title: WRC42, leaf, moderate drought, Day 5, rep 1

description: Library name: D31

value: moderate drought


title: 35A_coeliac

status: Public on Jul 30 2025

type: SRA

city: Spring House

first: Dylan

middle: Jack

last: Richards

state: PA

address: 1400 McKean Rd

country: USA

institute: Johnson & Johnson

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0
Cell Ranger output was immediately processed to remove ambient RNA using cellbender v0.3.0 to create ambient RNA adjusted matrix/tsv processed data
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: D2- Duodenum desending part

extract_protocol:
Cryopreserved biopsies were thawed by immersing in a 37°C water bath for ~ 2 min with periodic shaking. RPMI with 10% FCS was added to each biopsy, dropwise in a 50 ml tube. The biopsies were washed in serum free RPMI over a cell strainer. Single cell suspensions were made by placing biopsies in a mixture of Liberase TM (SIGMA – 5401127001) and DNase (SIGMA - D5025-15 KU) while slowly rotating at 37°C (Smilie et al.,). Dissocicated biopsies were washed with 0.1% BSA over a cell strainer. Dead cells were removed using EasySep™ Dead Cell Removal (Annexin V) Kit (Stemcell Technologies -  17899). Cells counts were determined using AOPI staining solution and a Nexcelom fluorescent cell counter.
scRNA libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics) according to manufacturer’s instruction on the Chromium Controller (10X Genomics). Sequence-ready libraries were validated and quantitated using the Agilent High Sensitivity D1000 ScreenTape Kit on the TapeStation 4200 System (Agilent Technologies). Individual libraries were normalized to 3nM and quantified by qPCR using the KAPA Library Quantification Kit – Illumina/ROX Low (Roche) on the QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems) according to manufacturer’s instructions. The libraries were then pooled to 3nM and quantified again by qPCR as described above. The quantified library pool was denatured and diluted according to the NovaSeq 6000 Denature and Dilute Libraries Guide and loaded onto a NovaSeq 6000 System (Illumina) for paired end sequencing. BCL conversion and demultiplexing was performed using the bcl2fastq2 script (v2.20, Illumina).

tag: tissue

value: D2- Duodenum desending part

tag: disease state

value: Coeliac

tag: histologic severity

value: Marsh 3b

tag: subject id


title: WRC35, leaf, moderate drought, Day 5, rep 1

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

description: Library name: D30

library_source: transcriptomic

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

molecule: polyA RNA

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were surface sterilized with 375 ppm of pefurazoate at 15°C for 24 h. Then the seeds were soaked in water to germinate in a dark place at 30°C for two days. The calcined clay (Profile Greens Grade, PROFILE Products LLC, http://www.profileevs.com) was used as the soil. The soil was washed with water before use, then dried, filled in the pots (24.5 cm upper outer diameter, 20 cm lower outer diameter, 30 cm height; SP2530P, Tecs Inc., http://www.tecs.ne.jp) up to a depth of 25cm, and irrigated with modified Kimura B (Yoshida et al., 1976) culture solution (273.2 µM K2SO4, 546.9 µM MgSO4.7H2O, 182.0 µM NaH2PO4.2H2O, 182.3 µM CaCl2.2H2O, 182.4 µM CaSO4.2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg L-1 FeC6H5O7.nH2O [pH 5.5]). The germinated seeds were individually planted in separate pots, and they were cultivated in a growth chamber (Nippon Medical & Chemical Instruments Co., http://www.nihonika.co.jp) under a 14 h light/ 10 h dark photoperiod, with 50% relative humidity (R.H.) at daytime and 60% R.H. at nighttime. The temperature in the growth chamber was maintained at 25°C at nighttime and varied from 25°C to 30°C at daytime.  We used iPOTs (Numajiri et al. 2021), which is a pot that incorporates auto-irrigation system to mimic soil condition similar to the drought stress in the field. The water level in the supply pot, connected in parallel with the pots through a hose, was maintained at a height of 10 cm to ensure that the upper layers of the pots were moistened during the irrigation period.

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: Plants at 14 days after sowing were subjected to severe drought treatment for 9 days, and then watered for 6 days. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf

tag: cultivar

tag: treatment

tag: days after_treatment

tag: replicate


title: 35 mer oligomer (100%D, 0%U), treated, HIV RT, 1mM dNTP

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

library_source: other

data_processing:
The sequencing data were all trimmed with cutadapt tool (v4.8) to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73), 5-mer random barcodes at reads ends were trimmed and low-quality or short reads (less than 20 nt) were removed using cutadapt tool.
For tRNAs, remaining reads were aligned to tRNA sequence obtained from GtRNAdb (https://gtrnadb.ucsc.edu/) using hisat-3n (v.2.2.1-3n-0.0.3). Mitochondria and chloroplast tRNA sequences are obtained from published papers.
Meanwhile, we have also aligned remaining reads to hg38, mm10, or TAIR10 genome using hisat3n to investigate D sites in other RNA species.
The generated table from hisat-3n were parsed and analyzed by inhouse scripts. Internal mutation ratio at each D candidate site suggested by hisat-3n, was further confirmed by direct IGV visualization (v.2.8.0).
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107), TAIR10
Supplementary files format and content: For samples with cellular RNA, the mutation ratio at D sites in treated, input samples are shown. For samples with RNA probes, mutations at D sites are shown.
Library strategy: Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI)

molecule: other

organism: synthetic construct

source_name: 35 mer oligomer (100%D

growth_protocol: Human HepG2 cell lines and mouse embryonic stem cells (mESC) used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell lines were maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). mESC cells were grown under a typical feeder-free culture condition: cells were cultured in DMEM (GIBCO, 11995), supplemented with 15% FBS, 1% Pen/Strep (GIBCO), 1X Glutamax (GIBCO), 1X non-essential amino acids (GIBCO), 1X 2-Mercaptoethanol (GIBCO), and 1000 U/ml leukemia inhibitory factor (Millipore, ESG1107), together with two inhibitors: 3 mM CHIR99021 (STEMCELL Technologies, dissolved in DMSO) and 1 mM PD0325901 (STEMCELL Technologies, dissolved in DMSO). mESC cells were distinctively cultured on gelatinized culture plates (0.2% Gelatin). The culture of mESC cells were passaged every 2 days. All cells were cultured at 37 Co under 5.0% CO2.

extract_protocol:
Generally, with harvesting cells as the first step, the media was aspirated, and the cells were washed once with proper volume of ice cold DPBS buffer for each plate. Then total RNA was isolated from cells with TRIzol reagent (Invitrogen) and then extracted following manufacturer’s protocol by isopropanol precipitation. Small RNA fraction was purified from total RNA with RNA Clean & Concentrator kit (Zymo Research) following manufacturer’s protocol. mRNA was extracted by two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion).
CRACI for D site detection Wild-type HepG2, mESC, and arabidopsis thaliana seedling cells (two replicates for each sample, one 10-cm plate per replicate); HepG2 siControl or DUS knockdown cells were prepared as described (two replicates for each sample, one 10-cm plate per replicate). After extracting the polyA+ RNA or small RNA from mammalian cells or plant cells, around 100 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with Oligomer Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by Oligomer Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water.  To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNNATCACG AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 45 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 45 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 10 µl RNase-free water. The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC -3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 12 µl RNase-free water.  A 2 µl aliquot of the purified RNA was saved for ‘Input1’ library construction, 2 µl aliquot of the purified RNA was saved for ‘Input2’ library construction, and the rest 6 µl was subjected to CRACI optimized reduction treatment, as the ‘Treated’ sample. The 6 µl RNA was mixed with 40 µl freshly prepared KBH4 (1 M KBH4, prepared by dissolving 54 mg KBH4 in 1000 µl RNase-free water) and Incubated the reaction mixture at 25 °C for 3 h, followed by purification with RNA Clean and Concentrator (Zymo Research) and elute with 10 µl H2O. ‘Input1’, ‘Input2’ and purified ‘Treated’ samples were diluted to 10 µl and mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. Then for ‘Input2’ and ‘Treated’ samples, a stock with 2 µl 10x AMV RT Buffer (New England BioLabs, cat. no. B0277AVIAL), 2 µl 1 mM dNTP Solution Mix (dilute from 10 mM dNTP Solution Mix, New England BioLabs, catalog no. N0447L), 2 µl 10mM dGTP (dilute from 100 mM dNTP Solution Mix, New England BioLabs, catalog no. N0442S), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 2 µl HIV RT (Worthington Biochemical, catalog no. LS05003) was added. For ‘Input1’ sample, a stock with 2 µl RNase-free water, 2 µl 10x AMV RT Buffer, 2 µl 10 mM dNTP Solution Mix (New England BioLabs, catalog no. N0447L), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor and 2 µl HIV RT was added.  The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina NovaSeqX with single-end 100 bp read length.

tag: cell line

value: 35 mer oligomer (100%D

tag: fraction

value: RNA probes


title: 33A_coeliac


title: FAC-sorted cells, DNMT1 control, rep 1

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Biology 2

country: Germany

institute: RWTH Aachen University

description:
Library name: Sst_WT_1_RNA
E14.5

data_processing:
FASTQ files were generated using bcl2fastq (Illumina, U.S.A.). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/rnaseq pipeline version 3.17.0 implemented in Nextflow 24.10.2 with the minimal command. In brief, lane-level reads were trimmed using Trim Galore 0.6.10 and aligned to the mouse genome (GRCm39) using STAR 2.7.11b. Gene-level and transcript-level quantification was done by Salmon v1.10.3. All analysis was performed using custom scripts in R version 4.3.3 using the DESeq2 v.1.42.1 framework.
Assembly: GRCm39
Supplementary files format and content: Comma-separated table listing the normalized counts of detected genes per sample

organism: Mus musculus

source_name: Cortex

extract_protocol:
The Cortex samples were collected in cold HBSS (w/ phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose; 4 µg/µL (600 U) of DNAse I (AppliChem GmbH, Germany). After treatment with 0.04% trypsin for 17 min at 37 °C, HBSS was replaced by DMEM with additional L-glutamine and 4.5 g/L D-glucose, 10% FBS and 1% P/S to stop the trypsinization. Subsequently, the cells were pelletized, resuspended and triturated in cold HBSS (w/o phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose, before being filtered through a nylon gauze (pore size 140 µm, Merck, U.S.A.) for FACS. Respective parameters for the procedure using a BD FACS Aria Fusion (BD Biosciences, U.S.A) were defined as follows: 5-laser (FCS, SSC, PE, BV421), 18-color (3-6-2-4-3). TdTomato-positive cells were collected in 100 µL of cold TRIzol™ (Thermo Fisher Scientific, U.S.A.) for subsequent RNA sequencing. Samples were mixed by inversion and stored at -80°C until processing. RNA was isolated from 50,000 cells pooled per genotype. The samples were filled up to 1 ml with TRIzol™ and dounced 25 times in a glass homogenizer using the small-clearance pestle. Samples were incubated for 5 min at room temperature, supplemented with 200 µL chloroform and mixed by shaking vigorously until a homogenous milky solution appeared. Following another incubation at room temperature (until a visible phase separation appeared) samples were centrifuged at 13,000x g and 4°C for 15 min in a tabletop centrifuge with cooling function. For precipitation, the clear upper phase was collected and mixed with 70% ethanol. Samples were bound onto RNeasy mini columns (Qiagen, Germany) and washed according to the instructions in the manual. RNA was eluted with 30 µL nuclease-free water.
Prior to library preparation, samples were digested with HL dsDNAseI (ArcticZymes Technologies ASA, Norway) for 10 min at 37°C to remove traces of gDNA. To avoid a digestion of the newly generated cDNA during library preparation, the dsDNAseI was heat inactivated for 5 min at 58°C. Thereafter, samples were subjected to library preparation using the  SMART-Seq Total RNA Pico Input with UMIs (ZapR Mammalian) for Illumina (Takara Bio, Japan). Fragmentation was done at 94°C for 4 min. Illumina adaptors and indices were ligated to cDNA in a PCR reaction with 5 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). RRNA depletion was performed on the amplified libraries. Final libraries were subjected to an upscale PCR with 15 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). Amplified libraries were cleaned with magnetic AMPure XP beads (Beckman Coulter, U.S.A.). Library concentration was determined with a Qubit™ 4 fluorometer using the 1x dsDNA HS reagent (Thermo Fisher Scientific, U.S.A.). Library size was assessed on a Tape Station 4200 using the DNA D1000 kit (Agilent Technologies, U.S.A.). Libraries were diluted, equimolarly pooled, denatured, and loaded for clustering onto an Illumina NovaSeq 6000 SP (200 cycles) flow cell (Illumina, U.S.A.) in conjunction with 1% PhiX control library, and run on an Illumina NovaSeq machine (Illumina, U.S.A.) in 75 bp paired-end mode. The 1% PhiX control library was spiked in to improve base calling accuracy.

value: Cortex

tag: cell type

value: Sst interneuron

tag: genotype

value: Sst-Cre/tdTomato


title: 34A_coeliac

value: Marsh 3c


title: 18A_coeliac


title: 35 mer oligomer (100%D, 0%U), treated, HIV RT, 1mM dGTP+100μM dNTP


title: 11A_control

value: control


title: WRC22, leaf, moderate drought, Day 5, rep 1

description: Library name: D28


title: Kidney, Pkd1KO+Glis3KO (ATAC, rep 2)

city: New Haven

first: Stefan

last: Somlo

state: CT

address: 333 Cedar Street

institute: Yale University

description: Library name: ZWDKO2

library_source: genomic

data_processing:
For RNA-Seq, raw fastq files were processed using fastq tool. Sequencing reads with low-quality bases were trimmed and filtered. Cleaned reads were aligned using STAR (version 2.7.9) with the mouse reference genome gencode version GRCm38.p6 with vM25 gene annotation. Expression quantification for aligned reads was performed using featureCounts (version 2.0.0). The filtered read counts matrix was normalized by the transcripts per million (TPM) method.
For ATAC-Seq, raw sequencing reads were trimmed using cutadapt and mapped to mm10 using bowtie2. Duplicates and mitochondrial reads were marked by Picard and removed by Samtools. Peak calling was performed using MACS2 with peaks falling into blacklist regions (mm10 blacklist v2) removed.
Assembly: mm10
Supplementary files format and content: csv files for RNA-Seq; bed files for ATAC-Seq

molecule: genomic DNA

source_name: Kidney

extract_protocol:
Total RNA from whole kidneys were isolated using (Themo Fisher Scientific, Cat. no. 15596026) and RNeasy Mini Kit (Qiagen, Cat. no. 74104). Tagmentated DNA were purified following ActiveMotif protocol.
RNA sequencing library was prepared using the ribosomal depletion method (KAPA RNA HyperPrep Kit with RiboErase, Roche). ATAC sequencing library were prepared following ActiveMotif protocol.

value: Kidney


title: 15A_coeliac


title: 35 mer oligomer (80%D, 20%U), treated

source_name: 35 mer oligomer (80%D

value: 35 mer oligomer (80%D


title: Kidney, Pkd1KO+Glis3KO (ATAC, rep 1)

description: Library name: ZWDKO1


title: Kidney, Pkd1KO (ATAC, rep 3)

description: Library name: ZWD1S3


title: 14A_coeliac


title: WRC47, leaf, moderate drought, Day 5, rep 1

description: Library name: D29


title: 35 mer oligomer (40%D, 60%U), treated

source_name: 35 mer oligomer (40%D

value: 35 mer oligomer (40%D


title: 35 mer oligomer (100%D, 0%U), treated


title: 35 mer oligomer (60%D, 40%U), treated

source_name: 35 mer oligomer (60%D

value: 35 mer oligomer (60%D


title: Kidney, Pkd1KO (ATAC, rep 2)

description: Library name: ZWD1S2


title: 10A_coeliac


title: 31A_coeliac


title: 26A_coeliac


title: WRC18, leaf, moderate drought, Day 5, rep 1

description: Library name: D27


title: Kidney, Glis3KO (ATAC, rep 3)

description: Library name: ZWG3S3


title: 20A_coeliac

value: Marsh 3a


title: Kidney, Glis3KO (ATAC, rep 2)

description: Library name: ZWG3S2


title: 35 mer oligomer (0%D, 100%U), treated

source_name: 35 mer oligomer (0%D

value: 35 mer oligomer (0%D


title: WRC50, leaf, moderate drought, Day 5, rep 1

description: Library name: D23

value: moderate drought


title: WRC46, leaf, moderate drought, Day 5, rep 1

description: Library name: D22


title: WRC37, leaf, moderate drought, Day 5, rep 1

description: Library name: D26


title: Kidney, Pkd1KO (ATAC, rep 1)

description: Library name: ZWD1S1


title: 35 mer oligomer (80%D, 20%U), input2


title: Kidney, Glis3KO (ATAC, rep 1)

description: Library name: ZWG3S1


title: 35 mer oligomer (60%D, 40%U), input2


title: WRC09, leaf, moderate drought, Day 5, rep 1

description: Library name: D24


title: 29A_coeliac

value: D2- Duodenum desending part

value: Coeliac


title: WRC32, leaf, moderate drought, Day 5, rep 1

description: Library name: D21

value: leaf


title: 32A_coeliac


title: WRC27, leaf, moderate drought, Day 5, rep 1

description: Library name: D25


title: IR64, leaf, moderate drought, Day 5, rep 1.

description: Library name: D20


title: 28A_coeliac


title: 35 mer oligomer (20%D, 80%U), treated

source_name: 35 mer oligomer (20%D

value: 35 mer oligomer (20%D


title: WRC01, leaf, moderate drought, Day 5, rep 1

description: Library name: D19


title: 35 mer oligomer (40%D, 60%U), input2

value: RNA probes


title: Kidney, WT (ATAC, rep 1)

description: Library name: ZWCTR1

value: WT


title: 27A_coeliac


title: Kidney, WT (ATAC, rep 2)

description: Library name: ZWCTR2


title: 35 mer oligomer (20%D, 80%U), input2


title: WRC13, leaf, moderate drought, Day 5, rep 1

description: Library name: D18


title: 35 mer oligomer (100%D, 0%U), input2

value: 35 mer oligomer (100%D


title: WRC16, leaf, moderate drought, Day 5, rep 1

description: Library name: D17


title: 35 mer oligomer (100%D, 0%U), input1


title: 35 mer oligomer (0%D, 100%U), input2


title: WRC06, leaf, moderate drought, Day 5, rep 1

description: Library name: D15


title: 24A_coeliac


title: 35 mer oligomer (80%D, 20%U), input1


title: Kidney, WT (ATAC, rep 3)

description: Library name: ZWCTR3


title: 23A_coeliac


title: Kidney, Pkd1KO+Glis3KO (RNA, rep 2)

description:
Library name: ZW12
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: Kidney, Pkd1KO+Glis3KO (RNA, rep 1)

description:
Library name: ZW11
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: 22A_coeliac


title: WRC33, leaf, moderate drought, Day 5, rep 1

description: Library name: D13


title: Kidney, Pkd1KO (RNA, rep 3)

description:
Library name: ZW10
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: 35 mer oligomer (60%D, 40%U), input1


title: 35 mer oligomer (40%D, 60%U), input1


title: 16A_coeliac


title: KP, leaf, moderate drought, Day 5, rep 1

description: Library name: D12

value: KP


title: WRC05, leaf, moderate drought, Day 5, rep 1

description: Library name: D14


title: 24A_rep2_coeliac


title: 8A_coeliac

value: Marsh 2


title: WRC03, leaf, moderate drought, Day 5, rep 1

description: Library name: D11


title: 35 mer oligomer (20%D, 80%U), input1


title: Kidney, Pkd1KO (RNA, rep 1)

description:
Library name: ZW8
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: WRC34, leaf, moderate drought, Day 5, rep 1

description: Library name: D10


title: 21A_coeliac


title: 35 mer oligomer (0%D, 100%U), input1


title: Kidney, Glis3KO (RNA, rep 4)

description:
Library name: ZW7
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: Kidney, Pkd1KO+Glis3KO (RNA, rep 3)

description:
Library name: ZW13
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: PS004_t3

city: Montreal

first: Luda

last: Diatchenko

state: Quebec

address: 3775 Rue University

country: Canada

institute: McGill University

data_processing:
The isolated RNA was stored in Eppendorf tubes at -80C
RNA QC was done by Nanodrop and Bioanalyzer
Assembly: GRCh38
Supplementary files format and content: transcript-per-million in tsv format

source_name: Blood

extract_protocol:
RNA extraction was performed using the PAXgene Blood RNA kit and a corresponding protocol
Standard Illumina Protocol

value: Blood


title: Kidney, Glis3KO (RNA, rep 2)

description:
Library name: ZW5
Glis3.RNAseq.tissue.RQ33140.counts.csv

value: Kidney


title: PS004_t2


title: Kidney, Glis3KO (RNA, rep 3)

description:
Library name: ZW6
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: Kidney, Pkd1KO (RNA, rep 2)

description:
Library name: ZW9
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: WRC23, leaf, moderate drought, Day 5, rep 1

description: Library name: D8


title: PS004_t0


title: Kidney, Glis3KO (RNA, rep 1)

description:
Library name: ZW4
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: WRC31, leaf, moderate drought, Day 5, rep 1

description: Library name: D7


title: Kidney, WT (RNA, rep 3)

description:
Library name: ZW3
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: UPN1_8h_r1

city: Valhalla

first: Seungha

middle: Alisa

last: Lee

state: New York

address: 15 Dana Road

institute: New York Medical College

description:
Library name: UPN1_8h_r1
Replicate 1

data_processing:
PRO-seq data is first trimmed off the 8 base unique molecular identifier and 3’ adaptor using cutadapt.
Trimmed sequences are aligned to hg38 genome using STAR aligner.
Read alignments are separated by the opposite strand they were aligned to.
Sum of readcounts per each genomic base coordinates at the 5’ end of aligned sequences are processed to strand specific bedgraph data.
Assembly: Hg38
Supplementary files format and content: bedgraph, sum of read counts in genomic coordinates

molecule: nuclear RNA

extract_protocol:
Approximately 4 million cells were collected from 10 cm culture dishes by rinsing the plates with cold PBS twice and resuspended in 50 µL of buffer D. Harvested cells were rapidly frozen in liquid nitrogen and stored at -80°C.
PRO-seq was performed on whole nuclei or nuclear condensate fractions in the storage buffer (Buffer D) as described previously (Kwat et al, 2013), with the following modifications. Briefly, isolated fractions were incubated in the nuclear run-on reaction condition (5 mM Tris-HCl pH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5% Sarkosyl, 0.4 units / μl of RNase inhibitor) with biotin-NTPs and rNTPs supplied (18.75 μM rATP, 18.75 μM rGTP, 1.875 μM biotin-11-CTP, 1.875 μM biotin-11-UTP for uPRO; 18.75 μM rATP, 18.75 μM rGTP, 18.75 μM rUTP, 0.75 μM CTP, 7.5 μM biotin-11-CTP for pChRO) for 5 min at 37°C. Run-On RNA was extracted using TRIzol, and fragmented under 0.2 N NaOH for 15 min on ice. Fragmented RNA was neutralized, and buffer exchanged by passing through P-30 columns (Biorad). 3′ RNA adaptor (/5Phos/NNNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT/) is ligated at 5 μM concentration for 1 hours at room temperature using T4 RNA ligase (NEB), followed by 2 consecutive streptavidin bead bindings and extractions. Extracted RNA is converted to cDNA using template switch reverse transcription with 1 μM RP1-short RT primer (GTTCAGAGTTCTACAGTCCGA), 3.75 μM RTP-Template Switch Oligo (GCCTTGGCACCCGAGAATTCCArGrGrG), 1x Template Switch Enzyme and Buffer (NEB) at 42°C for 30 min. After a SPRI bead clean-up, the cDNA is PCR amplified up to 20 cycles using primers compatible with Illumina Small RNA sequencing.

value: Mantle Cell Lymphoma

value: dTAG-47 8hr


title: UPN1_8h_r2

description:
Library name: UPN1_8h_r2
Replicate 2


title: PS001_t2


title: UPN1_2h_r1

description:
Library name: UPN1_2h_r1
Replicate 1

value: dTAG-47 2hr


title: PS001_t3


title: Kidney, WT (RNA, rep 2)

description:
Library name: ZW2
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: UPN1_2h_r2

description:
Library name: UPN1_2h_r2
Replicate 2


title: WRC51, leaf, moderate drought, Day 5, rep 1

description: Library name: D9


title: Neuroblastoma cell line

city: uppsala

first: Xiaonan

last: Zhang

state: Sweden

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

data_processing:
10x Genomics CellRanger 6.0.2 software was used to demultiplex cell barcodes. Reads were mapped to the GRCh38 human reference transcriptome using the STAR aligner. The number of cells in samples was identified with a cell barcode in a library. Cells containing the number of counts <100 and the number of detected feature genes <100 and mitochondrial percentage >0.3 will be filtered. R package DoubletFinder  was used to distinguish between empty droplets and droplets containing a cell. The raw matrix of gene counts versus cells from CellRanger output was filtered, removing unqualified cells. R package Seurat12 was used to perform the downstream analysis of the matrix. Expression normalization was performed using the LogNormalize() function in Seurat. To adjust for difference in library size and cell cycle, the number of UMIs, mitochondrial content and cell-cycle difference were regressed using a linear model during gene scaling and centering. The uninteresting differences in the cell cycle could be removed using the “Alternate Workflow” in Seurat based on the expression level of previously published G2/M and S-phase gene signatures.
Assembly: hg38
Supplementary files format and content: csv

source_name: nerve tissue

extract_protocol:
10,000 cells/well were plated in 96-well ultra-low attachment plates (#7007, Corning, NY, USA) in 200 μL medium. Then plates were centrifuged at 1500 rpm for 10 min. For single-cell RNA-Seq assay, plates were incubated for 8d before spheroids trypsinization.The volume of spheroids was calculated by the equation Volume = (4/3)*3.14*R3 (R = radius).  Preparation of sequencing material was performed in the single-cell system following the manufacturer’s protocols by Eukaryotic Single-Cell Genomics Facility (Karolinska Institute, Sweden).
Single-cell capture, lysis, reverse transcription, and pre-amplification were performed in the single-cell system following the manufacturer’s protocols by Eukaryotic Single-Cell Genomics Facility (Karolinska Institute, Sweden). Libraries were sequenced using the Illumina NovaSeq 6000 System.

value: nerve tissue

value: neuroblastoma

value: organoid


title: PS001_t0


title: WRC55, leaf, moderate drought, Day 5, rep 1

description: Library name: D3

value: moderate drought


title: WRC57, leaf, moderate drought, Day 5, rep 1

description: Library name: D4


title: WRC36, leaf, moderate drought, Day 5, rep 1

description: Library name: D6


title: MV_NT_r2

description:
Library name: MV_NT_r2
Replicate 2

value: Wild Type

value: No treatment


title: UPN1_0h_r1

description:
Library name: UPN1_0h_r1
Replicate 1


title: UPN1_0h_r2

description:
Library name: UPN1_0h_r2
Replicate 2


title: WRC44, leaf, moderate drought, Day 5, rep 1

description: Library name: D5

value: leaf


title: Kidney, WT (RNA, rep 1)

description:
Library name: ZW1
Glis3.RNAseq.tissue.RQ33140.counts.csv


title: Csnk2bfl/fl

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

description:
Library name: WT
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using 10X SpaceRanger pipeline.
Sequences were aligned to mm10 genome using SpaceRangers default settings.
Gene expression level of Refseq coding genes were quantified using SpaceRangers default settings.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx,gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json-json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hires images of the tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spacial_enrichment.csv: list with Feature ID,Feature Name,Feature Type,I,P value,Adjusted p value,Feature Counts in Spots Under Tissue,Median Normalized Average Counts,Barcodes Detected per Feature
Supplementary files format and content: CAVG files: CytAssist image files in TIFF format
Assembly: mm10
Library strategy: Spatial Transcriptomics

source_name: melanoma

growth_protocol: 2x105 B16.F10 cells were inoculated in wild-type mice (WT; Csnk2bfl/fl)  and Foxp3-Cre × CK2b-fl/fl (KO; Csnk2bTreg-/-) mice (8–16 weeks old).

extract_protocol:
B16.F10 tumors of comparable size were isolated on day 15 after inoculation B16.F10 tumors of comparable size were isolated on day 15 after inoculation, fixed in formalin and embedded in paraffin. 10µm FFPE embedded sections were cut with a microtome. The spatial transcriptomics workflow was performed using the Visium CytAssist Spatial Gene Expression for FFPE (10X document, Doc ID: CG000520 Rev C). Post-hybridization wash, probe ligation and post-ligation wash were conducted following 10X protocol (DOC ID: CG000495 Rev E).
Spatial transcriptome sequencing libraries were prepared with the 10x Genomics workflow according to manufacturer's instructions (10X document: CG000495 Rev E)

treatment_protocol: no treatment

value: melanoma

value: wild-type

value: untreated


title: MSCs, MFR50, rep3

city: Oxford

first: Jinrong

last: Lin

state: Oxfordshire

address: 22 Windmill Road, 22 Windmill Road, Headington

country: United Kingdom

institute: University of Oxford

data_processing:
The original image data file from the high-throughput Illumina sequencing platform was transformed into raw reads by the Illumina Casava (v1.8). These raw data were stored in FASTQ format files, which contain sequences of reads along with their corresponding base quality. Quality assessment of raw reads was accomplished using FASTQC and ReadQC tools. Alignment of raw reads to the GRCh38 reference genome was achieved using hisat2 (v 2.0.5). Visualisation of the mapped reads was conducted using IGV (v2.3.74) to further evaluate the mapping quality. The quantification of mapped reads against GCRh38 reference genome annotation was carried out using FeatureCounts (v1.5.0-p3), And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Subsequent analyses were completed using R 4.2.2. Differential expression analysis was performed using the EdgeR (v 3.28.1) by using quasilikelihood (QL) F-tests, genes with adjust P value < 0.05 and |log2(foldchange)| >= 1 were determined as significantly differential expressed. GO and KEGG analysis was performed using the enrichGO and enrichKEGG function of the clusterProfiler 3.14.3 package, respectively, where categories with p value ≤ 0.05 were considered significantly enriched. Heatmaps and volcano plots were visualized by using pheatmap 1.0.12 and EnhancedVolcano 1.4.0, respectively.
Assembly: hg18
Supplementary files format and content: fpkm and count values for each Sample

source_name: Green fluorescent protein (GFP)-modified human MSCshTERT

growth_protocol: mesenchymal stem cells were maintained in DMEM supplemented with with 10% fetal bovine serum and 1% penicillin-streptomycin solutio at the standard conditions of 37°C with a 5% CO2 atmosphere

extract_protocol:
RNA was extracted using Zymo Direct-zol RNA Miniprep Plus Kits (Cambridge Biosciences, UK) according to the manufacturer’s protocol.
Library preparation was done using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with poly-A selection (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.

treatment_protocol: After seeding each bioreactor chamber, they were cultured in static conditions for two days before introducing mechanical stimulation from day 3 to day 14, spanning a total of 12 days. Throughout the culture period, daily mechanical stimulations were conducted on the chambers using a humanoid shoulder arm or a uniaxial platform. For the dynamic stimulation on the humanoid robotic shoulder, before mounting the chambers onto the humanoid shoulder, a specific sequence of two adduction and abduction movements, each spanning approximately 60 degrees from a reference position parallel to the robot's trunk, was manually applied to the arm. The tension in the springs on the humanoid robotic shoulder and the uniaxial platform (the actuators attached to the chambers) was carefully adjusted to reach a pre-defined maximum force, which could be either 25 N (FR25) or 50 N (FR50). Once the loading parameters were configured, the chambers were transferred to both platforms, situated outside the incubator. To ensure an adequate supply of nutrients during stimulation, approximately 1 mL of medium was retained within each chamber. The adduction-abduction exercises on the humanoid robotic shoulder or the stretching exercises on the uniaxial platform, were repeated for 30 min at a frequency of approximately 0.08 Hz for both platforms. Deformations of the scaffold within the chambers, where cells adhered, were continuously monitored using sensors. The stimulation on uniaxial platform was performed by an X-LSM025A-E03 motorized linear stage (Zaber, Vancouver, Canada), and the stimulation conditions including time and strains were kept the same as those on the humanoid robotic shoulder.

value: mesenchymal stem cells

value: MFR50 mechanical stimulation


title: MSCs, MFR50, rep2

value: Green fluorescent protein (GFP)-modified human MSCshTERT


title: MSCs, MFR50, rep1


title: MV_NT_r1

description:
Library name: MV_NT_r1
Replicate 1


title: GEX + HTO (Sample tags: 7, 8, 9, 10, 11, 12)

description: Library name: Cartridge BD Rhapsody

data_processing:
Resulting raw data was preprocessed according to the Illumina standard protocol and transcript alignment, counting and demultiplexing was performed using the BD Rhapsody WTA analysis pipeline yielding to 5321 called putative cells overall with a mean of 1×105 aligned reads per cell. Pipeline output RSEC Mols per Cell files were imported into Partek Flow software (Version 10.0). Following quality control measures, cells were filtered out if they exhibited fewer than 500 or more than 4000 detected genes, or if their mitochondrial count exceeded 10%. After this filtering step, 3495 cells remained eligible for subsequent analyses. Additionally, noise reduction on low expressed genes (value<1 in 99%) was applied. Contaminating non-T cell populations, based on comparison of their gene-expression profiles with immune cell transcriptome profiles reported by ImmGen Consortium(https://www.immgen.org/), were removed from downstream analysis. Single cell counts were normalized by Partek Flows recommended normalization order (CPM (counts_per_million), Add:1 and log2).
Sampletag assignment: Sampletag 7 = Csnk2bfl/fl biol rep 1; Sampletag 8 = Csnk2bfl/fl biol rep 2; Sampletag 9 = Csnk2bfl/fl biol rep 3; Sampletag 10 = Foxp3-Cre × CK2b-fl/fl biol rep 1; Sampletag 11 = Foxp3-Cre × CK2b-fl/fl biol rep 2; Sampletag 12 = Foxp3-Cre × CK2b-fl/fl biol rep 1
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw molecule counts for every cell, gene and sample

source_name: B16.F10 melanomas

extract_protocol:
B16.F10 tumors were isolated on day 21 after inoculation. Excised tumors were cut into small pieces (2-4 mm), transferred into gentleMACS™ C tubes (Miltenyi Biotec; 130-093-237) and digested with the Tumor Dissocation Kit, mouse (Miltenyi Biotec; 130-096-730) according to the manufacturer's instructions using the gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec; 130-096-427). CD8+ and CD4+ tumor-infiltrating lymphocytes were isolated using CD4/CD8 (TIL) (Miltenyi Biotec; 130-116-480)  Microbeads according to the manufacturer's instructions using magnetic separation (magnetic activated cell sorting (MACS)).
Single cell capturing, isolation of RNA and synthesis of cDNA was performed using the BD Rhapsody Single-Cell Analysis System (BD Biosciences) according to manufacturer's instructions (All reagents required for this purpose are listed in document BD Biosciences, Doc ID: 210966 Rev1.0). Each sample was tagged with a special sample tag in order to allow multiplexing of samples on the same cartridge. Sequence of sample tags can be foundin the BD document Doc ID 210970. Whole transcriptome libraries and sample tag libraries were created using BD WTA Amplification Kit (BD Biosciences,633801) with random primers followed by amplification and insertion of sequencing adaptors following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation Protocol (BD Biosciences, Doc ID: 23-24119 Rev1.0). Quality and quantity of cDNA libraries were analyzed on a Bioanalyzer2100 (Agilent). Sequencing (paired end reads, PE150) was performed on a NovaSeq 6000 (Illumina) at Novogene (Cambridge; UK). For processing of the sequencing raw data BD Rhapsody WTA analysis pipeline version 2.0 was used.

value: B16.F10 melanomas

tag: sampletag assignment

value: Sampletag assignment:Sampletag 7 = Csnk2bfl/fl biol rep 1; Sampletag 8 = Csnk2bfl/fl biol rep 2; Sampletag 9 = Csnk2bfl/fl biol rep 3; Sampletag 10 = Foxp3-Cre × CK2b-fl/fl biol rep 1; Sampletag 11 = Foxp3-Cre × CK2b-fl/fl biol rep 2; Sampletag 12 = Foxp3-Cre × CK2b-fl/fl biol rep 1

value: tumor-infiltrating CD4+ and CD8+ T cells


title: Foxp3-Cre × CK2b-fl/fl

description:
Library name: KO
FFPE Spatial transcriptome sequencing

value: Foxp3-Cre x CK2b-fl/fl


title: WT.Vas.4

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

description: Library name: sample16

data_processing:
We aligned the raw reads to the mouse genome and estimated the gene counts using CellRanger software (v3.0) (10x Genomics). We then used Seurat (v4.3.0.1) package in R for downstream analysis. We selected cells with more than 500 detected unique molecular identifiers (UMIs) from protein-coding genes for further analysis. We also use the ratio of mitochondrial genes to measure the quality of cells (cells with higher than 5% were removed). We used DoubletFinder to remove the potential doublets and DecontX to remove the ambient RNA contamination ( https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1950-6)  from snRNA-seq data.
Assembly: mm10
Supplementary files format and content: ids files for count matrix of cell and gene and metadata for cells

source_name: Hippocampus

extract_protocol:
Mice were gently fixed in the strainer and quickly chopped, brains were harvested and dissected immediately on ice and dry ice mixture. Hippocampal dissections were flash frozen in liquid nitrogen and stored at -80C prior to further processing.
Paired vascular and non-vascular nuclei preparations were loaded onto a Chromium Next GEM Chip G (10xGenomics, PN-1000120) with libraries prepared using a Chromium Next GEM Single Cell 3’ Kit v3.1 following manufacturer recommendations (10xGenomics, PN-1000269).   In total four 5XFAD and four WT mice were profiled, corresponding to 16 total samples (bulk and vascular for each). For each sample we targeted 6000 nuclei on average. Libraries were sequenced on a NovaSeq S4 (Illumina) targeting 60,000 reads per nucleus.

value: Hippocampus

value: WT

value: Vascular enrichment


title: WRC57, leaf, control, Day 5, rep 3

description: Library name: C120

value: control


title: 5xFAD.Vas.4

description: Library name: sample15


title: MSCs, MFR25, rep3

value: MFR25 mechanical stimulation


title: KP, leaf, control, Day 5, rep 3

description: Library name: C119

value: KP


title: MV_FHD_r1

description:
Library name: MV_FHD_r1
Replicate 1

value: Mantle Cell Lymphoma

value: Wild Type


title: MSCs, MFR25, rep2


title: WT.Vas.3

description: Library name: sample14


title: MV_CCS_r2

description:
Library name: MV_CCS_r2
Replicate 2


title: WRC25, leaf, moderate drought, Day 5, rep 1

description: Library name: D2

value: leaf

value: moderate drought


title: MSCs, MFR25, rep1

value: mesenchymal stem cells


title: 5xFAD.Vas.3

description: Library name: sample13


title: MV_CCS_r1

description:
Library name: MV_CCS_r1
Replicate 1


title: WRC46, leaf, control, Day 5, rep 3

description: Library name: C117


title: WRC100, leaf, control, Day 5, rep 3

description: Library name: C116


title: MSCs, static, rep3

value: static


title: WRC100, leaf, moderate drought, Day 5, rep 1

description: Library name: D1


title: 5xFAD.All.4

description: Library name: sample11


title: MV_FHD_r2

description:
Library name: MV_FHD_r2
Replicate 2


title: MSCs, static, rep2

value: Green fluorescent protein (GFP)-modified human MSCshTERT


title: WRC16, leaf, control, Day 5, rep 3

description: Library name: C115


title: JEKO_NT_r1

description:
Library name: JEKO_NT_r1
Replicate 1

value: No treatment


title: WT.All.4

description: Library name: sample12


title: JEKO_NT_r2

description:
Library name: JEKO_NT_r2
Replicate 2


title: JEKO_FHD_r2

description:
Library name: JEKO_FHD_r2
Replicate 2


title: WRC21, leaf, control, Day 5, rep 3

description: Library name: C118


title: fCLIP IgG rep2

city: Seoul

first: Sunghan

state: South Korea

address: Building 203 Room 526, 1, Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
fCLIP-seq
gigyf2_fclip_seq_summary.txt
gigyf2_fclip_seq_sars_cov_2_coverage.csv

data_processing:
Sequencing reads were first mapped to the combined human-SARS-CoV-2 genome using STAR with options accommodating non-canonical viral junctions. Only uniquely mapped reads were used in the downstream analysis. Peak calling analysis was conducted using Piranha with the options -s -n -l -z 50. Adjacent peaks were merged, and those showing enrichment with an FDR < 0.05 in both replicates were selected for further analyses.
Assembly: STAR index were built using concatenated genome of human genome (GRCh38.primary_assembly) and SARS-CoV-2 genome (NC_045512.2).
Supplementary files format and content: Tab-delimited text file include the fCLIP-seq peak calling results generated by Piranha.
Supplementary files format and content: Comma-delimited csv file include the coverage of fCLIP reads on SARS-CoV-2 genome.
Library strategy: fCLIP-seq

extract_protocol:
Cells were fixed with 0.1% formaldehyde, quenched and lysed. After IP with specific antibodies, RNAs were extracted by ethanol precipitation.
RNAs were ligated with 3' adapter. After gel cut, RNAs were ligated with 5' adapter followed by reverse transcription and PCR amplifcation.

value: human lung cancer cell line

tag: antibody

value: IgG


title: WT.All.3

description: Library name: sample10


title: WRC44, leaf, control, Day 5, rep 3

description: Library name: C114


title: MSCs, static, rep1


title: JEKO_FHD_r1

description:
Library name: JEKO_FHD_r1
Replicate 1


title: 5xFAD.All.3

description: Library name: sample9


title: fCLIP IgG rep1


title: WT.Vas.2

description: Library name: sample8


title: IR64, leaf, control, Day 5, rep 3

description: Library name: C113


title: JEKO_CCS_r2

description:
Library name: JEKO_CCS_r2
Replicate 2


title: fCLIP antiGIGYF2 rep2


title: 5xFAD.Vas.2

description: Library name: sample7


title: WRC04, leaf, control, Day 5, rep 3

description: Library name: C112


title: JEKO_CCS_r1

description:
Library name: JEKO_CCS_r1
Replicate 1


title: WRC32, leaf, control, Day 5, rep 3

description: Library name: C111


title: Koshihikari, leaf, control, Day 5, rep 3

description: Library name: C110

value: Koshihikari


title: 5xFAD.All.2

description: Library name: sample5

value: Hippocampus


title: WT.All.2

description: Library name: sample6

value: WT


title: CM_8h_r2

description:
Library name: CM_8h_r2
Replicate 2

value: dTAG-47 8hr


title: Mesoderm Nucleus Repeat 3

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

description:
subcellular_rnaseq_mesoderm_loc.count.tsv.gz
subcellular_rnaseq_mesoderm_loc.tpm.tsv.gz
subcellular_rnaseq_combined_assembly_loc.count.tsv.gz
subcellular_rnaseq_combined_assembly_loc.tpm.tsv.gz

data_processing:
RSEM and STAR was used to align reads to the custon long-read transcripts and generate TPM/CPM or count tables.
Assembly: hg38
Supplementary files format and content: TSV files containing transcript counts or TPMs are provided. Each TSV is assmebled against the cell type-specific GTF, or against the combined_assembly of all transcripts in all four cell types. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have an accession number. Within each table all subcellular localisation values are contained. Nei=Nucleus; Np=Nucleoplasm; ch=chromatin; cp=cytoplasm

source_name: cell line

growth_protocol: H1 human pluripotent stem cell lines were maintained on a Matrigel treatment plate, cultured in mTeSR1 (STEMCELL TECHNOLOGIES, 85850) medium and digested with Accutase (Sigma, A6964) every 5-7 days. In vitro germ layers were generated by changing the medium and adding inhibitors or cytokines when human PSC reached 60-70% confluency as previously reported1. For endoderm differentiation, cells were cultured in RPMI supplemented with 2X GlutaMax (Thermo Fisher, 35050061), 0.2x MEM Non-Essential Amino Acids Solution (Thermo Fisher,11140050), 55 µM b-mercaptoethanol (BBI, A600194), 0.5% FBS (BIOWEST, S1580), 50nM/ml WNT3A (MedChemExpress, HY-P70453A), and 100ng/ml Activin A (PEPROTECH, 120-14E-100). For mesoderm differentiation, at the first 24 hour, Activin A was introduced to the culture medium. The cells were cultured in DMEM/F12 supplemented with 2X GlutaMax, 0.2X MEM Non-Essential Amino Acids Solution, 55µM b-mercaptoethanol, 0.5% FBS, 100ng/ml VEGF (PEPROTECH,100-20-50), 100ng/ml BMP4 (PEPROTECH, 120-05ET), 10 ng/ml bFGF (PEPROTECH, 100-18B-100), and 100ng/ml Activin A. Then Activin A was removed from the culture. For ectoderm differentiation from the PSC, the cells were cultured in DMEM/F12 supplemented with 0.2X MEM Non-Essential Amino Acids Solution, and 55 µM b-mercaptoethanol 15% KOSR (Life Technologies) 2µM A83-01(Tocris, 2939), 2µM PNU-74654(Tocris, 113906), and 2uM Dorsomorphin (Tocris, 3093). Media was changed daily and the cells were collected after 5 days

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol. Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). Short-read RNA sequencing was performed on Illumina Novaseq 6000 platform.
Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530).

treatment_protocol: RNA extraction from subcellular structures were performed according to the reported pipelines41. The plated cells were digested and washed once with ice-cold PBS. Cytoplasmic fractions were isolated by incubating the cells in ice-cold cytoplasmic lysis buffer containing 10 mM Tris-HCl pH 7.5, 0.05% NP-40, 150 mM NaCl, 25 μM α-amanitin (Sigma, A2263), 40 U/ml SUPERase.IN (Thermo Fisher, AM2694) and 1× complete protease inhibitor mix (Sigma, 11697498001). Cell lysate was carefully layered on top of a new 1.5 ml tube containing 500 μl of sucrose buffer (10 mM Tris-HCl pH 7.0,150 mM NaCl 25% (wt/vol) sucrose, 25 μM α-amanitin, 20 U SUPERase.IN, and 1x Protease inhibitor mix). The sample was centrifuged for 10 min at 2000 rpm in 4°C. The cytoplasmic fraction was collected in the supernatant, transfered to a new 1.5 ml tube and put on ice. The nuclear pellet was washed with 500 μl of ice-cold PBS. Nuclear RNA fraction was extracted from a portion of the RNA pellet.  The nuclear pellet was resuspended in 100 μl of nuclear resuspension buffer (20 mM Tris-HCl (pH 8.0), 75 mM NaCl, 0.5 mM EDTA, 50% (vol/vol) glycerol, 0.85 mM DTT, 25 μM α-amanitin, 10 U SUPERase.IN, and 1x Protease inhibitor mix). Next, 100 μl of nuclear lysis buffer (1% (vol/vol) NP-40, 20 mM HEPES (pH 7.5), 300 mM NaCl, 1M urea 0.2 mM EDTA, 1mM DTT 25 μM α-amanitin,10 U SUPERase.IN, and 1x Protease inhibitor mix) was introduced, and vortexed for 5 s. After 3 min of ice incubation, the sample was centrifuged at 18,500 rpm at 4°C for 2 min. Nucleoplasmic fraction was collected in a new 1.5-ml tube as the supernatant. The chromatin-associated fraction was collected as the pellet on ice-cold PBS. RNA extraction for nucleus- and chromatin-associated fraction was carried out by adding 100 ul PBS to resuspend the pellet. RNA was isolated by adding 500 ul RNAzol RT (MRC, RN190), according to manufacturer’s protocol. RNA suspended in supernatant fraction (including cytoplasmic and nucleoplasmic fraction) was extracted by the TRIZOL-PLS region. In short, 3.5x sample volumes RLT buffer introduced and mixed. The initial sample was added to 2.5x of the ice-cold absolute ethanol. The sample was mixed before centrifuging at 16,000 g at 4°C for 15 min. The ethanol was removed, resuspended and washed twice with 75% ethanol. The dry pellet was dissolved with RNase/DNase-free water. The success of the sub-cellular RNA extraction was confirmed by using Western blotting for the genes known to be preferentially localized to specific sub-cellular structure.

value: cell line

value: Mesoderm

tag: cell compartment

value: nucleus


title: CM_8h_r1

description:
Library name: CM_8h_r1
Replicate 1

value: Mantle Cell Lymphoma


title: WRC25, leaf, control, Day 5, rep 3

description: Library name: C109

value: control


title: Mesoderm Nucleus Repeat 2


title: WT.Vas.1

description: Library name: sample4

value: Vascular enrichment


title: CM_2h_r2

description:
Library name: CM_2h_r2
Replicate 2

value: dTAG-47 2hr


title: WRC47, leaf, control, Day 5, rep 3

description: Library name: C108

value: leaf


title: CM_2h_r1

description:
Library name: CM_2h_r1
Replicate 1


title: 5xFAD.Vas.1

description: Library name: sample3


title: Mesoderm Nucleoplasm Repeat 1

value: nucleoplasm


title: WRC33, leaf, control, Day 5, rep 3

description: Library name: C107


title: Mesoderm Nucleus Repeat 1


title: CM_0h_r2

description:
Library name: CM_0h_r2
Replicate 2


title: WT.All.1

description: Library name: sample2


title: WRC23, leaf, control, Day 5, rep 3

description: Library name: C106


title: CM_0h_r1

description:
Library name: CM_0h_r1
Replicate 1


title: Mesoderm Cytoplasm Repeat 1

value: cytoplasm


title: 5xFAD.All.1

description: Library name: sample1


title: fCLIP antiGIGYF2 rep1


title: WRC27, leaf, control, Day 5, rep 3

description: Library name: C105


title: Dro1-NIL, leaf, control, Day 5, rep 3

description: Library name: C104


title: WRC13, leaf, control, Day 5, rep 3

description: Library name: C103


title: Mesoderm Chromatin Repeat 3

value: chromatin


title: WRC09, leaf, control, Day 5, rep 3

description: Library name: C102


title: EmxDot E16.5 WT 469.1

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

description: Library name: EmxDot16WT1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger v7.0.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain hemispheres

extract_protocol:
The dorsal telencephalon was extracted from the embryos and the cells were dissociated using the Worthington papain dissociation system and resuspended in PBS.
The library was performed according to the manufacturer's instructions (single cell 3' v3.1 dual index protocol, 10x Genomics). Briefly, the dissociated brain cells resuspended in PBS were added to the master mix and loaded, together with gene expression beads and partitioning oil, into the chip and to generate the gel-bead emulsion using the Chromium machine. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, a unique molecular identifier (UMI), and 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the fragments with the appropriate sizeswere selected using SPRIselect beads for subsequent library construction. During the library construction Illumina R2 sequence, paired-end constructs with P5 and P7 sequence, and a sample (dual) index were added.

value: Brain hemispheres


title: Mesoderm Chromatin Repeat 2


title: BMC, 24 h, 5

city: Copenhagen

last: Anagho-Mattanovich

address: Blegdamsvej 3B

department: SUND

country: Denmark

institute: University of Copenhagen

description:
Library name: S17
Column name in salmon.merged.gene_counts.tsv: X17_S17

data_processing:
The data was aligned with the nf-core RNAseq workflow version 3.8.1 (Ewels, P.A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M.U., Di Tommaso, P., and Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276–278. https://doi.org/10.1038/s41587-020-0439-x.). Read counts were further processed using edgeR (Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140. https://doi.org/10.1093/bioinformatics/btp616.) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47. https://doi.org/10.1093/nar/gkv007.) and visualized with Glimma (Su, S., Law, C.W., Ah-Cann, C., Asselin-Labat, M.-L., Blewitt, M.E., and Ritchie, M.E. (2017). Glimma: interactive graphics for gene expression analysis. Bioinformatics 33, 2050–2052. https://doi.org/10.1093/bioinformatics/btx094.), following Law et al (Law, C.W., Alhamdoosh, M., Su, S., Dong, X., Tian, L., Smyth, G.K., and Ritchie, M.E. (2016). RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res. 5. https://doi.org/10.12688/f1000research.9005.3.).
Assembly: Mouse mm10
Supplementary files format and content: Tab-delimited file including raw counts for each sample

growth_protocol: Immortalized murine brown preadipocytes were grown in 6-well plates with DMEM media (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10 % FBS and 1 % penicillin-streptomycin (Thermo Fisher Scientific) at 37 °C and 5 % CO2 in a humidified incubator. For differentiation, cells were grown until confluence (day 0) and subsequently treated with differentiation media. On day 0, fresh growth media supplemented with an induction cocktail of 20 nM insulin (Sigma-Aldrich, St Louis, MO, USA), 1 nM triiodothyronine (Sigma-Aldrich), 1 µM dexamethasone (Sigma-Aldrich), 0.125 mM indomethacin (Sigma-Aldrich) and 0.5 mM isobutylmethylxanthine (Sigma-Aldrich). After 2 days of cultivation (day 2), the media was changed to growth media supplemented with 20 nM insulin and 1 nM triiodothyronine. The media was changed every 2 days (day 4 and day 6). All experiments were performed on day 7.

extract_protocol:
For proteomics and transcriptomics, samples were harvested by removing the media, washing each well with 1 mL PBS, lifting the cells off the plates using cell lifters, resuspending them in 500 µL PBS, centrifuging them at 300 g and removing the supernatant so that only the cell pellet remains. The pellets were split in two and frozen at -80 °C until further processing. Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit according to the manufacturer’s protocol.
Libraries were prepared using Universal Plus Total RNAseq with NuQuant kit (Tecan, Männedorf, Switzerland) as recommended by the manufacturer. In brief, 250 ng total RNA was fragmented followed by cDNA synthesis. Adaptors were ligated and after stand selection, the cDNA was depleted from rRNA using AnyDeplete probes (Tecan). Following the final bead clean-up, libraries were quantified with NuQuant, quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were stimulated with 1 µM L-(−)-norepinephrine (+)-bitartrate salt monohydrate (Sigma-Aldrich) and samples were taken at the specified sampling time points.

value: BMC

value: differentiated brown adipocytes

tag: time

value: 24 h induced

tag: batch


title: BMC, 24 h, 6

description:
Library name: S18
Column name in salmon.merged.gene_counts.tsv: X18_S18

tag: tissue


title: WRC28, leaf, control, Day 5, rep 3

description: Library name: C101

source_name: leaf


title: Mesoderm Chromatin Repeat 1


title: Mesoderm Cytoplasm Repeat 3


title: BMC, 24 h, 4

description:
Library name: S16
Column name in salmon.merged.gene_counts.tsv: X16_S16


title: hPSCs Nucleus Repeat 3

description:
subcellular_rnaseq_hPSC_loc.count.tsv.gz
subcellular_rnaseq_hPSC_loc.tpm.tsv.gz
subcellular_rnaseq_combined_assembly_loc.count.tsv.gz
subcellular_rnaseq_combined_assembly_loc.tpm.tsv.gz

value: hPSCs


title: BMC, 24 h, 3

description:
Library name: S15
Column name in salmon.merged.gene_counts.tsv: X15_S15


title: hPSCs Nucleus Repeat 2


title: WRC05, leaf, control, Day 5, rep 3

description: Library name: C98


title: WRC02, leaf, control, Day 5, rep 3

description: Library name: C97


title: hPSCs Nucleus Repeat 1


title: EmxDot E16.5 WT 469.6

description: Library name: EmxDot16WT6

value: WT


title: BMC, 24 h, 1

description:
Library name: S13
Column name in salmon.merged.gene_counts.tsv: X13_S13

value: cell line


title: WRC24, leaf, control, Day 5, rep 3

description: Library name: C99


title: hPSCs Nucleoplasm Repeat 3


title: BMC, 24 h, 2

description:
Library name: S14
Column name in salmon.merged.gene_counts.tsv: X14_S14


title: Mesoderm Cytoplasm Repeat 2

value: Mesoderm


title: BMC, 4 h, 6

description:
Library name: S12
Column name in salmon.merged.gene_counts.tsv: X12_S12

value: 4 h

value: 4 h induced


title: WRC19, leaf, control, Day 5, rep 3

description: Library name: C96

value: control


title: BMC, 4 h, 5

description:
Library name: S11
Column name in salmon.merged.gene_counts.tsv: X11_S11


title: WRC06, leaf, control, Day 5, rep 3

description: Library name: C95


title: hPSCs Nucleoplasm Repeat 1


title: BMC, 4 h, 4

description:
Library name: S10
Column name in salmon.merged.gene_counts.tsv: X10_S10


title: WRC03, leaf, control, Day 5, rep 3

description: Library name: C100


title: BMC, 4 h, 3

description:
Library name: S9
Column name in salmon.merged.gene_counts.tsv: X9_S9


title: WRC51, leaf, control, Day 5, rep 3

description: Library name: C94


title: hPSCs Cytoplasm Repeat 3


title: WRC36, leaf, control, Day 5, rep 3

description: Library name: C93


title: hPSCs Cytoplasm Repeat 2


title: BMC, 4 h, 2

description:
Library name: S8
Column name in salmon.merged.gene_counts.tsv: X8_S8


title: WRC48, leaf, control, Day 5, rep 3

description: Library name: C92


title: hPSCs Cytoplasm Repeat 1


title: BMC, 4 h, 1

description:
Library name: S7
Column name in salmon.merged.gene_counts.tsv: X7_S7


title: WRC37, leaf, control, Day 5, rep 3

description: Library name: C91


title: BMC, 0 h, 5

description:
Library name: S5
Column name in salmon.merged.gene_counts.tsv: X5_S5

value: 0 h

value: not induced


title: BMC, 0 h, 6

description:
Library name: S6
Column name in salmon.merged.gene_counts.tsv: X6_S6


title: WRC01, leaf, control, Day 5, rep 3

description: Library name: C90

value: leaf


title: hPSCs Chromatin Repeat 2


title: Endoderm Nucleus Repeat 2

description:
subcellular_rnaseq_endoderm_loc.count.tsv.gz
subcellular_rnaseq_endoderm_loc.tpm.tsv.gz
subcellular_rnaseq_combined_assembly_loc.count.tsv.gz
subcellular_rnaseq_combined_assembly_loc.tpm.tsv.gz

value: Endoderm

value: nucleus


title: hPSCs Chromatin Repeat 1

value: chromatin


title: WRC35, leaf, control, Day 5, rep 3

description: Library name: C87


title: BMC, 0 h, 4

description:
Library name: S4
Column name in salmon.merged.gene_counts.tsv: X4_S4


title: WRC15, leaf, control, Day 5, rep 3

description: Library name: C88


title: WRC18, leaf, control, Day 5, rep 3

description: Library name: C89


title: hPSCs Nucleoplasm Repeat 2

value: nucleoplasm


title: Endoderm Nucleus Repeat 3


title: BMC, 0 h, 2

description:
Library name: S2
Column name in salmon.merged.gene_counts.tsv: X2_S2

value: BMC


title: BMC, 0 h, 1

description:
Library name: S1
Column name in salmon.merged.gene_counts.tsv: X1_S1

value: differentiated brown adipocytes


title: WRC31, leaf, control, Day 5, rep 3

description: Library name: C85


title: WRC42, leaf, control, Day 5, rep 3

description: Library name: C86


title: Endoderm Nucleus Repeat 1


title: Endoderm Nucleoplasm Repeat 3


title: hPSCs Chromatin Repeat 3


title: BMC, 0 h, 3

description:
Library name: S3
Column name in salmon.merged.gene_counts.tsv: X3_S3


title: WRC34, leaf, control, Day 5, rep 3

description: Library name: C84


title: Endoderm Nucleoplasm Repeat 2


title: Endoderm Nucleoplasm Repeat 1


title: PBS 72h -1

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

description: Library name: Sample 31

data_processing:
Paired-end raw reads (there are some samples with two sets of paired-end raw reads due to insufficient reads output in first attempt) were uploaded onto Genialis Expressions web-based application for RNA sequencing analysis (Genialis, Inc., Boston, MA). We used their “General RNA-seq pipeline (featureCounts)” pipeline to analyze our raw data with their default settings. Description for this pipeline is adopted from their website as follow: “First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming. Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool. FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool. RNA-SeQC is initiated only when ENSEMBL annotation is selected.” Trimmed reads were aligned to Mus musculus GRCm39 transcriptome (Ensembl release 109) with STAR aligner. We would like to note that we performed data analysis around July 2023 to January 2024; Genialis Expressions application version might have changed a little bit since then according to vendor’s routine maintenance. We downloaded output data of featureCounts, PCA, and DESeq2 to generate figures and downstream analysis.
Assembly: Mus musculus GRCm39 Ensembl release 109
Supplementary files format and content: txt files of raw counts for each sample (featureCounts data output)

source_name: mouse bone marrow-derived macrophages (BMDMs)

growth_protocol: BMDMs were cultured from the femurs and tibias of mice in DMEM medium (DMEM, 10% fetal bovine serum, 10 ng/ml of M-CSF) and incubated at 37°C in 5% CO2 for 7 days, with the addition of new medium containing M-CSF every 2-3 days

extract_protocol:
Total RNA was isolated from the infected BMDMs using EZ-10 DNAaway RNA Mini-Preps Kit (Bio Basic, Canada). TapeStation (Agilent Technologies 4200) was used to analyze RNA integrity of the preparation, and RNA quantification was done using Nanodrop (Thermo Scientific, USA).
After the QC procedures, 4 ug of total RNA with >9 RIN (RNA Integrity Number) was used for RNA-Seq library preparation. PolyA RNA was enriched using oligo (dT) beads. PolyA RNA was then fragmented by heating to 94°C for 6 min. The first-strand cDNA was synthesized by SuperScript III reverse transcription kit (Invitrogen) using random hexamers, in the presence of RNasin Plus RNase Inhibitor, Actinomycin D, and DTT. Second-strand cDNA was synthesized with dUTP for strand-specific RNA sequencing, with DNA polymerase I (Enzymatics) in the presence of RNase H. Library preparation continued with end repairing, dA tailing for adapter ligation, and library purification with SparQ PureMag beads. Purified double-stranded cDNA libraries were lastly PCR-enriched and final purification. Quality control of the library consists of three steps: Quibit 2.0 (in-house) and q-PCR (at Novogene Inc.) for library quantification, and using Agilent 2100 (in-house & at Novogene Inc.) for library integrity and purity check. At Novogene Inc (Sacramento, CA), qualified libraries were fed into Illumina sequencers (NovaSeq 6000) for polyA RNA sequencing after pooling according to their effective concentration and expected data volume. Some libraries got sequenced twice due to insufficient data output in the first trial.

treatment_protocol: Mouse BMDMs (1 x10^6 cells/well) in each well of a 6-well culture plate were infected  with Mtb wild-type H37Rv and all mycobacterial vaccine strains  at an MOI of 1:5 or uninfected (control cells) and incubated for 4 h at 37°C in a CO2 incubator. After the incubation, the cells were washed with D-PBS to remove the extracellular bacteria and replaced with fresh DMEM containing 10% fetal bovine serum for further incubation at 24 and 72 h.

value: PBS control for 72h


title: BCG 72h -2

description: Library name: Sample 30

value: mouse bone marrow-derived macrophages (BMDMs)

value: Infected with BCG TB vaccine strain for 72h


title: WRC50, leaf, control, Day 5, rep 3

description: Library name: C82


title: Endoderm Cytoplasm Repeat 3

value: cell line

value: cytoplasm


title: BCG 72h -1

description: Library name: Sample 29


title: WRC22, leaf, control, Day 5, rep 3

description: Library name: C81


title: Endoderm Cytoplasm Repeat 1


title: Endoderm Cytoplasm Repeat 2


title: QKO 72h -2

description: Library name: Sample 28

value: Infected with QKO TB vaccine strain for 72h


title: WRC19, leaf, control, Day 5, rep 2

description: Library name: C79


title: TKO-Z 72h -2

description: Library name: Sample 26

value: Infected with TKO-Z TB vaccine strain for 72h


title: PBS 72h -2

description: Library name: Sample 32


title: WRC02, leaf, control, Day 5, rep 2

description: Library name: C78

value: control


title: QKO 72h -1

description: Library name: Sample 27


title: Endoderm Chromatin Repeat 2


title: TKO-Z 72h -1

description: Library name: Sample 25


title: Endoderm Chromatin Repeat 1


title: TKO-D 72h -2

description: Library name: Sample 24

value: Infected with TKO-D TB vaccine strain for 72h


title: WRC46, leaf, control, Day 5, rep 2

description: Library name: C76


title: WRC55, leaf, control, Day 5, rep 3

description: Library name: C83


title: Ectoderm Nucleus Repeat 3

description:
subcellular_rnaseq_ectoderm_loc.count.tsv.gz
subcellular_rnaseq_ectoderm_loc.tpm.tsv.gz
subcellular_rnaseq_combined_assembly_loc.count.tsv.gz
subcellular_rnaseq_combined_assembly_loc.tpm.tsv.gz

value: Ectoderm


title: TKO-D 72h -1

description: Library name: Sample 23


title: WRC48, leaf, control, Day 5, rep 2

description: Library name: C75

value: leaf


title: Ectoderm Nucleus Repeat 2


title: DKO 72h -2

description: Library name: Sample 22

value: Infected with DKO TB vaccine strain for 72h


title: WRC16, leaf, control, Day 5, rep 2

description: Library name: C80


title: Ectoderm Nucleus Repeat 1

value: nucleus


title: WRC35, leaf, control, Day 5, rep 2

description: Library name: C74


title: WRC50, leaf, control, Day 5, rep 2

description: Library name: C77


title: Ectoderm Nucleoplasm Repeat 3


title: Endoderm Chromatin Repeat 3

value: Endoderm

value: chromatin


title: SKO 72h -1

description: Library name: Sample 19

value: Infected with SKO TB vaccine strain for 72h


title: SKO 72h -2

description: Library name: Sample 20


title: Dro1-NIL, leaf, control, Day 5, rep 2

description: Library name: C70


title: WRC09, leaf, control, Day 5, rep 2

description: Library name: C69


title: H37Rv 72h -2

description: Library name: Sample 18

value: Infected with H37Rv TB vaccine strain for 72h


title: Ectoderm Nucleoplasm Repeat 1

value: nucleoplasm


title: H37Rv 72h -1

description: Library name: Sample 17

value: mouse bone marrow-derived macrophages (BMDMs)


title: WRC04, leaf, control, Day 5, rep 2

description: Library name: C71


title: DKO 72h -1

description: Library name: Sample 21


title: Ectoderm Cytoplasm Repeat 2


title: Ectoderm Cytoplasm Repeat 3


title: PBS 24h -2

description: Library name: Sample 16

value: PBS control for 24h


title: WRC44, leaf, control, Day 5, rep 2

description: Library name: C68


title: Ectoderm Cytoplasm Repeat 1

value: cell line


title: PBS 24h -1

description: Library name: Sample 15


title: WRC34, leaf, control, Day 5, rep 2

description: Library name: C67


title: BCG 24h  -2

description: Library name: Sample 14

value: Infected with BCG TB vaccine strain for 24h


title: Ectoderm Chromatin Repeat 3


title: WRC42, leaf, control, Day 5, rep 2

description: Library name: C66


title: WRC13, leaf, control, Day 5, rep 2

description: Library name: C72


title: Ectoderm Chromatin Repeat 2


title: Ectoderm Nucleoplasm Repeat 2


title: BCG 24h  -1

description: Library name: Sample 13


title: QKO 24h -2

description: Library name: Sample 12

value: Infected with QKO TB vaccine strain for 24h


title: WRC32, leaf, control, Day 5, rep 2

description: Library name: C65


title: Ectoderm Chromatin Repeat 1


title: Bulk RNA-seq Mesoderm Repeat 2

description:
bulk_shortread_rnaseq_mesoderm_bulk_SR.count.tsv.gz
bulk_shortread_rnaseq_mesoderm_bulk_SR.cpm.tsv.gz
bulk_shortread_rnaseq_combined_assembly.count.tsv.gz
bulk_shortread_rnaseq_combined_assembly.cpm.tsv.gz

data_processing:
The short read sequences were first filtered with fastp37. The filtered SR sequences were then used for quantification using STAR and RSEM.
For short read quantification, RSEM STAR references were made using the assembled transcripts.
Assembly: hg38
Supplementary files format and content: TSV files containing transcript counts or TPMs are provided. Each TSV is assmebled against the cell type-specific GTF, or against the combined_assembly of all transcripts in all four cell types. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have ant accession number.

treatment_protocol: No special treatment

value: Mesoderm


title: WRC01, leaf, control, Day 5, rep 2

description: Library name: C64

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

value: control


title: QKO 24h -1

description: Library name: Sample 11


title: WRC33, leaf, control, Day 5, rep 2

description: Library name: C63


title: Bulk RNA-seq Mesoderm Repeat 1


title: KP, leaf, control, Day 5, rep 2

description: Library name: C62

value: KP


title: WRC24, leaf, control, Day 5, rep 2

description: Library name: C61


title: TKO-Z 24h -2

description: Library name: Sample 10

value: Infected with TKO-Z TB vaccine strain for 24h


title: TKO-Z 24h -1

description: Library name: Sample 9


title: TKO-D 24h -2

description: Library name: Sample 8

value: Infected with TKO-D TB vaccine strain for 24h


title: Bulk RNA-seq hPSC Repeat 3

description:
bulk_shortread_rnaseq_hPSC_bulk_SR.count.tsv.gz
bulk_shortread_rnaseq_hPSC_bulk_SR.cpm.tsv.gz
bulk_shortread_rnaseq_combined_assembly.count.tsv.gz
bulk_shortread_rnaseq_combined_assembly.cpm.tsv.gz

value: hPSCs


title: WRC37, leaf, control, Day 5, rep 2

description: Library name: C60

value: leaf


title: DKO 24h -2

description: Library name: Sample 6

value: Infected with DKO TB vaccine strain for 24h


title: WRC05, leaf, control, Day 5, rep 2

description: Library name: C59


title: WRC47, leaf, control, Day 5, rep 2

description: Library name: C73


title: WRC18, leaf, control, Day 5, rep 2

description: Library name: C58


title: Bulk RNA-seq Endoderm Repeat 2

description:
bulk_shortread_rnaseq_endoderm_bulk_SR.count.tsv.gz
bulk_shortread_rnaseq_endoderm_bulk_SR.cpm.tsv.gz
bulk_shortread_rnaseq_combined_assembly.count.tsv.gz
bulk_shortread_rnaseq_combined_assembly.cpm.tsv.gz

value: Endoderm


title: DKO 24h -1

description: Library name: Sample 5


title: WRC55, leaf, control, Day 5, rep 2

description: Library name: C57


title: Bulk RNA-seq Ectoderm Repeat 2

description:
bulk_shortread_rnaseq_ectoderm_bulk_SR.count.tsv.gz
bulk_shortread_rnaseq_ectoderm_bulk_SR.cpm.tsv.gz
bulk_shortread_rnaseq_combined_assembly.count.tsv.gz
bulk_shortread_rnaseq_combined_assembly.cpm.tsv.gz

value: Ectoderm


title: WRC28, leaf, control, Day 5, rep 2

description: Library name: C56


title: SKO 24h -2

description: Library name: Sample 4

value: Infected with SKO TB vaccine strain for 24h


title: Bulk RNA-seq Endoderm Repeat 1


title: Bulk RNA-seq Ectoderm Repeat 1


title: Bulk RNA-seq hPSC Repeat 2


title: WRC31, leaf, control, Day 5, rep 2

description: Library name: C55


title: H37Rv 24h -2

description: Library name: Sample 2

value: Infected with H37Rv TB vaccine strain for 24h


title: WRC100, leaf, control, Day 5, rep 2

description: Library name: C54


title: Bulk RNA-seq hPSC Repeat 1


title: Mesoderm Half-life 8h Repeat 3

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_8h.rp3.p1

data_processing:
RSEM and STAR was used to align reads to the custon long-read transcripts assembled from the long-read RNA-seq data
Assembly: hg38
Supplementary files format and content: TSV files containing transcript counts or TPMs are provided. Each TSV is assmebled against the cell type-specific GTF, or against the combined_assembly of all transcripts in all four cell types. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have ant accession number. Each table contains 0, 1 and 8 hour treated cells with Actinomycin D

treatment_protocol: Human PSC and differentiated three germ cells were cultured in 6-well plates. Then Actinomycin B was added to inhibit the synthesis of new RNA. RNA was extracted at 0, 1, and 8 hours after the addition of Actinomycin B. Short-read sequencing was then done for RNA extracted at the time points after transcription stoppage. For each time point, short-read transcript quantification was first done using RSEM and STAR as highlighted above. Relative stability was then computed using the average expression of each transcript as the specified time, relative to the expression at time 0 hour after actinomycin treatment. For transcript x with the average TPM expressions x0 at time 0hr and xT at time T hour, relative stability is given as;    Relative stability=(log2(xT+0.01))/(log2(x0+0.01))


title: Bulk RNA-seq Endoderm Repeat 3


title: Mesoderm Half-life 8h Repeat 2

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_8h.rp2.p1


title: TKO-D 24h -1

description: Library name: Sample 7

value: mouse bone marrow-derived macrophages (BMDMs)


title: WRC21, leaf, control, Day 5, rep 2

description: Library name: C53


title: DRG, WT vehicle treated, sample 6

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

description: Library name: WV_6

data_processing:
Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/
mapped reads of each sample were assembled using StringTie
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts
Assembly: GRCm38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes FPKM values for each sample

source_name: L3-L5 dorsal root ganglia

extract_protocol:
RNA was extracted by Trizol and Qiagen RNeasy Micro kit.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: L3-L5 dorsal root ganglia

value: WT

value: vehicle


title: Mesoderm Half-life 8h Repeat 1

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_8h.rp1.p1

value: cell line


title: WRC51, leaf, control, Day 5, rep 2

description: Library name: C52

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.


title: DRG, WT vehicle treated, sample 5

description: Library name: WV_5


title: Mesoderm Half-life 1h Repeat 3

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_1h.rp3.p1

value: Mesoderm


title: SKO 24h -1

description: Library name: Sample 3


title: WRC22, leaf, control, Day 5, rep 2

description: Library name: C51

value: control


title: Mesoderm Half-life 1h Repeat 2

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_1h.rp2.p1


title: WRC57, leaf, control, Day 5, rep 2

description: Library name: C50


title: DRG, WT vehicle treated, sample 4

description: Library name: WV_4


title: DRG, WT vehicle treated, sample 3

description: Library name: WV_3


title: DRG, WT vehicle treated, sample 2

description: Library name: WV_2


title: Koshihikari, leaf, control, Day 5, rep 2

description: Library name: C49

value: Koshihikari


title: Mesoderm Half-life 0h Repeat 3

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_0h.rp3.p1


title: MCF7 H2B-E76Q replicate2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: MCF7_H2B-Q_rep2_S38_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

growth_protocol: MCF-7 human epithelia cells from breast adenocarsinoma cells from American Type Cell Culture (ATCC) were maintained in MEM supplemented with 5% calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin. MCF-7 cells were maintained in phenol red-free MEM supplimented with 5% charcoal-dextrantreated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin for at least 3 days prior to experimentation.

extract_protocol:
MCF-7 cells were seeded at at density of 0.5x10^6 cells per well in a 6-well plate and treated as described above. Total RNA was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol.
RNA-seq libraries were generated as previously described with the following modifications [24]. Total RNA from MCF-7 cells treated as indicated was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol. Total RNA was then enriched for mRNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002). Further fragmentation, first-strand cDNA synthesis, and subsequent procedures have been done as described [25].The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Illumina TruSeq RNA Prep kit, multiplexed, and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded at a density of 0.5 x 10^6 cells per well in a 6-well dish one day prior to experimentation. At least biological replicates were used for each experimental condition. For E2 continuous treatment, 100 nM E2 was applied to the cells for the indicated times prior to collection. For E2 washout treatments, cells were treated with 100 nM of E2 for 40 mins., washed onced in stripped medium, then inclubated in stripped medium for the remainder of the experiment.

value: Epithelia cells from breast adenocarsinoma cells

value: Cells ectipically express H2B-E76Q mutant


title: DRG, WT vehicle treated, sample 1

description: Library name: WV_1


title: H37Rv 24h -1

description: Library name: Sample 1


title: MCF7 H2B-E76Q replicate1

description:
Library name: MCF7_H2B-Q_rep1_S35_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: Mesoderm Half-life 0h Repeat 2

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_0h.rp2.p1


title: DRG, WT NGF treated, sample 6

description: Library name: WN_6

value: NGF


title: WRC25, leaf, control, Day 5, rep 2

address: 3-1-3 Kan-nondai

institute: National Agriculture and Food Research Organization

description: Library name: C46

value: leaf


title: MCF7 H2Bwt replicate2

description:
Library name: MCF7_H2Bwt_rep2_S36_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: Cells ectipically express wild-type H2B


title: Mesoderm Half-life 0h Repeat 1

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_0h.rp1.p1


title: hPSC Half-life 8h Repeat 1

description:
hPSCs treated with actinomycin D
half_life_hPSC_0_1_8.count.tsv.gz
half_life_hPSC_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_hpsc_8h.rp1

value: hPSCs


title: MCF7 H2Bwt replicate1

description:
Library name: MCF7_H2Bwt_rep1_S33_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: DRG, WT NGF treated, sample 5

description: Library name: WN_5


title: WRC06, leaf, control, Day 5, rep 2

description: Library name: C45


title: DRG, WT NGF treated, sample 4

description: Library name: WN_4


title: Mesoderm Half-life 1h Repeat 1

description:
hPSCs differnetiated to mesoderm and treated with actinomycin D
half_life_mesoderm_0_1_8.count.tsv.gz
half_life_mesoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_mesoderm_1h.rp1.p1


title: MCF7 H3-E105K replicate2

description:
Library name: MCF7_H3-105K_rep2_S31_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: Cells ectipically express H3-E105K mutant


title: DRG, WT NGF treated, sample 3

description: Library name: WN_3


title: IR64, leaf, control, Day 5, rep 2

description: Library name: C48


title: WRC36, leaf, control, Day 5, rep 2

description: Library name: C43


title: WRC27, leaf, control, Day 5, rep 2

description: Library name: C42


title: MCF7 H3-E105K replicate1

description:
Library name: MCF7_H3-105K_rep1_S28_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: DRG, WT NGF treated, sample 2

description: Library name: WN_2


title: WRC03, leaf, control, Day 5, rep 2

description: Library name: C44


title: hPSC Half-life 0h Repeat 1

description:
hPSCs treated with actinomycin D
half_life_hPSC_0_1_8.count.tsv.gz
half_life_hPSC_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_hpsc_0h.rp1


title: WRC15, leaf, control, Day 5, rep 2

description: Library name: C47


title: MCF7 H3-E97K replicate2

description:
Library name: MCF7_H3-97K_rep2_S32_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: Cells ectipically express H3-E97K mutant


title: WRC23, leaf, control, Day 5, rep 2

description: Library name: C41


title: DRG, WT NGF treated, sample 1

description: Library name: WN_1


title: MCF7 H3-E97K replicate1

description:
Library name: MCF7_H3-97K_rep1_S29_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: Endoderm Half-life 8h Repeat 1

description:
hPSCs differnetiated to endoderm and treated with actinomycin D
half_life_endoderm_0_1_8.count.tsv.gz
half_life_endoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_endoderm_8h.rp1

value: Endoderm


title: WRC04, leaf, control, Day 5, rep 1

description: Library name: C40


title: Treg, CTRL, Foxp3CreERT2, WT5

city: San Francisco

first: Victoire

last: Gouirand

state: CALIFORNIA

address: 513 Parnassus av

department: Dermatology

institute: UCSF

data_processing:
Read alignment done with kallisto (v. 0.46.2) using Ensembl reference genome GRCm39 (110)
Assembly: GRCm39
Supplementary files format and content: Abundance tsv files for individual samples

source_name: Skin

extract_protocol:
Treg cells were isolated respectively by gating on live CD45+CD3+CD4+CD8-CD25hiCD62LhiGFP+  cells. Cells were sorted into lysis buffer from the kit and frozen on dry ice before being processed using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) according to the manufacture’s protocol.
100pg of amplified cDNA obtained was used to generate a library using Nextera XT DNA prep-aration kit (Illumina).

value: Skin

value: Treg

value: Imiquimod


title: Endoderm Half-life 1h Repeat 1

description:
hPSCs differnetiated to endoderm and treated with actinomycin D
half_life_endoderm_0_1_8.count.tsv.gz
half_life_endoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_endoderm_1h.rp1


title: MCF7 H3wt replicate2

description:
Library name: MCF7_H3wt_rep2_S30_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO

value: Cells ectipically express wild-type H3


title: WRC28, leaf, control, Day 5, rep 1

city: Tsukuba

last: Kawakatsu

description: Library name: C39


title: Endoderm Half-life 0h Repeat 2

description:
hPSCs differnetiated to endoderm and treated with actinomycin D
half_life_endoderm_0_1_8.count.tsv.gz
half_life_endoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_endoderm_0h.rp2

value: cell line


title: Treg, CTRL, Foxp3CreERT2, WT3


title: WRC02, leaf, control, Day 5, rep 1

description: Library name: C38


title: Endoderm Half-life 8h Repeat 2

description:
hPSCs differnetiated to endoderm and treated with actinomycin D
half_life_endoderm_0_1_8.count.tsv.gz
half_life_endoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_endoderm_8h.rp2


title: Endoderm Half-life 0h Repeat 1

description:
hPSCs differnetiated to endoderm and treated with actinomycin D
half_life_endoderm_0_1_8.count.tsv.gz
half_life_endoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_endoderm_0h.rp1


title: hPSC Half-life 1h Repeat 1

description:
hPSCs treated with actinomycin D
half_life_hPSC_0_1_8.count.tsv.gz
half_life_hPSC_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_hpsc_1h.rp1


title: Treg, CTRL, Foxp3CreERT2, WT2


title: WAT_RD_2WK_M_7

city: Barcelona

first: Vicent

last: Ribas

state: Choose a State or Province

address: Rosselló 149, 5th floor, Centre Esther Koplowitz

department: Pathogenesis and prevention of diabetes

country: Spain

institute: IDIBAPS

data_processing:
Reads quality control performed using Fast!C software
Raw reads were then mapped to the reference genome (Mus_musculus_GRCm38) using the pseudo-aligner Kallisto.
Transcript counts were imported to R statistical software using the Tximport package, where data was filtered and normalized with EdgeR, and differentially expressed genes were obtained through the Deseq2 package.
Assembly: Mus_musculus_GRCm38
Supplementary files format and content: Raw counts in a tab-delimited text spreadheet, genes in rows and samples in columns.

source_name: White adipose tissue (visceral)

growth_protocol: Animals were fed from 8 weeks of age, either with regular chow or High-fat diet.

extract_protocol:
Tissues were homogenized in trizol, and purified by Rneasy columns. RNA was initially quantified with Nanodrop, and
Messenger RNA strand-specific RNA libraries were created from 200 ng of total RNA using the Illumina® Stranded mRNA Prep Ligation

treatment_protocol: Animals were fed at libitum with diets for 2 weeks or 12 weeks

value: White adipose tissue (visceral)

tag: diet

value: RD

tag: time on_diet

tag: Sex

value: M

tag: group number


title: Ectoderm Half-life 8h Repeat 2

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_8h.rp2

value: Ectoderm


title: Treg, CTRL, Foxp3CreERT2, WT4

tag: treatment


title: Koshihikari, leaf, control, Day 5, rep 1

first: Taiji

description: Library name: C36

tag: cultivar

value: Koshihikari

value: control

tag: days after_treatment


title: Treg, LAYN_flox, Foxp3CreERT2;Laynfl/fl, K05


title: WAT_RD_2WK_M_6


title: WRC24, leaf, control, Day 5, rep 1

description: Library name: C35

value: leaf

tag: replicate


title: Ectoderm Half-life 8h Repeat 1

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_8h.rp1

tag: cell line


title: Ectoderm Half-life 1h Repeat 2

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_1h.rp2

tag: cell type


title: WAT_HFD_2WK_M_14

value: HFD


title: Treg, CTRL, Foxp3CreERT2, WT1

tag: genotype


title: Treg, LAYN_flox, Foxp3CreERT2;Laynfl/fl, K04


title: WAT_HFD_2WK_M_13


title: WAT_HFD_2WK_M_12


title: WRC19, leaf, control, Day 5, rep 1

description: Library name: C34


title: Treg, LAYN_flox, Foxp3CreERT2;Laynfl/fl, K03