen. The ground tissues were stored at -80 ℃ prior to DNA isolation.

extract_protocol:
DNA was isolated with TIANamp Genomic DNA Kit (Tiangen)
The biochemistry part of 3’ ends tailing was based on the SSiNGLe-ILM protocol from our previous study (PMID: 31862872). Briefly, 100 ng of the purified DNA was denatured at 95℃ for 5 min in 19 µl volume containing 2 µl of 10x TdT buffer and 2 µl of 2.5 mM CoCl2 followed by rapid snap-cooling on ice. TdT (5 units, NEB) and 2 µl of 10 mM dATP (Takara) were then added to denatured DNA to a total volume of 22 µl and incubated at 37°C for 30 min. To block free 3′-OH ends, samples was mix with 2 µl of 10 mM ddNTP (Roche) and incubated at 37℃ for additional 30 min, followed by enzyme of VAHTS DNA clean beads to a final volumn of 15 μl and mixed with 2 µl of 10x Taq buffer (Tiangen), 1.6 µl of 2.5 mM dNTP mix (Takara), 1 µl of 10 µM of polyT primer (a chimeric DNA-RNA oligo-d(T)50-r(T)3 oligonucleotide) and 1 unit of Taq DNA polymerase (Tiangen). The amplification conditions were as follows: initial denaturation at 94℃ for 3 min, followed by 10 cycles of denaturation at 94 °C for 30 s, annealing at 55℃ for 30 s and extension at 72℃ for 30 s. The PCR products were purified with 2x volumes of VAHTS DNA clean beads and tailed with dCTP (Takara) with the same procedure used for polyA tailing, followed by blocking of 3’-OH ends as described above. The tailing products were purified with 2x volume of VAHTS DNA clean beads and all purified DNA was PCR-amplified with P5_10N10G (CTACACGACGCTCTTCCGATCTAGTTGCGGATGGGGGGGGGGHN) and P7_T12 (GTTCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTVN) primers with the following amplification conditions: initial denaturation at 94℃ for 3 min; 1 cycle of denaturation at 94℃ for 30 s, annealing at 55℃ for 1 min and extension at 72℃ for 1 min; 1 cycle of denaturation at 94℃ for 30 s, annealing at 37℃ for 1 min and slow ramp at 2℃ per minute to 72℃; 30 cycles at 94℃ for 30 s, annealing at 60℃ for 30 s, and extension at 72℃ for 30 s; final extension at 72℃ for 7 min. The amplified DNA was purified with 2x volumes of VAHTS DNA clean beads to a final volumn of 17 μl of water, and 4 µl PCR products were used as the template for the second round of nested PCR with lIlumina_P5 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and primer Illumina_P7 (CAAGCAGAAGACGGCATACGAGATcgtgatGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) as primers under the following conditions.: 94℃ for 3 min; 6 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. PCR products were purified with 2x volumes of VAHTS DNA Clean Beads.

tag: cell line

value: WT


title: w1118_ZT7_1_S4_

status: Public on Jun 14 2023

type: SRA

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

department: Biology department

country: USA

institute: Brandeis University

library_source: transcriptomic

data_processing:
data were aligned to the Drosophila melanogaster dm6 genome and transcriptome version using STAR
quantification was done with ESAT
The circadian analysis was performed using the package MetaCycle
For each circadian timepoint, three replicates were analyzed. Since each replicate was sequenced separately, the counts were divided by the maximum value in each replicate after normalizing by library size. Genes with more than two zero counts at any time point were discarded. The amplitude for each replicate was calculated as the maximum divided by the minimum for each gene. The JTK algorithm was used for the circadian analysis
A gene was considered a cycler if the JTK p-adjusted value was less than 0.05 and the amplitude was more than 2.
Assembly: dm6
Supplementary files format and content: normalized counts

molecule: total RNA

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All crosses were performed and raised at 25 °C in a 12:12 Light/Dark cycle (LD) conditions.

extract_protocol:
RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DnaseI (NEB, M0303L).
150 ng of RNA as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol

tag: tissue

value: Brain

tag: genotype

tag: treatment


title: Old (24 month) Vertebrae 3

city: Rochester

first: David

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Analysis was performed using the edgeR package in R and normalized expression was used to determine the log fold-change
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw values for each sample

organism: Mus musculus

source_name: Vertebrae (L4-5)

extract_protocol:
RNA was harvested using QIAzol reagent and purified using the Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Lib NEBNEXT Small RNA v2 Kit following manufacturer's protocols.

value: Vertebrae (L4-5)

tag: Sex

value: Male

tag: age

value: 24 month


title: K562-2.Nova

country: China

description: K562 cells, sequenced on Illumina NovaSeq 6000 platform, replica2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: human chronic myeloid leukemia cell line


title: w1118_ZT11_2_S18_


title: Myc-Cap-M-D3

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)

source_name: ATCC cell line cells

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

value: ATCC cell line cells

tag: patient donor/cell_line

value: Myc-Cap

tag: genome build

tag: cpg coverage

tag: bisulfite conversion_rate

tag: qc

value: fail


title: BP02, scRNA

city: Epalinges

first: Mathilde

last: Foglierini-Perez

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

description: 10X genomics

data_processing:
BCL-files were demultiplexed into samples using bcl2fastq 2.20
scRNA: The barcoded processing and gene counting were made using the Cell Ranger v6.0.0 software with method count
VDJ: The barcoded processing, V(D)J sequences and annotations were made using the Cell Ranger v6.0.0 software with method vdj
Assembly: mRNA: cellranger gex-GRCh38-2020-A
Assembly: VDJ: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Assembly: hg38
Supplementary files format and content: mRNA: h5 of count matrix
Supplementary files format and content: VDJ: tsv table of cell annotations (AIRR format)

source_name: biopsed skin

extract_protocol:
4 mm punch biopsies were harvested from the IDR site 24h after skin test from 3 vaccinated controls. Skin biopsies were mechanically and enzymatically digested using DNAse I and collagenase D. Single-cell suspensions were stained with APC conjugated anti-CD45 antibodies. Fluorescence-activated cell sorting (FACS) of CD45-labelled cells was performed on a BD aria sorter for 10x RNA sequencing.
Library construction was performed according to the manufacture's protocol (single cell 5' v2 (dual index) + human TCR amplification). To generate gel beads-in-emulsion (GEMs), T cells were loaded to Chromium Next GEM Chip K together with master mix, gel beads and partitioning oil. After GEM generation, poly-A RNA was retrotranscripted to cDNA and Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode were included. For final library construction, pooled cDNA was cleaned up with Silane DynaBeads, further amplified by PCR and size-restricted by using SPRIselect reagent. To generate TCR libraries, a part of the amplified cDNA was used for V(D)J amplification followed by SPRIselect cleanup steps. During final library construction and V(D)J amplification, Illumina R2 primer and paired-end constructs were included. scRNA-seq and TCR seq

value: biopsed skin

value: CD45 immune cell

tag: antibodies/tag

tag: library type

value: mRNA


title: BP02, TCRseq

description: 10X genomics


title: Myc-Cap-M-D2

value: pass


title: Myc-Cap-M-C3


title: HeLa-2.Nova

description: HeLa cells, sequenced on Illumina NovaSeq 6000 platform, replica2

source_name: HeLa

value: HeLa

value: human cervical carcinoma cell line


title: Old (24 month) Vertebrae 2


title: Pooled PTGs from Gcm2-/- mice complemented with Pth-tdTomato mouse ESCs, biological replicate 2

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequence data were mapped to the mouse reference genome with Gfp and tdTomato using Cell Ranger v.7.0.0.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Mouse ESC-derived PTG

extract_protocol:
We performed a series of experiments twice (each experiment was titled para10_215 and para10_222). Adult Gcm2-/- mice complemented with mESCs showing 50‒70% chimerism of peripheral blood cells were used (three for para10_215 and five for para10_222). A pair of mESC-derived PTGs was removed and placed in a 20-μl PBS drop. Isolated mESC-derived PTGs were cut into small pieces using Vannas scissors. Minced mESC-derived PTGs were transferred into a 1.5 ml siliconized tube (Watson). They were incubated in 25μl of papain solution (Worthington) for 15 min at 37°C under 5% CO2 in air. Twenty-five μl of 10 mg/ml collagenase XI (Sigma) / HBSS (Wako) supplemented with 120 μl of 170mM CaCl2 was added into the same tube, which was incubated for 15 min at 37°C under 5% CO2 in air. Finally, 10μl of 0.25% trypsin-EDTA was added. After 1 min, pipetting was done several times, yielding single cells that were suspended in 140 μl of medium containing equal volumes of 10% FBS/DMEM and ovomucoid protease inhibitor (Worthington) and placed on ice. Doublets were discriminated using FACSAria Fusion Flow Cytometer. Sorted single cells were collected in 500μl 0.1% BSA /PBS in a 1.5 ml siliconized tube. The cell suspension was centrifuged at 300g at room temperature for 5 min.
Single-cell gel beads-in-emulsion were generated using the Chromium Controller (10x Genomics). Libraries were generated using the Single Cell 3’ Reagent Kit v.3.1 for dual index (10x Genomics) according to manufacturer’s instructions.

value: Mouse ESC-derived PTG

tag: strain

value: Gcm2-/- on an BDF1B6 background complemented with Pth-tdTomato mouse ESCs

value: 6-13 weeks old

value: pooled male and female

tag: number of_mice

tag: chimerism of_peripheral_blood_cells


title: HepG2-1.Nova

description: HepG2 cells, sequenced on Illumina NovaSeq 6000 platform, replica1

tag: cell line

value: human liver cancer cell line

value: WT


title: HeLa-1.Nova

description: HeLa cells, sequenced on Illumina NovaSeq 6000 platform, replica1


title: Myc-Cap-M-C2


title: Pooled PTGs from Gcm2-/- mice complemented with Pth-tdTomato mouse ESCs, biological replicate 1

description: 10x Genomics

tag: tissue

value: 9-12 weeks old


title: Old (24 month) Vertebrae 1

value: Vertebrae (L4-5)

value: Male

value: 24 month


title: w1118_ZT23_1_S12_

value: Brain

tag: genotype


title: Myc-Cap-M-B3

value: ATCC cell line cells

value: Myc-Cap


title: Mouse Calvarial Osteoblasts, miR-19a-3p miRNA mimic [DM5]

data_processing:
RNA-sequencing was performed on a HiSeq4000 (Illumina®) using TruSeq SBS sequencing software (v3) and SCS data collection software (v.1.4.8)
Fastq files were mapped to the murine reference genome mm10
Assembly: mm10
Supplementary files format and content: tab-delimited files include raw counts for each gene per sample

source_name: Mouse Calvaria

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

extract_protocol:
48 hours after transfection, RNA was harvested using QIAzol reagent and purified using the Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Total RNA Prep Kit following manufacturer's protocols.

treatment_protocol: Negative control or miR-19a-3p miRNA mimics (purchased from QIAGEN) were transfected using Dharmacon Transfection reagent.

value: Mouse Calvaria

value: Primary Osteoblast

value: Female

tag: treatment

value: miR-19a-3p miRNA mimic transfected


title: Control PTG cells, Experiment 2, biological replicate 4

description: SMART-Seq HT

data_processing:
RNA-seq datasets were analyzed using Galaxy software (https://usegalaxy.org/). Sequence data were annotated by the reference genome (GRCm39_version104) using the Salmon quant in Galaxy.
Assembly: GRCm39
Supplementary files format and content: Salmon output files (.tabular.txt)

source_name: PTG cells

extract_protocol:
Under fluorescent-light illumination, 10–20 tdTomato-expressing PTG cells were manually collected using a micromanipulator (IX73, Olympus).
The SMART-Seq® HT Kit (634438, Takara) was used according to manufacturer’s instructions, minimally modified, to synthesize cDNA from total RNA derived from PTG cells.

value: PTG cells

value: 11 weeks old

tag: Sex

value: female


title: Myc-Cap-M-E3

value: pass


title: BT549-2.Nova

description: BT549 cells, sequenced on Illumina NovaSeq 6000 platform, replica2

value: human breast cancer cell line


title: Mouse Calvarial Osteoblasts, miR-19a-3p miRNA mimic [DM6]


title: Control PTG cells, Experiment 2, biological replicate 3

description: SMART-Seq HT

tag: age


title: Control PTG cells, Experiment 2, biological replicate 2

description: SMART-Seq HT

tag: cell type


title: Mouse Calvarial Osteoblasts, Negative Control miRNA mimic [DM3]

value: Negative Control miRNA mimic transfected


title: w1118_ZT11_1_S6_


title: Mouse Calvarial Osteoblasts, miR-19a-3p miRNA mimic [DM4]


title: Myc-Cap-M-A3

tag: patient donor/cell_line


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 4, biological replicate 4

description: SMART-Seq HT

value: Gcm2-/- on an BDF1B6 background complemented with Pth-tdTomato mouse ESCs

value: 9 weeks old

value: male


title: Control PTG cells, Experiment 2, biological replicate 1

description: SMART-Seq HT


title: T900_GS6_M_B8

source_name: Single prostate tumor cell

value: Single prostate tumor cell

tag: genome build


title: Mouse Calvarial Osteoblasts, Negative Control miRNA mimic [DM2]


title: Myc-Cap-M-A2

tag: cpg coverage


title: T900_GS6_M_B7

tag: bisulfite conversion_rate

value: fail


title: HepG2-2.Nova

description: HepG2 cells, sequenced on Illumina NovaSeq 6000 platform, replica2

value: human liver cancer cell line

value: WT


title: T900_GS6_M_B6

tag: qc


title: Mouse Calvarial Osteoblasts, Negative Control miRNA mimic [DM1]

value: Mouse Calvaria


title: BT549-1.Nova

description: BT549 cells, sequenced on Illumina NovaSeq 6000 platform, replica1


title: T900_GS6_M_B4


title: miRNA_768_T1

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

description:
Female - NO ICU
768_S92

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed reads were further processed with the FASTX Toolkit v0.0.14 to filter out reads with tail quality < 15 nucleotides and retain reads of 16-25 nucleotides length for downstream analyses.
High-quality reads were subject to small RNAs annotation and quantification using the online tool OASIS
Assembly: Grch38

source_name: Female - NO ICU

extract_protocol:
Small RNA libraries were prepared from 400ng of high-quality total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina
The library size distribution was checked using a 2100 Bioanalyzer instrument to ensure correct size amplicons are selected for sequencing.
ndividual libraries were quantified, and equimolar quantities of each library pooled and sequenced on an S1 flow cell using a NovaSeq instrument

tag: disease state

value: Blood

tag: visit

tag: outcome

value: NO ICU


title: miRNA_766_T1

description:
Female - ICU
766_S84

source_name: Female - ICU

value: Female

value: ICU


title: miRNA_757_T1

description:
Male - NO ICU
757_S76

source_name: Male - NO ICU

value: Male


title: miRNA_769_T1

description:
Male - NO ICU
769_S5


title: T900_GS6_M_B5


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 4, biological replicate 2

description: SMART-Seq HT

value: PTG cells

tag: strain


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 3, biological replicate 4

description: SMART-Seq HT

value: female


title: miRNA_754_T1

description:
Male - NO ICU
754_S70


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 3, biological replicate 3

description: SMART-Seq HT


title: miRNA_750_T1

description:
Male - NO ICU
750_S25


title: cKO1

city: New York

first: Jianlong

last: Wang

state: NY

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized expression levels for every gene and every sample

source_name: Tex10 conditional knockout testis 1

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using Ovation Mouse RNA-seq kit (NuGEN, #0348-32) for batch 1 and 3 RNA samples, and Universal Plus mRNA-Seq with NuQuant Kit (TECAN, 0520-A01) for batch 2 RNA samples according to manufactory protocol.

tag: cell types

value: cells from mouse testis

value: untreated


title: cKO2

source_name: Tex10 conditional knockout testis 2


title: miRNA_740_T1

description:
Male - NO ICU
740_S17


title: EpiLC_OE1

source_name: Tex10 overexpression clone 1 EpiLCs

value: EpiLCs


title: WT2

source_name: Wildtype testis 2


title: EpiLC_EV

source_name: empty-vector control EpiLCs


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 3, biological replicate 2

description: SMART-Seq HT

value: Gcm2-/- on an BDF1B6 background complemented with Pth-tdTomato mouse ESCs

value: 9 weeks old


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 4, biological replicate 1

description: SMART-Seq HT

value: male


title: T900_GS6_M_A8

value: Single prostate tumor cell

value: fail


title: WT1

source_name: Wildtype testis 1


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 3, biological replicate 1

description: SMART-Seq HT


title: miRNA_737_T1

description:
Male - ICU
737_S9

source_name: Male - ICU


title: T900_GS6_M_B3

value: pass


title: miRNA_728_T1

description:
Female - NO ICU
728_S95


title: T900_GS6_M_A6


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 4, biological replicate 3

description: SMART-Seq HT


title: EpiLC_OE2

source_name: Tex10 overexpression clone 2 EpiLCs


title: miRNA_732_T1

description:
Female - NO ICU
732_S1


title: T900_GS6_M_B1


title: miRNA_731_T1

description:
Female - NO ICU
731_S75


title: miRNA_726_T1

description:
Male - NO ICU
726_S87


title: Grafted mESC-derived PTG cells from Gcm2-/- mice, biological replicate 2

description: SMART-Seq HT

value: 12 weeks old


title: miRNA_730_T1

description:
Female - NO ICU
730_S8

value: Blood


title: T900_GS6_M_A5


title: Grafted mESC-derived PTG cells from Gcm2-/- mice, biological replicate 4

description: SMART-Seq HT


title: T900_GS6_M_B2


title: T900_GS6_M_A4


title: Grafted mESC-derived PTG cells from Gcm2-/- mice, biological replicate 3

description: SMART-Seq HT


title: D4PGCLC_OE2

source_name: Day4 Tex10 overexpression clone 2 PGCLCs

value: PGCLCs derived from EpiLCs


title: D6PGCLC_OE2

source_name: Day6 Tex10 overexpression clone 2 PGCLCs


title: miRNA_725_T1

description:
Female - NO ICU
725_S59

value: Female

value: NO ICU


title: T900_GS6_M_A7


title: miRNA_722_T1

description:
Female - NO ICU
722_S51


title: D4PGCLC_EV

source_name: Day4 empty-vector control PGCLCs


title: T900_GS6_M_A3


title: D6PGCLC_OE1

source_name: Day6 Tex10 overexpression clone 1 PGCLCs


title: miRNA_719_T1

description:
Female - NO ICU
719_S35


title: Mouse ESC-derived PTG cells from the Gcm2-/- rat, biological replicate 4

description: SMART-Seq HT

source_name: PTG cells

value: Gcm2-/- Wistar rat complemented with Pth-tdTomato mouse ESCs

value: Neonate

value: unknown


title: Mouse ESC-derived PTG cells from the Gcm2-/- rat, biological replicate 2

description: SMART-Seq HT

value: PTG cells


title: T900_GS6_M_A2

source_name: Single prostate tumor cell


title: miRNA_716_T1

description:
Female - NO ICU
716_S27

source_name: Female - NO ICU


title: miRNA_721_T1

description:
Female - NO ICU
721_S43


title: T1519_GS6_M_H3


title: Mouse ESC-derived PTG cells from the Gcm2-/- rat, biological replicate 1

description: SMART-Seq HT


title: T900_GS6_M_A1


title: D2PGCLC_OE1

source_name: Day2 Tex10 overexpression clone 1 PGCLCs

value: untreated


title: D2PGCLC_EV

source_name: Day2 empty-vector control PGCLCs


title: miRNA_715_T1

description:
Female - NO ICU
715_S56


title: T1519_GS6_M_G3


title: D2PGCLC_OE2

source_name: Day2 Tex10 overexpression clone 2 PGCLCs


title: miRNA_714_T1

description:
Female - NO ICU
714_S48


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 2, biological replicate 3

description: SMART-Seq HT

value: female


title: Mouse ESC-derived PTG cells from the Gcm2-/- rat, biological replicate 3

description: SMART-Seq HT


title: T1519_GS6_M_H2


title: D6PGCLC_EV

source_name: Day6 empty-vector control PGCLCs


title: dD4PGCLC_rep1

source_name: dTAG13-treated Day 4 PGCLCs rep 1


title: Grafted mESC-derived PTG cells from Gcm2-/- mice, biological replicate 1

description: SMART-Seq HT

value: Gcm2-/- on an BDF1B6 background complemented with Pth-tdTomato mouse ESCs


title: D4PGCLC_OE1

source_name: Day4 Tex10 overexpression clone 1 PGCLCs


title: dD4PGCLC_rep2

source_name: dTAG13-treated Day 4 PGCLCs rep 2


title: miRNA_711_T1

description:
Male - NO ICU
711_S40

source_name: Male - NO ICU

value: Male


title: T1519_GS6_M_F3


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 2, biological replicate 1

description: SMART-Seq HT

value: 9 weeks old


title: dD2PGCLC_rep1

source_name: dTAG13-treated Day 2 PGCLCs rep 1


title: T1519_GS6_M_G2

value: Single prostate tumor cell


title: miRNA_710_T1

description:
Female - NO ICU
710_S32


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 2, biological replicate 2

description: SMART-Seq HT


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 1, biological replicate 3

description: SMART-Seq HT


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 1, biological replicate 2

description: SMART-Seq HT


title: T1519_GS6_M_G1

value: fail


title: EpiLC_rep1

source_name: EpiLCs rep 1

value: EpiLCs


title: miRNA_709_T1

description:
Male - ICU
709_S24

source_name: Male - ICU

value: ICU


title: dD2PGCLC_rep2

source_name: dTAG13-treated Day 2 PGCLCs rep 2


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 2, biological replicate 4

description: SMART-Seq HT


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 1, biological replicate 4

description: SMART-Seq HT


title: Mouse ESC-derived PTG cells from Gcm2-/- mice, Experiment 1, biological replicate 1

description: SMART-Seq HT


title: T1519_GS6_M_E3


title: miRNA_701_T1

description:
Male - NO ICU
701_S88

value: Blood


title: miRNA_708_T1

description:
Male - ICU
708_S16


title: miRNA_700_T1

description:
Male - NO ICU
700_S80


title: T1519_GS6_M_D3


title: miRNA_707_T1

description:
Female - NO ICU
707_S96


title: T1519_GS6_M_F1


title: EpiLC_rep2

source_name: EpiLCs rep 2


title: Control PTG cells, Experiment 1, biological replicate 3

description: SMART-Seq HT

value: 8 weeks old

value: male


title: T1519_GS6_M_E1


title: D4PGCLC_rep2

source_name: Day4 PGCLCs rep 2

value: PGCLCs derived from EpiLCs

value: DMSO


title: T1519_GS6_M_E2


title: D2PGCLC_rep2

source_name: Day2 PGCLCs rep 2


title: D2PGCLC_rep1

source_name: Day2 PGCLCs rep 1


title: D4PGCLC_rep1

source_name: Day4 PGCLCs rep 1


title: Control PTG cells, Experiment 1, biological replicate 4

description: SMART-Seq HT

source_name: PTG cells


title: miRNA_441_T1

description:
Male - ICU
441_S64


title: miRNA_443_T1

description:
Male - ICU
443_S72


title: miRNA_438_T1

description:
Male - ICU
438_S2


title: miRNA_440_T1

description:
Male - ICU
440_S10


title: T1519_GS6_M_D2

source_name: Single prostate tumor cell


title: T1519_GS6_M_C3


title: Control PTG cells, Experiment 1, biological replicate 2

description: SMART-Seq HT


title: Inprep1

data_processing:
Alignment was done by using Bowtie2 (v2.3.4.3)
PCR duplicates were removed using Samtools (v1.9).
Peaks were called using MACS2 (v2.1.2) to compare IP samples with input samples using parameter p-value 0.05 for Tex10 and 0.01 for H3K4me3, respectively. Only peaks called from both replicates were kept.
Annotation was done by using the script annotatePeaks.pl of HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: peak bed files

source_name: Day 2 PGCLCs- input DNA rep 1

extract_protocol:
ChIP DNA was extracted by using SampleChIPR Enzymatic Chromatin IP Kit (Cell Signaling, #9005).
library was prepared using NEBNext® Ultra™ II DNA Library Prep (E7103S)

value: Day 2 PGCLCs

tag: tatreatment

tag: chip antibody


title: miRNA_437_T1

description:
Male - ICU
437_S71

tag: tissue


title: HAD2rep2

source_name: Day 2 PGCLCs- HA-Tex10 rep 2

value: HA-tag (Abcam, ab9110 )


title: T1519_GS6_M_D1


title: Control PTG cells, Experiment 1, biological replicate 1

description: SMART-Seq HT

value: PTG cells


title: Inprep2

source_name: Day 2 PGCLCs- input DNA rep 2

value: untreated


title: Treg cells, Helios gRNA, rep1

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description: Hi-C library

library_source: other

data_processing:
Hi-C and PLAC-seq data were aligned to the mm9 reference genome using BWA-MEM. Reads were filtered (MAPQ >= 30) and manually paired. PCR duplicate reads were removed using Picard. Contact matrices were generated and normalized using the iterative correction method. Enriched contacts in the PLAC-seq data were identified using HICCUPs
Assembly: mm9
Supplementary files format and content: hic files (Hi-C)

source_name: Thymus

extract_protocol:
A single cell suspension from the thymus or the spleen was prepared, then pre-enriched using EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, Cat# 19852), and stained with fluorescent-conjugated primary antibodies on ice for 30 minutes. In situ Hi-C experiments were performed as previously described (Rao et al. Cell 2014) using restriction enzyme MboI (NEB) with minor modifications. Briefly, 0.5×106 cells per each developmental stage from DN to mature thymic Treg cells, and 1×106 splenic Tcon and Treg cells were FACS-sorted and collected for individual biological replicate. Cells were resuspended in RMPI1640 medium at a concentration of 1×106 cells per mL, cross-linked with 1% formaldehyde for 10 minutes at room temperature with rotating, and subsequently lysed and digested with 100 Units of MboI/1 million cells at 37 °C for 2 hours. The following steps including Making of DNA ends, Proximity ligation and Crosslink Reversal. For PLAC-seq experiments, Briefly, 20×106 cells per biological replicate were crosslinked in 1% formaldehyde for 10 minutes at room temperature with rotating. After DNA cutting with the restriction enzyme MboI, marking DNA ends with biotin-14-dATP, and proximity ligation of DNA ends, the resultant chromatin was sonicated to 200-600 bp using Covaris E229 sonicator for 10 min. Sonicated chromatin was pre-cleared with Protein A+G magnetic beads followed by overnight chromatin immunoprecipitations with 5 µg Foxp3 antibody.
DNA Shearing and Size Selection, Biotin pull-down and Preparation for Illumine Sequencing, Final amplification and Purification were processed as previously described (Rao et al. Cell 2014). Libraries were prepared using NuGen Ovation Ultralow Library System V2 kit according to the manufacturer’s instructions, and sequenced by an Illumina sequencing.

value: Thymus

value: CD45+CD4+CD8-CD25+Foxp3-Thy1.1+ wild-type Treg cells

tag: genotype

tag: treatment

value: Helios enhancer gRNA


title: Treg cells, Foxp3 gRNA, rep2

description: Hi-C library

value: Foxp3 gRNA


title: Treg cells, Helios gRNA, rep2

description: Hi-C library


title: miRNA_433_T1

description:
Male - ICU
433_S81

tag: Sex

value: Male


title: H3K4me3rep2

source_name: Day 2 PGCLCs- H3K4me3 rep 2

value: H3K4me3 (Abcam, ab8580)


title: miRNA_432_T1

description:
Male - ICU
432_S73


title: T1519_GS6_M_B2

tag: cell type

value: Single prostate tumor cell

value: fail


title: miRNA_431_T1

description:
Male - ICU
431_S57

value: Blood

value: ICU


title: T1519_GS6_M_C1

tag: patient donor/cell_line


title: T1519_GS6_M_B3

tag: genome build


title: miRNA_434_T1

description:
Female - ICU
434_S89

source_name: Female - ICU

value: Female


title: Treg cells, Ctrl_sgRNA, rep2

description: Hi-C library

value: control gRNA


title: Treg cells, Ctrl_sgRNA, rep1

description: Hi-C library


title: HAD2rep1

source_name: Day 2 PGCLCs- HA-Tex10 rep 1


title: Treg cells, Foxp3 gRNA, rep1

description: Hi-C library


title: miRNA_425_T1

description:
Female - ICU
425_S41


title: Treg_GFP_Foxp3_WT2

description: Hi-C library

data_processing:
Hi-C and PLAC-seq data were aligned to the mm9 reference genome using BWA-MEM. Reads were filtered (MAPQ >= 30) and manually paired. PCR duplicate reads were removed using Picard. Contact matrices were generated and normalized using the iterative correction method. Enriched contacts in the PLAC-seq data were identified using HICCUPs
Assembly: mm9
Supplementary files format and content: cool files (Hi-C)
Supplementary files format and content: hic files (PLAC-seq)

value: CD45+CD4+CD8-CD25+Foxp3-GFP+ Foxp3 WT T-cells

value: Foxp3 WT


title: miRNA_419_T1

description:
Male - ICU
419_S33


title: H3K4me3rep1

source_name: Day 2 PGCLCs- H3K4me3 rep 1

value: Day 2 PGCLCs


title: N900_2N_M_H5

source_name: Single normal prostate cell

value: Single normal prostate cell

tag: cpg coverage

value: pass


title: MF 14

type: RNA

first: Rachael

middle: A

last: Clark

address: 221 Longwood Ave EBRC 501

department: Dermatology

institute: Brigham and Women's Hospital

hyb_protocol: RNA was hybridized to probes in the NanoString Human PanCancer Immune Profiling Panel, washed, and processed according to manufacturer's protocol

scan_protocol: Hybridized probes were imaged and measured on a NanoString nCounter instrument according to manufacturer's protocol

data_processing: Normalization and analysis of NanoString data were carried out using nSolver software. Normalization factors were calculated based on 40 reference genes included in the Human PanCancer Immune Profiling Panel.

label: NanoString PanCancer Immune Profiling CodeSet

source_name: Skin

extract_protocol: Total RNA was extracted from samples with the Qiagen Rneasy Mini Kit as per manufacturer's protocol

treatment_protocol: Skin biopsies were taken from untreated lesional skin from mycosis fungoides patients or from healthy skin obtained from plastic surgery procedures

tag: disease

value: Untreated mycosis fungoides


title: MF 13

label_protocol: RNA was hybridized to probes in the NanoString Human PanCancer Immune Profiling Panel, washed, and processed according to manufacturer's protocol


title: MF 17


title: MF 15


title: T1519_GS6_M_B1

tag: bisulfite conversion_rate

tag: qc


title: T1519_GS6_M_C2


title: MF 12


title: miRNA_427_T1

description:
Male - ICU
427_S49

source_name: Male - ICU

tag: disease state

tag: visit


title: T1519_GS6_M_A3


title: TReg2

description: Hi-C library

source_name: Spleen

value: Spleen


title: Treg_Foxp3_PLACseq

description: PLAC-seq library

value: Thymus


title: Treg_GFP_Foxp3_WT1

description: Hi-C library


title: T1519_GS6_M_A2


title: N900_2N_M_H6


title: miRNA_410_T1

description:
Male - ICU
410_S30

tag: outcome


title: N900_2N_M_G4


title: MF 16


title: miRNA_422_T1

description:
Male - ICU
422_S65


title: T1519_GS6_M_A1


title: MF 11


title: miRNA_414_T1

description:
Male - ICU
414_S38


title: miRNA_404_T1

description:
Female - NO ICU
404_S22

source_name: Female - NO ICU

value: NO ICU


title: Treg_GFP_Foxp3_KIKO2

description: Hi-C library

value: CD45+CD4+CD8-CD25+Foxp3-GFP+ Foxp3 KO T-cells

value: Foxp3 KO


title: TCon2

description: Hi-C library


title: Treg_GFP_Foxp3_KIKO1

description: Hi-C library


title: miRNA_412_T1

description:
Male - ICU
412_S63

value: Male


title: MF 9


title: miRNA_409_T1

description:
Male - ICU
409_S62


title: N900_2N_M_G6


title: miRNA_121_T1

description:
Female - NO ICU
121_S6


title: TReg1

description: Hi-C library


title: N900_2N_M_G5


title: N900_2N_M_F6


title: MF 10


title: N900_2N_M_E6


title: MF 7


title: miRNA_124_T1

description:
Male - NO ICU
124_S14

source_name: Male - NO ICU


title: N900_2N_M_F5


title: N900_2N_M_E5


title: MF 8


title: miRNA_118_T1

description:
Male - NO ICU
118_S93


title: N900_2N_M_F4


title: DSMwt_Treg2

description: Hi-C library

value: CD45+CD4+CD8-CD25+Foxp3-Thy1.1+ DSM mutant T-cells

value: wild type


title: DP_rep2

description: Hi-C library

value: CD45+CD4+CD8+ T-cells


title: DSMwt_Treg1

description: Hi-C library


title: miRNA_105_T1

description:
Female - NO ICU
105_S52

value: Female

value: Blood


title: miRNA_106_T1

description:
Female - NO ICU
106_S60


title: MF 6


title: DSMmt_Treg2

description: Hi-C library

value: DSM mutant


title: MF 3


title: DSMmt_Treg1

description: Hi-C library


title: miRNA_114_T1

description:
Male - NO ICU
114_S86


title: N900_2N_M_D4

value: fail


title: MF 5


title: MF 1


title: miRNA_113_T1

description:
Male - NO ICU
113_S68


title: miRNA_100_T1

description:
Female - NO ICU
100_S54


title: N900_2N_M_E4


title: CD8_rep2

description: Hi-C library

value: CD45+CD4-CD8+ T-cells


title: MF 4


title: N900_2N_M_D5

value: Single normal prostate cell


title: N900_2N_M_D6

value: pass


title: DN_rep2

description: Hi-C library

value: CD45+CD4-CD8- T-cells


title: N900_2N_M_C4


title: DN_rep1

description: Hi-C library


title: miRNA_103_T1

description:
Male - NO ICU
103_S44


title: DP_rep1

description: Hi-C library


title: MF 2

value: Untreated mycosis fungoides


title: N900_2N_M_C5


title: healthy_skin 2

value: Healthy


title: healthy_skin 4


title: miRNA_98_T1

description:
Male - NO ICU
98_S36

value: NO ICU


title: TCon1

description: Hi-C library

value: Spleen


title: N900_2N_M_B5


title: miRNA_97_T1

description:
Male - NO ICU
97_S28


title: healthy_skin 3


title: CD8_rep1

description: Hi-C library

value: Thymus


title: N900_2N_M_B6


title: CD4_Q4_rep2

description: Hi-C library


title: CD4_Q3_rep2

description: Hi-C library


title: miRNA_87_T1

description:
Female - NO ICU
87_S46


title: N900_2N_M_A6


title: miRNA_86_T1

description:
Male - NO ICU
86_S55

value: Male


title: Pt 14 Post PUVA

treatment_protocol: Skin biopsies were taken from lesional skin from mycosis fungoides patients before or after phototherapy treatment (PUVA), or from healthy skin obtained from plastic surgery procedures

value: Mycosis fungoides

value: Post-PUVA


title: CD4_Q4_rep1

description: Hi-C library


title: N900_2N_M_B4


title: CD4_Q3_rep1

description: Hi-C library


title: N900_2N_M_A5


title: CD4_Q2_rep2

description: Hi-C library


title: N900_2N_M_A4


title: CD4_Q2_rep1

description: Hi-C library


title: Pt 5 Post PUVA


title: Pt 8 Post PUVA


title: miRNA_79_T1

description:
Male - NO ICU
79_S23


title: healthy_skin 1


title: Pt 4 Post PUVA


title: miRNA_80_T1

description:
Female - NO ICU
80_S31


title: Pt 3 Post PUVA


title: miRNA_75_T1

description:
Female - NO ICU
75_S7


title: N1519_2N_M_H3


title: miRNA_81_T1

description:
Male - NO ICU
81_S39


title: Pt 6 Post PUVA


title: CD4_Q1_rep2

description: Hi-C library


title: Pt 1 Post PUVA


title: WT_Treg2_RNA

description: RNA-seq

data_processing:
RNA-seq data was aligned using STAR 11 to the mm9 reference genome. PCR duplicates were removed, and read counts were quantified over GENCODE genes (vM1) using HTSeq.
Assembly: mm9
Supplementary files format and content: Gene counts using ENSEMBL gene models

extract_protocol:
Briefly, a single cell suspension from the thymus or the spleen was prepared, then pre-enriched using EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, Cat# 19852), and stained with fluorescent-conjugated primary antibodies on ice for 30 minutes. The individual cell population was sorted by FACS. 1×104 cells were FACS-sorted into TRIzol RNA isolation reagent (Invitrogen) and RNA was isolated according to the protocol.
RNA-seq libraries were constructed using Illumina TruSeq Stranded mRNA kit (Illumina) following manufacturer’s instructions.

tag: strain


title: miRNA_77_T1

description:
Female - NO ICU
77_S15


title: N1519_2N_M_G2


title: Pt 14 Pre PUVA

value: Pre-PUVA


title: miRNA_85_T1

description:
Male - NO ICU
85_S47


title: N1519_2N_M_H2


title: CD4_Q1_rep1

description: Hi-C library


title: N1519_2N_M_H1


title: N1519_2N_M_G1


title: miRNA_73_T1

description:
Female - NO ICU
73_S79

value: Female


title: WT_Treg3_RNA

description: RNA-seq


title: miRNA_68_T1

description:
Male - NO ICU
68_S82

value: Blood


title: Pt 2 Post PUVA


title: N1519_2N_M_G3


title: miRNA_67_T1

description:
Male - ICU
67_S74

value: ICU


title: miRNA_65_T1

description:
Female - NO ICU
65_S66


title: miRNA_72_T1

description:
Male - NO ICU
72_S94


title: N1519_2N_M_F2


title: Pt 5 Pre PUVA


title: WT_Treg1_RNA

description: RNA-seq


title: miRNA_71_T1

description:
Female - NO ICU
71_S85


title: Pt 8 Pre PUVA


title: Pt 4 Pre PUVA


title: WT_Tcon3_RNA

description: RNA-seq


title: Pt 3 Pre PUVA


title: Pt 7 Pre PUVA


title: Treg_GFP2_RNA

description: RNA-seq

value: CD45+CD4+CD8-CD25+Foxp3-GFP+ Foxp3 WT T-cells


title: N1519_2N_M_F3


title: WT_Tcon2_RNA

description: RNA-seq


title: N1519_2N_M_E1

value: fail


title: DSMwt_Treg3_RNA

description: RNA-seq


title: N1519_2N_M_D3

value: Single normal prostate cell


title: Treg_GFP1_RNA

description: RNA-seq


title: Pt 6 Pre PUVA


title: WT_Tcon1_RNA

description: RNA-seq


title: N1519_2N_M_F1

value: pass


title: Treg_KIKO2_RNA

description: RNA-seq

value: CD45+CD4+CD8-CD25+Foxp3-GFP+ Foxp3 KO T-cells

value: Foxp3 KO


title: Pt 1 Pre PUVA


title: N1519_2N_M_E3


title: Treg_KIKO1_RNA

description: RNA-seq


title: N1519_2N_M_E2


title: healthy skin 2

value: Healthy


title: healthy skin 3


title: miRNA_55_T1

description:
Male - NO ICU
55_S50

value: NO ICU


title: N1519_2N_M_C3


title: miRNA_54_T1

description:
Male - NO ICU
54_S19


title: DSMwt_Treg2_RNA

description: RNA-seq


title: DSMmt_Treg3_RNA

description: RNA-seq

value: CD45+CD4+CD8-CD25+Foxp3-Thy1.1+ DSM mutant T-cells

value: DSM


title: Pt 2 Pre PUVA


title: miRNA_48_T1

description:
Female - NO ICU
48_S77


title: miRNA_46_T1

description:
Male - NO ICU
46_S69

value: Male


title: miRNA_53_T1

description:
Male - ICU
53_S11


title: healthy skin 1


title: healthy skin 4


title: N1519_2N_M_D1


title: miRNA_51_T1

description:
Female - NO ICU
51_S3


title: miRNA_57_T1

description:
Female - NO ICU
57_S58


title: N1519_2N_M_D2


title: miRNA_50_T1

description:
Male - ICU
50_S13


title: DSMwt_Treg1_RNA

description: RNA-seq

value: Thymus


title: miRNA_52_T1

description:
Male - NO ICU
52_S90


title: miRNA_43_T1

description:
Male - ICU
43_S53


title: miRNA_44_T1

description:
Female - NO ICU
44_S61


title: DSMmt_Treg2_RNA

description: RNA-seq


title: ASO3 (pyG), replicate3

city: Yokohama

first: Takayuki

last: Kanagawa

address: Midori-ku Nagatsuta-cho

institute: Tokyo Institute of Technology

description: Gene expression after 24h

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: The scanned images were pre-processed using R 4.1 with filtering by probe quality, log 2-based transformation and quantile normalization.

source_name: HeLa, 10nM, 24h, replicate3

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal inactivated bovine serum , 100 U/mL penicillin-100 μg/mL streptomycin at 37 °C under 5% CO2.

extract_protocol: The total RNA was prepared using the QIAGEN, RNeasy Plus Mini kit (Qiagen, USA) following the manufacturer's instruction.

treatment_protocol: Rluc-targeting antisense oligonucleotides were transfected using Lipofectamine 2000 (Invitrogen, USA)  according to the manufacturer’s protocol. Final concentration of antisense oligonucleotides was 10nM.

tag: cell line

value: HeLa


title: N1519_2N_M_C2


title: N1519_2N_M_C1


title: N1519_2N_M_B3


title: DP_rep2_RNA

description: RNA-seq

value: CD45+CD4+CD8+ T-cells


title: N1519_2N_M_B2


title: DN_rep2_RNA

description: RNA-seq

value: CD45+CD4-CD8- T-cells


title: miRNA_41_T1

description:
Male - ICU
41_S78

value: Blood


title: DSMmt_Treg1_RNA

description: RNA-seq


title: ASO3 (pyG), replicate2

description: Gene expression after 24h

source_name: HeLa, 10nM, 24h, replicate2


title: N1519_2N_M_B1


title: DN_rep1_RNA

description: RNA-seq


title: ASO3 (pyG), replicate1

description: Gene expression after 24h

source_name: HeLa, 10nM, 24h, replicate1


title: N1519_2N_M_A3


title: N1519_2N_M_A1


title: CD8_rep1_RNA

description: RNA-seq

value: CD45+CD4-CD8+ T-cells


title: N1519_2N_M_A2


title: miRNA_39_T1

description:
Male - NO ICU
39_S29


title: CD8_rep2_RNA

description: RNA-seq


title: miRNA_40_T1

description:
Male - ICU
40_S37

value: ICU


title: ASO2 (cmG), replicate3

description: Gene expression after 24h


title: miRNA_42_T1

description:
Male - NO ICU
42_S45


title: DP_rep1_RNA

description: RNA-seq


title: miRNA_36_T1

description:
Female - NO ICU
36_S21

value: Female


title: ASO2 (cmG), replicate2

description: Gene expression after 24h


title: ASO2 (cmG), replicate1

description: Gene expression after 24h


title: CD4_Q4_rep2_RNA

description: RNA-seq


title: CD4_Q4_rep1_RNA

description: RNA-seq


title: T826_GS8_M_H1

source_name: Single prostate tumor cell

value: Single prostate tumor cell


title: miRNA_26_T1

description:
Male - ICU
26_S12


title: T826_GS8_M_G3

value: fail


title: miRNA_23_T1

description:
Male - NO ICU
23_S4


title: ASO1 (G), replicate2

description: Gene expression after 24h


title: ASO1 (G), replicate3

description: Gene expression after 24h


title: T826_GS8_M_G2

value: pass


title: CD4_Q3_rep1_RNA

description: RNA-seq


title: miRNA_22_T1

description:
Female - NO ICU
22_S91


title: T826_GS8_M_G1


title: Rluc vehicle, replicate2

description: Gene expression after 24h

value: no ASO


title: ASO1 (G), replicate1

description: Gene expression after 24h


title: CD4_Q2_rep2_RNA

description: RNA-seq


title: T826_GS8_M_F3


title: CD4_Q2_rep1_RNA

description: RNA-seq


title: Rluc vehicle, replicate1

description: Gene expression after 24h


title: miRNA_20_T1

description:
Male - NO ICU
20_S83


title: T826_GS8_M_H2


title: miRNA_33_T1

description:
Male - NO ICU
33_S20


title: miRNA_17_T1

description:
Male - ICU
17_S42


title: ASO7 (pyG), replicate3

description: Gene expression after 24h

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal inactivated bovine serum, 100 U/mL penicillin-100 μg/mL streptomycin at 37 °C under 5% CO2.

treatment_protocol: MALAT1-targeting antisense oligonucleotides were transfected using Lipofectamine 2000 (Invitrogen, USA)  according to the manufacturer’s protocol. Final concentration of antisense oligonucleotides was 10nM.


title: CD4_Q3_rep2_RNA

description: RNA-seq


title: CD4_Q1_rep2_RNA

description: RNA-seq


title: T826_GS8_M_F1


title: T826_GS8_M_F2


title: miRNA_13_T1

description:
Male - NO ICU
13_S26


title: T826_GS8_M_E3


title: miRNA_15_T1

description:
Male - ICU
15_S34


title: miRNA_12_T1

description:
Male - NO ICU
12_S18


title: T826_GS8_M_E2


title: CD4_Q1_rep1_RNA

description: RNA-seq


title: IgG_CnT_WT

description: Cut&Tag

data_processing:
Reads were aligned using BWA MEM to the mm9 genome. Peaks were called with MACS2. Differential peaks were determined using edgeR
Assembly: mm9
Supplementary files format and content: bed files
Library strategy: CUT&RUN

extract_protocol:
Briefly, a single cell suspension from the thymus or the spleen was prepared, then pre-enriched using EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, Cat# 19852), and stained with fluorescent-conjugated primary antibodies on ice for 30 minutes. The individual cell population was sorted by FACS. CUT&RUN experiments were performed as previously described with minor modifications.  To avoid the potential activation of T cells by Concanavalin-A (ConA) beads in the standard protocol, we instead used a spin-down method to collect cells as previously reported. Briefly, 0.5×106 cells per biological replicate were collected in V-bottom 96-well plate. Cells were first washed twice in Antibody Buffer (2mM EDTA, 1X EDTA-free protease inhibitors, 0.5mM spermidine, 1x permeabilization buffer from eBioscience Foxp3/Transcription Factor Staining Buffer Set) by centrifugation at 1900rpm for 6min, at 4°C, and then incubated with IgG and Foxp3 antibodies on ice for 1 hour. After two washes with buffer 1 (1X EDTA-free protease inhibitors, 0.5mM spermidine, 1x permeabilization buffer), cell pellets were incubated with pA/G-MNase (20X) enzyme in 50µl buffer 1 and incubated at 4°C for 1 hour. Cells were washed twice in saponin buffer (0.05% (w/v) saponin, 1X EDTA-free protease inhibitors, 0.5mM spermidine in PBS) and resuspended in 100µl calcium buffer (2mM CaCl2 in buffer 2) on ice for 30 min. 100µl 2x stop buffer (20mM EDTA, 4mM EGTA in saponin buffer) was then added and incubated in a 37°C incubator for 10-20 min to release cleaved chromatin fragments. Last, the supernatant containing chromatin fragments was collected by centrifugation and DNA was extracted using a QIAGEN MinElute kit according to manufacturer’s protocol.
CUT&RUN libraries were prepared using the NEBNext UltraTM II DNA Library Prep Kit for Illumina® (E7645) according to manufacturer’s instructions.

tag: antibody

value: IgG


title: miRNA_7_T1

description:
Male - ICU
7_S67

tag: tissue


title: IgG_CnT_DSM

description: Cut&Tag

tag: genotype


title: ASO7 (pyG), replicate2

description: Gene expression after 24h

tag: treatment


title: T826_GS8_M_E1


title: Rluc vehicle, replicate3

description: Gene expression after 24h


title: Foxp3_CnT_WT3

description: Cut&Tag


title: Foxp3_CnT_WT2

description: Cut&Tag


title: mRNA_769_T1

data_processing:
Fastqc
Trimming of reads using trimmomatic and fastp
Hisat2 alignment using Ensemble Grch38
Raw Gene ocunt generation using htseq-count program
Assembly: Grch38
Supplementary files format and content: htseq-Count text fiile

extract_protocol:
Total RNA
NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads

tag: Sex

value: NO ICU


title: T826_GS8_M_D3

tag: cell type


title: mRNA_768_T1


title: Foxp3_CnT_WT1

description: Cut&Tag


title: T826_GS8_M_D2

tag: patient donor/cell_line


title: ASO6 (cmG), replicate2

description: Gene expression after 24h


title: mRNA_766_T1


title: ASO6 (cmG), replicate1

description: Gene expression after 24h


title: T826_GS8_M_D1

tag: genome build


title: Foxp3_CnT_DSM3

description: Cut&Tag

value: CD45+CD4+CD8-CD25+Foxp3-Thy1.1+ DSM mutant T-cells


title: T826_GS8_M_C3

tag: cpg coverage


title: ASO6 (cmG), replicate3

description: Gene expression after 24h


title: mRNA_757_T1


title: ASO7 (pyG), replicate1

description: Gene expression after 24h


title: ASO5 (G), replicate2

description: Gene expression after 24h


title: Foxp3_CnT_DSM2

description: Cut&Tag

value: DSM


title: mRNA_754_T1

value: Male


title: mRNA_750_T1


title: Menopause8

city: chengdu

first: Xia

last: Yu

address: No.1617 Ri Yue Street, Chengdu, Sichuan

institute: Chengdu women and Children's hospital

data_processing:
mRNA was purified from total RNA using poly-T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.
In order to select cDNA fragments of preferentially 250~300 bp in length, the library ragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR.
Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Atlast, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: vaginal wall

extract_protocol:
The samples were selected for total RNA extract, which using the Trizol reagent (Invitrogen, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: vaginal wall

value: ovariectomy


title: mRNA_740_T1


title: T826_GS8_M_C1


title: T826_GS8_M_B3


title: T826_GS8_M_B2


title: ASO5 (G), replicate1

description: Gene expression after 24h

value: HeLa


title: vehicle, replicate3

description: Gene expression after 24h


title: Foxp3_CnT_DSM1

description: Cut&Tag

value: Thymus


title: ASO5 (G), replicate3

description: Gene expression after 24h


title: CD82+NCAM+ adult SC, sample 3

city: Irvine

first: Michael

last: Hicks

address: 845 Health Sciences Road, Room 3101

institute: University of California, Irvine

data_processing:
FASTQ Groomer
HISATx2 (hierarchical indexing for spliced alignment of transcripts)
StringTie
DESeq2
Assembly: Homo Sapiens (Hg38) genome
Supplementary files format and content: FASTQ Files
Supplementary files format and content: Microscoft Excel files include StringTie Normalized HISATx2 Transcript Counts for each sample

source_name: Quadriceps

growth_protocol: To generate a defined directed differentiation strategy from hPSCs, cells were dissociated as single cells in ROCK inhibitor and treated with CHIR99021 to induce mesoderm lineage. FGF2 is used to capture and expand pre-myogenic cells, and IGF1 Inhibition of TGFb (TGFbi) is used to mature PAX7+ skeletal muscle progenitor cells. After 6 days, hPSC skeletal muscle progenitor cells (SMPCs) are enriched by flow cytometry on ERBB3 and NGFR

extract_protocol:
RNA was harvested using RNA-micro kit (Qiagen):
RNA amplification was performed using a Universal Plus mRNA-Seq Library Preparation Kit (Nugen). Adult SCs had lower starting yield and were amplified by Ribo-Zero Plus rRNA Depletion Kit (Illumina).

value: Quadriceps

value: WT


title: CD82+NCAM+ adult SC, sample 2


title: T826_GS8_M_B1

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)


title: vehicle, replicate2

description: Gene expression after 24h


title: Menopause5


title: T826_GS8_M_A3


title: ERBB3+NGFR+ fetal week 18 SMPC, sample 2

source_name: Limb

value: Limb


title: mRNA_731_T1

value: Female

value: Blood


title: vehicle, replicate1

description: Gene expression after 24h


title: Menopause4


title: mRNA_730_T1


title: mRNA_737_T1

value: ICU


title: T826_GS8_M_A2

value: Single prostate tumor cell

value: fail


title: Menopause3


title: T826_GS8_M_A1


title: CD82+NCAM+ adult SC, sample 1


title: T826_GS8_M_C2


title: Menopause6


title: mRNA_732_T1


title: ERBB3+NGFR+ fetal week 18 SMPC, sample 3


title: Menopause2


title: ERBB3+NGFR+ fetal week 18 SMPC, sample 1


title: mRNA_728_T1


title: T1646_GS8_M_H2

value: pass


title: mRNA_726_T1

value: NO ICU


title: Control8

value: sham operation


title: Menopause7


title: mRNA_722_T1


title: ERBB3+NGFR+ fetal week 10 SMPC, sample 1


title: T1646_GS8_M_H1


title: T1646_GS8_M_G3


title: ERBB3+NGFR+ hPSC SMPC, sample 5

value: Myogenic differentiation


title: T1646_GS8_M_F3


title: ERBB3+NGFR+ fetal week 10 SMPC, sample 2


title: ERBB3+NGFR+ hPSC SMPC, sample 2


title: Menopause1


title: mRNA_716_T1


title: mRNA_715_T1


title: Control7


title: mRNA_725_T1


title: ERBB3+NGFR+ hPSC SMPC, sample 1


title: T1646_GS8_M_G1


title: mRNA_721_T1


title: T1646_GS8_M_E3


title: mRNA_714_T1


title: Control2


title: Control3


title: ERBB3+NGFR+ hPSC SMPC, sample 4


title: T1646_GS8_M_E2


title: mRNA_711_T1

value: Male


title: Control6

value: vaginal wall


title: mRNA_719_T1


title: Control5


title: ERBB3+NGFR+ fetal week 10 SMPC, sample 3


title: mRNA_710_T1


title: ERBB3+NGFR+ hPSC SMPC, sample 3


title: Control4


title: mRNA_709_T1


title: T1646_GS8_M_F2


title: mRNA_708_T1


title: C480  rep3

city: shijiazhuang

first: jiaojiao

last: bai

address: huaizhong road No.286

institute: UCAS

description:
12-day-old seedlings
C480minvsC000_deg

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)(Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: Arabidopsis thaliana
Supplementary files format and content: tab-delimited text files include reads and FPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Total seedling

value: wild type (Col-0)

value: seedling treated with H2O

tag: time (min)


title: C480 rep2

description:
12-day-old seedlings
C480minvsC000_deg


title: Control1


title: T1646_GS8_M_F1

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: bisulfite conversion_rate


title: T1646_GS8_M_E1

tag: qc


title: T1646_GS8_M_D3


title: C360  rep3

description:
12-day-old seedlings
C360minvsC000_deg


title: T1646_GS8_M_D1


title: mRNA_707_T1

tag: disease state


title: mRNA_701_T1

tag: visit


title: T1646_GS8_M_D2


title: T1646_GS8_M_C2


title: C480rep1

description:
12-day-old seedlings
C480minvsC000_deg


title: mRNA_443_T1

tag: outcome


title: C360rep1

description:
12-day-old seedlings
C360minvsC000_deg


title: C360 rep2

description:
12-day-old seedlings
C360minvsC000_deg


title: mRNA_700_T1


title: C240 rep2

description:
12-day-old seedlings
C240minvsC000_deg


title: Yangben3

type: genomic

city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

description: whole genomic promoter expression

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Microarrays were scanned using Agilent Scanner G2505C

data_processing: We perform Median-centering, quantile normalization and linear smoothing in this analysis process by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data was created for each sample.

source_name: pSTAT3 ChIP DNA from CAF cells

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen ChIP-on-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: For each immunoprecipitate (IP), cells were cross-linked with 1% formaldehyde for 10 min, washed in cold PBS buffer, resuspended in lysis buffer, and sonicated to obtain chromatin fragments between 200 bp and 1000 bp. Sonicated chromatin was resuspended in IP buffer and incubated overnight at 4°C with ChIP grade pStat3 Tyr705 antibdy. The IP was then washed with lysis buffer, LiCl buffer and TE buffer, eluted in elution buffer. The DNA was then recovered by reversing the crosslinks, and purified by QIAGEN Purification Kit. An un-enriched sample of DNA was treated in a similar manner to serve as input.

treatment_protocol: 1x10E7 cells were collected for ChIP assay per antibody

value: CAF cells

source_name: Input DNA from CAF cells


title: T1646_GS8_M_B3


title: mRNA_438_T1


title: T1646_GS8_M_B2


title: C120  rep3

description:
12-day-old seedlings
C120minvsC000_deg


title: Sample3

description: whole genomic promoter expression

source_name: pSTAT3 ChIP DNA from ESCC cells

value: ESCC cells

source_name: Input DNA from ESCC cells


title: T1646_GS8_M_C3


title: C240  rep3

description:
12-day-old seedlings
C240minvsC000_deg


title: Yangben2

description: whole genomic promoter expression


title: mRNA_440_T1


title: C120  rep2

description:
12-day-old seedlings
C120minvsC000_deg


title: mRNA_437_T1


title: Yangben1

description: whole genomic promoter expression


title: mRNA_441_T1


title: T1646_GS8_M_A2


title: Sample2

description: whole genomic promoter expression


title: T1646_GS8_M_A3


title: C120  rep1

description:
12-day-old seedlings
C120minvsC000_deg


title: C060  rep3

description:
12-day-old seedlings
C060minvsC000_deg


title: mRNA_432_T1


title: mRNA_433_T1


title: T1646_GS8_M_B1


title: T1646_GS8_M_C1


title: mRNA_434_T1

source_name: Female - ICU


title: T1636_GS8_M_H2


title: C060 rep2

description:
12-day-old seedlings
C060minvsC000_deg


title: T1646_GS8_M_A1


title: C060 rep1

description:
12-day-old seedlings
C060minvsC000_deg


title: C240rep1

description:
12-day-old seedlings
C240minvsC000_deg


title: mRNA_427_T1

source_name: Male - ICU


title: mRNA_431_T1


title: T1636_GS8_M_G3


title: Sample1

description: whole genomic promoter expression


title: mRNA_425_T1


title: C030  rep3

description:
12-day-old seedlings
C030minvsC000_deg


title: T1636_GS8_M_G1


title: T1636_GS8_M_G2


title: mRNA_422_T1


title: T1636_GS8_M_H1


title: C015 rep1

description:
12-day-old seedlings
C015minvsC000_deg


title: C030  rep1

description:
12-day-old seedlings
C030minvsC000_deg


title: mRNA_419_T1


title: mRNA_414_T1


title: mRNA_412_T1


title: C015 rep2

description:
12-day-old seedlings
C015minvsC000_deg


title: T1636_GS8_M_F3


title: C015  rep3

description:
12-day-old seedlings
C015minvsC000_deg


title: T1636_GS8_M_E3


title: C000  rep1

description:
12-day-old seedlings
C015minvsC000_deg


title: T1636_GS8_M_E2


title: mRNA_124_T1


title: C000  rep3

description:
12-day-old seedlings
C015minvsC000_deg


title: mRNA_409_T1


title: T1636_GS8_M_D3


title: T1636_GS8_M_E1


title: RNASeq_mESC Embryoid Body_Zmym2KO_Sample 2

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

description:
Zmym2_normalized_and_raw_counts_EB.txt
Zmym2_RNAseq_matrixRPKM_mESC.txt

data_processing:
Reads were trimmed using Trimmomatic (v0.34)
Trimmed reads wre then mapped to the GRCm38/mm10 genome using STAR (v2.7.8a) using default parameters
Picard (v2.9.0) was used to sort, mark and remove duplicates.
Raw and normalized counts were quanitified using HTSeq-counts and the StringTie suite(v1.3.5)
Differential expression analysis was then measured using DESeq2 and EdgeR
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimted text file showing raw and normalized read counts
Supplementary files format and content: tab-delimted text file showing RPKM of samples

extract_protocol:
Total RNA was isolated using a Rneasy Micro Kit (Qiagen, 74084)
Sequencing libraries were prepared by the Genome Quebec Innovation Center using the NEB mRNA stranded library preperation kit

value: embryoid body

tag: strain

value: Zmym2 Knockout

tag: time

value: Day 3


title: C000  rep2

description:
12-day-old seedlings
C015minvsC000_deg


title: C030  rep2

description:
12-day-old seedlings
C030minvsC000_deg


title: T1636_GS8_M_D2


title: RNASeq_mESC Embryoid Body_NT_Sample 2

tag: cell line

value: Wild-Type


title: RNASeq_mESC Embryoid Body_NT_Sample 1


title: mRNA_410_T1

tag: tissue

value: Blood

value: ICU


title: T1636_GS8_M_C1

value: Single prostate tumor cell

value: pass


title: RNASeq_mESC Serum+Lif_Zmym2KO_Sample 2

description:
Zmym2_normalized_and_raw_counts_SL.txt
Zmym2_RNAseq_matrixRPKM_mESC.txt

value: embryonic stem cell

tag: genotype

value: Day 0


title: RNASeq_mESC Embryoid Body_Zmym2KO_Sample 1


title: T1636_GS8_M_D1


title: mRNA_121_T1

value: Female

value: NO ICU


title: T1636_GS8_M_C2


title: mRNA_404_T1


title: GM-Mphage macrophage donor1 treated with 50nM MTX

city: Amsterdam

first: Ittai

middle: Bernardo

last: Muller

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC

description: GM-Mphage_A  + MTX

data_processing:
HiSeq 4000 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  STAR with the following additional parameters: --sdjbOverhang 150 --OutSAMType BAM
Gene expression levels were determined in R with the edgeR package
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files include Entrez Gene ID and raw counts or CPM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-Mphage) or in the presence of 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-Mphage).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using Takara Bio SMARTer Stranded Total RNA-Seq - Pico Input Mammalian

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing M-CSF or GM-CSF in combination with 50nM MTX for 7 days.

tag: cell

value: Monocyte-derived GM-CSF macrophages


title: T1636_GS8_M_C3


title: mRNA_118_T1

tag: Sex

value: Male


title: GM-Mphage macrophage donor2 treated with 50nM MTX

description: GM-Mphage_B  + MTX


title: mRNA_114_T1


title: T1636_GS8_M_B3

tag: cell type


title: M-Mphage macrophage donor2 treated with 50nM MTX

description: M-Mphage_B  + MTX

value: Monocyte-derived M-CSF macrophages


title: M-Mphage macrophage donor3 treated with 50nM MTX

description: M-Mphage_C  + MTX


title: mRNA_106_T1

source_name: Female - NO ICU


title: mRNA_113_T1

source_name: Male - NO ICU


title: RNASeq_mESC Serum+Lif_Zmym2KO_Sample 1


title: T1636_GS8_M_B2

tag: patient donor/cell_line


title: M-Mphage macrophage donor1 treated with 50nM MTX

description: M-Mphage_A + MTX


title: mRNA_103_T1


title: RNASeq_mESC Serum+Lif_NT_Sample 2


title: T1636_GS8_M_B1

tag: genome build


title: GM-Mphage macrophage donor3 treated with 50nM MTX

description: GM-Mphage_C  + MTX


title: mRNA_105_T1


title: Hypothalamic neurons, MKRN3-KO III

first: Ursula

last: Kaiser

state: Massachusetts

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing:
Data were processed using bcbio-nextgen v1.0.8
Reads were quantified using Salmon v0.9.0 mapped against hg19 of the human reference.
Counts were imported into R using tximport (Soneson, Love, and Robinson 2016) and DESeq2 (Love, Huber, and Anders 2014).
Assembly: hg19
Supplementary files format and content: tab delimited text file containing combined  salmon counts for all samples

source_name: Hypothalamic neurons derived from hiPSCs

extract_protocol:
Total RNA was extracted from the hiPSC-derived hypothalamic neurons on day 30 of differentiation using the RNeasy Mini Kit (Qiagen).
Sample mRNA libraries were prepared using the Illumina Tru-Seq Stranded mRNA kit.


title: T1636_GS8_M_A3

tag: cpg coverage


title: T1636_GS8_M_A2


title: NAc MDMA 2 days replicate 3

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description:
27MDMA2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

data_processing:
Reads were pseudoaligned to the mouse GENCODE vM25 (PMID: 30357393) reference transcriptome using kallisto (v0.46.2) with 100 bootstrapped samples and 6 threads. Defaults were used for all other parameters.
Estimated transcript-level abundances were collapsed to gene-level expression estimates and analyzed using the sleuth (v0.30.0) R/Bioconductor package.
To identify genes with differential expression as a function of samples where the critical period is reopened we performed a likelihood ratio test comparing a full model which included batch, and critical period to a reduced model that only included batch. Time was not used as an explanatory variable in this model fitting.
To identify genes with differential expression as a function of any drug treatment (including cocaine) vs saline we performed a likelihood ratio test comparing a full model which included batch, and ‘treated vs untreated’ to a reduced model that only included batch.
Assembly: GENCODE vM25 Transcriptome
Supplementary files format and content: Tab-separated genesXsample expression matrix in normalized transcripts per million (tpm)
Supplementary files format and content: Tab-separated data frame of sleuth likelihood ratio test results for all expressed genes comparing open vs closed critical periods

source_name: Nucleus Accumbens macrodissection

growth_protocol: Male wild-type C57BL6/J mice were bred in house and weaned at 3 weeks or obtained from Jackson Laboratories (stock # 000664). All mice were maintained on a 12:12 hour natural light/dark cycle, starting at 7:30 am with food and water provided ad libitum.

extract_protocol:
At P98-P112 mice were sacrificed, brains were rapidly removed and ~1mm thick coronal slice (n = 3 mice for each conditions) containing the nucleus accumbens were sectioned using a mouse brain matrix. To microdissect the NAc, slices were placed in a petri dish containing ice-cold, ACSF (125 mM NaCl, 2.5 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 1.25 mM NaH2PO4, 10 mM glucose and 26 mM NaHCO3) supplement with RNase Inhibitor and oxygenated with carbogen gas (95% O2 and 5% CO2) to pH 7.3 - 7.4. The NAc was identified using the anterior commissure and other structural markers. Between each dissection, blades were replaced and all the instruments and the matrix were cleaned with a solution containing RNase inhibitor. Following dissection, tissue was immediately placed into 0.5 ml trizol and subjected to a 15 second burst with a tissue homogenizer to lyse the cells.  Samples were kept on ice prior to storage at -20C. Total RNA were extracted using the RNeasy Kit from Qiagen. The quality of purified RNA was assessed via both a nanodrop and 2100 Bioanalyzer from Agilent.
Library preparation was performed using a TruSeq Stranded mRNA kit (Illumina) using the recommended protocol. Individual dual-indexed libraries were quality controlled, pooled, and sequenced on the NovaSeq 6000 platform on a single S1 flowcell to an average depth of 76,841,745 (± 8,066,939.82) paired-end 100bp reads per sample.

treatment_protocol: Male wild-type C57BL6/J mice were injected i.p. with LSD, ketamine, MDMA, cocaine (20 mg/kg) or saline solution either 2 weeks or 48h before the mice were sacrificed.

value: Nucleus Accumbens macrodissection

tag: treatment -_drug

value: MDMA

tag: treatment -_time_(days)

tag: treatment -_critical_period

value: open


title: Hypothalamic neurons, MKRN3-KO II

value: Hypothalamic neurons derived from hiPSCs


title: NAc MDMA 2 days replicate 2

description:
26MDMA2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: T1636_GS8_M_A1

tag: bisulfite conversion_rate

tag: qc


title: Hypothalamic neurons, MKRN3-WT III


title: mRNA_97_T1

tag: disease state

tag: visit

tag: outcome


title: Hypothalamic neurons, MKRN3-KO I


title: T1484_GS6_4N_M_H2

value: fail


title: NAc MDMA 2 days replicate 1

description:
25MDMA2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: strain


title: NAc LSD 2 days replicate 3

description:
24LSD2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: tissue

value: LSD


title: NAc LSD 2 days replicate 2

description:
23LSD2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: T1484_GS6_4N_M_H1


title: mRNA_86_T1

value: Blood


title: Hypothalamic neurons, MKRN3-WT II

tag: genotype


title: Hypothalamic neurons, MKRN3-WT I


title: mRNA_87_T1


title: 19G02977, Patient 4, Spatial Transcriptomics (Visium)

city: Montpellier

first: Andrei

last: Turtoi

address: 208 avenue des Apothicaires

country: France

institute: Inserm U1194

description: 10X Genomics

data_processing:
Sequencing fastq files passing Illumina quality control criteria were further analyzed using 10X Genomics SpaceRanger 1.3  pipeline.
Assembly: hg38
Supplementary files format and content: *_filtered_feature_bc_matrix.tar.gz contains gene expression matrices produced by spaceranger : barcodes.tsv, features.tsv and matrix.tsv.
Supplementary files format and content: *_spatial.tar.gz contains mainly images : aligned_fiducials, detected_tissue_image, scalefactors_json.json, tissue_hires_image, tissue_lowres_image and tissue_positions_list.
Supplementary files format and content: *_filtered_feature_bc_matrix.h5 is a compressed binary format file to access gene expression matrices produced by spaceranger.

source_name: Liver Metastasis

extract_protocol:
Selected formalin-fixed paraffin-embedded (FFPE) tumor samples were firstly analyzed for RNA quality by evaluating the percentage of fragments with a length greater than 200 nucleotides (DV200). Samples with a DV200 higher than 50% were considered as usable for Visium analysis
Briefly, one to two 10 µm-thin FFPE sections were cut, dewaxed and lysed. RNA was extracted and purified using the High Pure FFPE RNA Isolation Kit (cat. no.: 06650775001, Roche) and analyzed by microfluidics-based automated electrophoresis (Bioanalyzer; Agilent)
All samples tested in this study had a DV200 > 50%. Serial sections, stained with Hematoxylin Eosin Saffron (HES), were used to identify an area of ~6 x 6 mm containing liver metastasis, in order to provide optimal coverage of the 6.5 x 6.5 mm capture area on the Visium slide.
Following macrodissection, 10 µm-thin sections of the selected areas were fixed on the Visium slide, dewaxed, HES-stained, imaged, and decrosslinked according to manufacturer’s instruction (10X Genomics Visium Spatial Gene Expression for FFPE kit, Human Transcriptome, Protocol no.: GC000408 and GC000409).
Library preparation was then carried out according to manufacturer’s instruction (Protocol no., GC000407)

value: Liver Metastasis

tag: primary tumor_location

value: Recto-sigmoid hinge

tag: neo-adjuvant chemotherapy

value: FOLFOX+Cetuximab/Xeloda+Cetuximab

tag: age

value: F


title: RNASeq_mESC Serum+Lif_NT_Sample 1

tag: cell line

tag: cell type

value: embryonic stem cell

value: Wild-Type

tag: time

value: Day 0


title: NAc LSD 2 days replicate 1

description:
22LSD2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_drug


title: T1484_GS6_4N_M_G2

first: Ben

last: Wittner

institute: Massachusetts General Hospital

source_name: Single prostate tumor cell

value: Single prostate tumor cell

tag: patient donor/cell_line

tag: genome build

tag: cpg coverage


title: NAc ketamine 2 days replicate 3

description:
21ketamine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: ketamine

tag: treatment -_time_(days)

tag: treatment -_critical_period


title: mRNA_85_T1

tag: disease state

tag: Sex

value: Male

tag: visit

value: NO ICU


title: T1484_GS6_4N_M_G1

tag: bisulfite conversion_rate

tag: qc


title: NAc ketamine 2 days replicate 2

description:
20ketamine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: strain

tag: tissue

value: Nucleus Accumbens macrodissection


title: 19G0635, Patient 3, Spatial Transcriptomics (Visium)

description: 10X Genomics

tag: primary tumor_location

value: Inferior rectum

tag: neo-adjuvant chemotherapy

value: FOLFOX

tag: age

value: M


title: mRNA_81_T1

tag: outcome


title: mRNA_100_T1

value: Female


title: 19G0619, Patient 2, Spatial Transcriptomics (Visium)

description: 10X Genomics

value: High rectum


title: T1484_GS6_4N_M_F3

tag: cell type

value: fail


title: mRNA_98_T1

value: Blood


title: T1484_GS6_4N_M_F2

tag: patient donor/cell_line


title: NAc cocaine 2 days replicate 3

description:
18cocaine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_drug

value: cocaine

value: closed


title: mRNA_79_T1


title: NAc ketamine 2 days replicate 1

description:
19ketamine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: open


title: 19G081,  Patient 1, Spatial Transcriptomics (Visium)

description: 10X Genomics

value: Liver Metastasis

value: Sigmoid

value: FOLFIRI+Cetuximab/Irinotecan+Cetuximab

value: F


title: T1484_GS6_4N_M_F1

value: Single prostate tumor cell

tag: genome build

tag: cpg coverage


title: T1484_GS6_4N_M_G3


title: mRNA_77_T1

value: NO ICU


title: NAc cocaine 2 days replicate 2

description:
17cocaine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: Nucleus Accumbens macrodissection

tag: treatment -_time_(days)

tag: treatment -_critical_period


title: T1484_GS6_4N_M_E3


title: 171012_Con

city: Hatfield

first: Ross

middle: Eric

last: Beaumont

state: Hertfordshire

address: Hawkshead Ln

department: Clinical science and services

country: United Kingdom

institute: Royal Veterinary College

data_processing:
RNA sequencing was performed on a NovaSeq6000 (Illumina) by external providers (Oxford Genomics, Oxford, UK & Novagene, Cambridge, UK).
30.7 – 46.2 million reads of 150 base pair paired-end data were generated per sample.
Resulting FASTQ files generated were quality control (QC) checked using FASTQC and MultiQC (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensembl version v95 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (v.1.24; Soneson et al. 2015) was used to import the quantified gene-level abundance data into R (v.4.2.1) and differential expression analysis conducted using R/Bioconductor DESeq2 (v.1.36) as described in Love et al., 2014.
Assembly: Genes with adjusted pvalue of less than 0.05 and log2 fold change of ± 2 were considered as differentially expressed.
Supplementary files format and content: Ensembl version v95 EquCab 3.0.
Supplementary files format and content: Control_vs_IL1B_First_Batch_Count_Data.csv: Comma-Separated Value (CSV) files include raw counts of sequencing reads for each sample from the first batch (n=5 biological replicates, two conditions).
Supplementary files format and content: Control_vs_IL1B_vs_IL1Ra_Second_Batch_Count_Data.csv: Comma-Separated Value (CSV) files include raw counts of sequencing reads for each sample from the second batch (n= 3 biological replicates, three conditions).

organism: Equus caballus

source_name: Superficial digital flexor tendon tenocytes

growth_protocol: Adult tenocytes were cultured in Dulbecco’s modified eagle medium (DMEM) high glucose (4.5 g/L), 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen, Renfrewshire, UK) and passaged using 0.25% trypsin-EDTA (Sigma-Aldrich) every 3-4 days.

extract_protocol:
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK).

treatment_protocol: Tenocytes were seeded in type 1 collagen gels (bovine; Advanced Biomatrix, California, USA) to generate a three-dimensional matrix and stimulated with IL-1ß (1 nM), IL-1ß (1 nM) + IL1Ra (100 ng/mL) or control for 14 days, with fresh media changes every 3-4 days before harvesting at day 14.

tag: genotype

value: WT

tag: treatment

value: Control

tag: batch

value: Second


title: mRNA_75_T1

tag: disease state

tag: Sex

value: Female

tag: visit


title: 171012_IL1B

tag: tissue

value: Superficial digital flexor tendon tenocytes

value: Interleukin 1 beta


title: NAc cocaine 2 days replicate 1

description:
16cocaine2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: strain


title: 171012_Both

value: Interleukin 1 beta + interleukin 1 receptor antagonist protein


title: T1484_GS6_4N_M_E2

address: 149 13th Street

tag: bisulfite conversion_rate

tag: qc

value: fail


title: mRNA_72_T1

value: Male

value: Blood

tag: outcome


title: mRNA_80_T1


title: T1484_GS6_4N_M_E1

tag: cell type

tag: patient donor/cell_line


title: NAc saline 2 days replicate 3

description:
15saline2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_drug

value: saline

value: closed


title: NAc saline 2 days replicate 2

description:
14saline2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: 120911_IL1B


title: T1484_GS6_4N_M_D3

tag: genome build

tag: cpg coverage


title: 120911_Con


title: mRNA_71_T1


title: T1484_GS6_4N_M_D2


title: NAc saline 2 days replicate 1

description:
13saline2
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_time_(days)

tag: treatment -_critical_period


title: mRNA_68_T1


title: NAc LSD 14 days replicate 3

description:
12LSD14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: LSD

value: open


title: NAc LSD 14 days replicate 2

description:
11LSD14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: mRNA_67_T1

value: ICU


title: T1484_GS6_4N_M_D1

value: Single prostate tumor cell


title: NAc LSD 14 days replicate 1

description:
10LSD14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: Nucleus Accumbens macrodissection


title: 030221_IL1B

tag: genotype

value: WT

tag: treatment


title: T1484_GS6_4N_M_C3


title: mRNA_65_T1

tag: disease state

value: NO ICU


title: mRNA_73_T1

tag: Sex


title: NAc ketamine 14 days replicate 3

description:
9ketamine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: ketamine


title: mRNA_55_T1

tag: visit


title: 120911_Both

tag: tissue

tag: batch

value: Second


title: T1484_GS6_4N_M_C2

tag: bisulfite conversion_rate


title: 090811_IL1B

value: Superficial digital flexor tendon tenocytes

value: First


title: 030221_Con

value: Control


title: T1484_GS6_4N_M_C1

tag: qc

value: fail


title: NAc ketamine 14 days replicate 2

description:
8ketamine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: strain


title: 090811_Control


title: NAc ketamine 14 days replicate 1

description:
7ketamine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: T1484_GS6_4N_M_B3

tag: cell type


title: mRNA_54_T1

value: Male

tag: outcome


title: 180412_IL1B

value: Interleukin 1 beta


title: mRNA_53_T1

value: Blood


title: NAc cocaine 14 days replicate 3

description:
6cocaine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_drug

value: cocaine

value: closed


title: 030221_Both

value: Interleukin 1 beta + interleukin 1 receptor antagonist protein


title: NAc cocaine 14 days replicate 2

description:
5cocaine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: mRNA_52_T1


title: 180412_Control


title: T1484_GS6_4N_M_B1

tag: patient donor/cell_line

tag: genome build


title: NAc cocaine 14 days replicate 1

description:
4cocaine14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: treatment -_time_(days)


title: 250718B_IL1B


title: mRNA_50_T1

value: ICU


title: T1484_GS6_4N_M_A2

value: Single prostate tumor cell

tag: cpg coverage


title: T1484_GS6_4N_M_A3


title: mRNA_57_T1

value: Female


title: NAc saline 14 days replicate 3

description:
3saline14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

value: Nucleus Accumbens macrodissection

value: saline

tag: treatment -_critical_period


title: CD_IL1B

tag: genotype

value: WT

tag: treatment


title: T1484_GS6_4N_M_A1

value: pass


title: NAc saline 14 days replicate 2

description:
2saline14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv


title: CD_Control

description: CDTendonControl

value: Superficial digital flexor tendon tenocytes


title: mRNA_46_T1

tag: disease state

tag: Sex

value: NO ICU


title: T1245_GS6_4N_M_H3


title: T1484_GS6_4N_M_B2


title: NAc saline 14 days replicate 1

description:
1saline14
20230425_psychadelic_study_tpm_matrix.tsv
criticalPeriodDE_all_test_results.tsv

tag: tissue


title: mRNA_48_T1

tag: visit


title: ID8_R_Combo_rep2

city: Denver

first: Lily

last: Nguyen

state: CO

address: 220 Roslyn Street, Apt 706

institute: UNIVERSITY OF COLORADO DENVER

data_processing:
quality assessement using FastQC (v0.11.8) and MultiQC (v1.7)
adapter trimming using BBDuk/BBMap (v38.05)
genome alignment using using hisat2 (v2.1.0)
Assembly: hg38, mm10
Supplementary files format and content: bigwig tracks were generated using the bamCoverage function of deepTools (v3.0.1)

source_name: OC

growth_protocol: Cell Culture- PEO1 (RRID:CVCL_2686), Kuramochi (RRID:CVCL_1345), and OVCA420 (RRID:CVCL_3935) cell lines were provided through the Gynecologic Tumor and Fluid Bank (GTFB). ID8 cell line was kindly gifted from Dr. Iain McNeish lab (Imperial College London). All cells were authenticated via STR at The University of Arizona Arizona Genetics Core (RRID:SCR_012429). All cells undergo monthly mycoplasma testing using Sigma LookOut Mycoplasma Detection kit (Cat. #MP0035) and are only culture up to 20 passages or two months. Cells are cultured in RPMI1640 (Gibco) in 10% FBS (Phoenix Scientific Cat. #PS-100) and Penicillin Streptomycin (Cat. #SV30010) at 37C in 5% CO2. ID8 cells are cultured in DMEM (Gibco, Cat. #11995-065) supplemented with 4% FBS, Penicillin Streptomycin and 1x ITS (Gibco Cat. #41400-045).   Ex vivo Culture - Primary ovarian cancer tumors (Table S1) were collected at The University of Colorado Cancer Center under the Colorado Multiple Institutional Review Board (COMIRB) Gynecologic Tumor and Fluid Bank protocol #07-935. All patients are consented under the GTFB protocol and collected specimens are deidentified. Tumors are collected by the Biorepository Shared Resource and delivered to the lab within one hour of surgical dissection. Tumors are sliced using a Krumdeick Tissue Slicer into 300 micron thick discs and placed in warmed culture media. Tumor sections treated for 72 hours, are either stored at -80C  in RLT plus buffer (Qiagen, Cat. #74136 ) or fixed in 10% buffered formalin. RNA was extracted from tissues stored in the RLT buffer and used for RNA-sequencing. Fixed tissues were embedded in paraffin at the University of Colorado Histopathology Shared Resources.   Cell culture and generation of EHMT1 and 2 overexpression - PEO1 cells were maintained in RPMI+ 10% heat inactivated FBS (Avantor, Cat. #10803-034) + 100 μg/mL Penicilin/Streptomycin (Lonza, Cat. #09-757F). EHMT1 or EHMT2 overexpression cells were obtained by using lentivirus to infect cells with either TRE_EHMT1_hygromycin or TRE_EHMT2_hygromycin. To produce lentivirus, 500,000 Lenti-X 293T cells were seeded on 6-well plate. Twenty-four hours later, the cells were transfected with packaging plasmids (0.5µg pCMV-VSV-G, 1.1µg pD8.9), 0.85µg transfer plasmid, 7.35µg of PEI MAX (Polysciences Inc., Cat. #24765-1) and 10mM HEPES. Media was changed 24 hours later. Supernatant with virus was collected 48 and 72 hours post transfection. The supernatant was filtered using a 0.45µm PES Filter membrane (Whatman Uniflo, Cat. #9914-2504). Cells were then infected using 1mL of supernatant with 5 µg/mL polybrene (EMD Millipore, Cat. #TR-1003-G). Media was changed 24 hours later. 48 hours post transduction, cells were selected using 200μg/ml Hygromycin B (Biosciences, Cat. #31282-04-9). Cells were selected until death of non-transduced cells. Once cells were selected, they were induced for EHMT1 or EHMT2 expression using Doxycycline (1µg/ml, TCI, Cat. #D4116) for four days and collected. Cells were immunoblotted for EHMT1 (Bethyl, Cat. #A301-642A; dilution 1:500), EHMT2 (Cell Signaling, Cat. #3306; RRID:AB_2097647; dilution 1:1000), alpha-tubulin (Cell Signaling Cat. #3873; RRID:AB_1904178; dilution 1:3000), and H3K9me2 (Cell Signaling Cat. #4658; RRID:AB_10544405; diluted 1:1000).

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Sequencing libraries were prepared from RNA harvested from treatment or transfection replicates. Total RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Cat. #D4209). Ribosome depletion and library preparation was performed using the Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581) according to the manufacturer’s protocols. Briefly, 500ng of RNA was used as input, and KAPA BioSystems single-index adapters were added at a final concentration of 1.5mM. Purified, adapter-ligated library was amplified for a total of 11 cycles following the manufacturer’s protocol. The final libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150 bp paired-end reads.

treatment_protocol: Cells were treated with DMSO, olaparib, UNC0642, or olaparib + UNC0642 for 72 hours

tag: phenotype

tag: timepoint


title: 130911_IL1B

tag: batch

value: First


title: T1245_GS6_4N_M_H2

city: Boston

tag: cell type

tag: bisulfite conversion_rate

tag: qc


title: 130911_Control

value: Control


title: ID8_R_Combo_rep1


title: mRNA_51_T1

first: Youssef

last: Idaghdour

institute: NYUAD

tag: outcome


title: T1245_GS6_4N_M_H1

tag: patient donor/cell_line

tag: genome build

value: fail


title: mRNA_44_T1


title: 250718B_Control


title: T1245_GS6_4N_M_G3

tag: cpg coverage


title: CD8+ T cells, FIH/VHL_DKO_4

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

institute: University of Cambridge

data_processing:
RNA-sequencing: 2x75-nt sequence reads using Illumina NextSeq 550.
Basecalling and demultiplexing was performed using Illumina bcl2fastq.
Reads were aligned to the mm10 reference genome using STAR.
Read summarization to gene counts was performed using featureCounts.
Normalization of raw counts and differential gene expression were performed using DESeq2.
Assembly: mm10.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Spleen

growth_protocol: Splenic CD8+ T cells from Hif1an-floxed dLck Cre- or Vhl-floxed dLck Cre- (‘WT’) , Hif1an-floxed dLck Cre+ (‘FIH KO’), Vhl-floxed dLck Cre+ (‘VHL KO’) and Hif1an--floxed/Vhl--floxed dLck Cre+ (‘FIH/VHL KO’) C57BL6/J mice were activated in complete RPMI (Gibco) with anti-CD3/anti-CD28 Dynabeads and 10units/ml recombinant human IL-2 for 3 days.

extract_protocol:
On day 3 CD8+ T cells were washed twice with ice cold PBS (Gibco) and lysed with RLT buffer containing 1% β-mercaptoethanol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD8+ T cells were activated in complete RPMI (Gibco) with anti-CD3/anti-CD28 Dynabeads and 10units/ml recombinant human IL-2 for 3 days.

value: Spleen

value: CD8+ T cells

value: fih vhl double knockout


title: mRNA_43_T1

address: Saadiyat Marina District

value: Male

value: Blood


title: mRNA_41_T1

value: ICU


title: ID8_R_UNC_rep1


title: CD8+ T cells, FIH/VHL_DKO_2


title: T1245_GS6_4N_M_G2

value: Single prostate tumor cell


title: T1245_GS6_4N_M_G1


title: ID8_R_Ola_rep2

value: olaparib


title: mRNA_42_T1


title: CD8+ T cells, FIH/VHL_DKO_1


title: mRNA_40_T1


title: T1245_GS6_4N_M_F3


title: CD8+ T cells, VHL_KO_4

value: vhl knockout


title: T1245_GS6_4N_M_F2


title: ID8_R_DMSO_rep2

value: DMSO


title: mRNA_36_T1

value: Female


title: T1245_GS6_4N_M_F1


title: mRNA_33_T1


title: ID8_R_DMSO_rep1


title: ID8_R_UNC_rep2


title: CD8+ T cells, VHL_KO_2


title: mRNA_26_T1


title: CD8+ T cells, VHL_KO_1


title: T1245_GS6_4N_M_E3

value: pass


title: ID8_S_DMSO_rep2

value: wildtype


title: mRNA_23_T1

value: NO ICU


title: CD8+ T cells, FIH/VHL_DKO_3


title: ID8_S_DMSO_rep1


title: CD8+ T cells, FIH_KO_4

value: fih knockout


title: CD8+ T cells, FIH_KO_3


title: mRNA_39_T1