title: spike-in, 128A

status: Public on Jan 05 2024

city: Poznan

first: Zbigniew

last: Warkocki

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: spikein.txt

data_processing:
From 3'RACE-Seq raw reads, adapters were removed with cutadapt (v4.0) and sequences shorter than 20 nt were discarded. Low-quality nucleotides from 3’ end of reads were removed using ConDeTri (v2.3) with the following settings hq=37, ml=1, mh=5 and minlen=40.
Specific amplicons were selected based on a sequence of forward primers with bbduk from BBTools. For further analyses only reads containing a unique molecular identifier (UMI) in length 15 nt and delimiter (GTCAG) on 5’ end of read R2 were kept.
UMI and delimiter sequences were removed from read sequences and moved to the read name with the extract mode of UMI-tools (v1.1.2). As references for control transcripts (GAPDH, ACTB, PABPC4) were used gene sequences provided by the Ensembl database (GRCh38).
Reads were mapped to reference using STAR (v2.7.9a) with soft-clipping allowed (with the following settings outFilterMatchNmin 20, outFilterScoreMinOverLread 0.1 and outFilterMatchNminOverLread 0.1). Mapped reads were deduplicated with UMIcollapse.
For pair of reads in which both reads mapped non-templated tails and their nucleotide compositions were retrieved from the sam file from the soft-clipped fragments of read R2 using the previously published script (get_softclipped_reads_from_sam.pl) [Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022)]. For pair of reads in which only R1 mapped due to presence of long homopolymeric sequence in the read R2 length sequence of tails were extracted directly from the read R2.
Statistical analyses were performed in R (v4.2). In these analyses were included reads with no tails and those with the following composition: tails containing only A (A tails), only U (U tails), A with U on their 3’ (AU tails). In AU tails were allowed tails with U between A but not at the beginning of the tail. All operations on bam and sam files were performed with samtools (v1.13).
Assembly: Gene sequences of GAPDH, ACTB and PABPC4 from GRCh38 and LINE-1 sequence from the L1.3 nomarker L1 reporter plasmid
Supplementary files format and content: tails_X1KO.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_X1D2KO.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: spikein.txt; tab-delimited text file containing tails lengths of Spikes-IN
Library strategy: 3' RACE-seq to assess non-templated 3' ends

organism: synthetic construct

source_name: synthesized

growth_protocol: 293T cells were grown in DMEM (Gibco ref no. 41966052) supplemented with 9% FBS (Gibco ref no. 10270106), and penicillin/streptomycin at 1x concnetration (Merck ref. no. P4458) at 37C in an atmosphere supplemented to 5% CO2 in a humidified incubator

extract_protocol:
~42-48hrs post-transfection total RNA was extracted using home-made Trizol reagent (according to Chomczynski and Sacchi, 1987, 10.1016/0003-2697(87)90021-2), 1ml trizol was used per 1 well, following precipitation RNA was repurified following treatment with proteinase K at 20ng per microliter in a Tris-buffered 1% SDS solution with 2mM EDTA and 100mM NaCl, purified by phenol-chloroform extraction, then samples  were deprived of DNA by treatment with Tubro DNase (Ambion) and again purified by phenol-chloroform extraction
For the 12 home-made 293T cell lines (this paper) including the wild-type and the XRN1 KO each biological replicate was a single technical replicate (one index per cell line). For the 4 acquired cell lines (10.1021/acs.biochem.0c00069) three technical replicates (starting at the RT step) of each biological replicate were performed and marked with a different index. Synthetic spike-ins had defined index sequences see Supplementary Table 1. Libraries were prepared as described in (10.1016/j.cell.2018.07.022) with modifications. Briefly, 2µg total RNA after DNase treatment were ligated with 100pmole RA3_15N 5’ preadenylated adapter comprising a 15-nucleotide unique molecular identifier (UMI) in 20µl of 1x enzyme-supplied buffer, 15% PEG 8000 by T4 RNA ligase 2 truncated (NEB, M0242) for 18h at 18˚C. Nucleic acids of each reaction were purified using 20µl Ampure XP magnetic beads, eluted in and used for reverse transcription in 20µl with 100pmoles RPI primer (containing an 6-nucleotide index) using Superscript III (ThermoScientific) enzyme according to the manufacturer’s protocol (2mins at 50˚C, 30mins at 45˚C, 15mins at 85˚C), followed by purification on 1,25 volume of Ampure XP magnetic beads. Nested PCR was performed with PrimeSTAR GLX polymerase (TaKaRa, R050B) since it proofed best at elongating long poly(A) tracts (as compared to Phusion of ThermoScientific and Q5 polymerases of NEB; not shown). First round PCR were performed in 25µl with an equivalent of 500ng input total RNA (input to RT step) per reaction. Primers at 0,35µM were either of: 3UNP1f, GAPDH_3R0, PABPC4_3R0 for L1, GAPDH, and PABPC4 respectively, universal reverse primer, RP_uni, was added at 0,4µM. Reactions were carried out: 98˚C 2mins, [98˚C 12sec, 52˚C 15sec, 70˚C 40sec]x21, 68˚C 1min, 1/5 of each reaction was used without purification as template for second round PCR with 0,36µM transcript-specific forward primer: L1_NGS4, or GAPDH_NGS, or PABPC4_NGS, and 0,4µM universal reverse primer RP_uni. PCRs were carried out: 98˚C 2mins, [98˚C 12sec, 55˚C 15sec, 70˚C 30sec]x21, 70˚C 1min. The reactions were purified on 1,3 volume Ampure XP magnetic beads, eluted, measured and diluted to ~5ng/µl, and analysed on TapeStation (Agilent). Before running on Illumina Novaseq libraries were quantitated by qPCR to adjust the number of reads to ~3-5 MRds for each transcript for each biological/technical replicate (each index).

treatment_protocol: ~200,000 to 350,000 cells were transfected in wells of a 6-well plate with 1microgram of L1.3 nomarker L1 reporter plasmid using Lipofectamine 2000, 5microliters per well.

value: synthesized


title: spike-in, 8A

type: SRA

description: spikein.txt

library_source: genomic

molecule: genomic DNA

tag: tissue


title: Macrophage, CTR1

status: Public on Jan 06 2024

city: Jinan

first: Chang

last: Ma

state: Shandong

address: Wenhuaxi Road107#

country: China

institute: Shandong University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Macrophage

growth_protocol: Peritoneal macrophages were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (P/S) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Standard cell culture conditions are applied, with no additional treatments.

tag: cell type

value: Macrophage

tag: genotype

value: CTR


title: spike-in, 64A

description: spikein.txt


title: spike-in, 16A

description: spikein.txt


title: pHBEC_COPD-IV_LPS_rep3

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with LPS, biological replicate 3

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

label: biotin

organism: Homo sapiens

source_name: Human bronchial epithelial cells

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: As described in the paper. Briefly, isolated pHBECs seeded on CollagenIV-coated transwell inserts were cultured in PneumaCultTM - Ex Plus Media (STEMCELL Technologies, REF:05041) until 95% cell confluency before airlift (ALId0; basal medium PneumaCultTM with 100x PneumaCultTM - ALI Maintenance Supplement, STEMCELL Technologies, REF:05006). Basal medium was changed every second day; ALI apical side was washed 1/week (HBSS Ca2+/Mg2+, Gibco Life Technologies, REF:14065-049). Cellular frequencies in main stem bronchi were in line with previously reported data for multi-ciliated cells (47-49% [31–33]) and secretory cells (6-21% [32, 33]) on ALI cultures.

extract_protocol: Total RNA was isolated by RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: As described in the paper. Briefly, ALI-cultured pHBECs were exposed to aerosolized carbon nanoparticles (NP) CNPs (Printex 90; primary particle diameter: 14nm; Degussa, Germany), zinc oxide NPs (ZnO; JRC reference material NM110; primary particle diameter: 158nm) or LPS (Lipopolysaccharides from Escherichia coli O55:B5, Sigma-Aldrich, REF:2974730) using the ALICE CLOUD technology (VITROCELL® CLOUD 12, VITROCELL Systems, Waldkirch, Germany). The VITROCELL® CLOUD 12 system provides uniform aerosol deposition onto the cells in approx. 3-5min, taking advantage of effects related cloud dynamics. After nebulization of 200µl of a NP suspension, the cell deposited NP dose is measured by an integrated quartz crystal microbalance (QCM), which provides accurate NP dosimetry. NP exposure was performed at 37°C applying the following doses: Sham controls (saline solution 0.9%), CNP 10.8cm2/cm2, ZnO low dose 0.14cm2/cm2 at ALId30±2 after air-lift. NP suspensions of 5.1mg/ml (CNP) and 1.8mg/ml for ZnO low dose were prepared in 1:100 diluted saline (saline solution/ NaCl 0.009% in water) using a probe sonicator (Bachofer GmbH, Reutlingen, Germany; 30% output energy, 30s for CNP (37J/mL sonication energy) and 160s for ZnO (195J/mL)) obtaining NP agglomerates with 160nm and 260nm (volumetric median) diameter for CNP and ZnO NPs as confirmed by DLS (Dynamic Light Scattering; Zetasizer, Malvern Instruments, GBR). LPS was nebulized (200μl; 1mg/ml; 0.699µg/cm2) as an inflammation reference.

tag: disease state

value: COPD-IV

tag: treatment

value: LPS


title: spike-in, 0A

description: spikein.txt


title: pHBEC_COPD-IV_LPS_rep2

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with LPS, biological replicate 2


title: male_T1_female_dsWhite_piRNA_2

city: Ithaca

first: Yicheng

last: Luo

state: NY

address: 215 Tower Rd

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

data_processing:
Degradome-seq reads were trimmed by Trimmomatic (version 0.33) and cutadapt (version 1.15) and filter out those shorter than 50 bp after trimming
Ribosomal RNA removal by bowtie
The first 50bp of reads were mapped to dm6 genome and vectors sequence respectively, using STAR alignment
smRNA-seq reads were trimmed by Cutadapt to rRNA and filter out those shorter than 15 bp after trimming
Select reads size 21-22bp (siRNA) and 23-29bp (piRNA) and 21-30bp (small RNA)
mapped to dm6 genome and extracted regions 20A cluster(20A) and 42AB cluster(42A), mapped to vector maps, Ubi-GFP(UBIG), non-RMCE Ubi-GFP(originalUBIG), double-stranded GFP reporter(UBIGasG) (parameters: -v 0 -a -m 1 -t --best --strata), and plus, minus strand of genome regions and vectors were separate.
smRNA profilings were generated by Matlab after mapping
Assembly: dm3(ChIP-seq) and dm6(smRNA-seq)
Supplementary files format and content: bg4

organism: Drosophila melanogaster

source_name: adult fly ovaries total small RNA

growth_protocol: Fly stocks were maintained at 24C on standard diet

extract_protocol:
Total smRNA from ovary was isolated with Ribozol reagent and do size selection from 19nt to 30nt. Total smRNA from ovary was isolated with Ribozol reagent and do ribosomal RNA depeltion.
smRNA-seq libraries were made by using NEBNext® Small RNA Library Prep Set for Illumina®. Degradome-seq libraries were prepared by using protocol from Zamore lab. Libraries were sequenced on the Illumina HiSeq 2000 platform.
smRNA-seq follow NEBNext® Small RNA Library Prep Set for Illumina®

treatment_protocol: Flies were fed with yeast for 2-3 days prior to dissection

value: adult fly ovaries

tag: chipantibody

tag: reporter

value: T1 BX reporter

tag: molecule subtype

value: total small RNA


title: male_T1_female_TM3_piRNA_2


title: pHBEC_COPD-IV_LPS_rep1

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with LPS, biological replicate 1


title: male_T1_female_TM3_piRNA_1


title: male_BX2_female_TM3_piRNA_2


title: male_T1_female_DB_piRNA_2


title: male_T1_female_dsWhite_piRNA_1


title: male_T1_female_DB_piRNA_1


title: male_BX2_female_TM3_piRNA_1


title: spike-in, 32A

description: spikein.txt


title: male_BX2_female_dsWhite_piRNA_2


title: M20-X_FAgo2414_dsGFP_TM3_piRNA_1

value: 20A-X 20A cluster reporter


title: M20-X_FAgo2414_dsGFP_Ago2414_piRNA_2


title: M20-X_FAgo2414_dsGFP_Ago2414_piRNA_1


title: dsGFP_Piwi_IP_piRNA_1

value: 66A6 double-stranded GFP insertion


title: dsGFP_Piwi_IP_piRNA_2


title: male_BX2_female_dsWhite_piRNA_1


title: dsGFP_Piwi_Input_piRNA_2


title: F94dsGFP_M20A-X_piRNA_2


title: F94dsGFP_TM3_M20A-X_piRNA_2


title: F94dsGFP_TM3_M20A-X_piRNA_1


title: F94dsGFP_M20A-X_piRNA_1


title: dsGFP_Piwi_Input_piRNA_1


title: Fwt_M20A-X_TM3_piRNA_1


title: female_T1_male_DB_piRNA_2


title: 20A-X_Paternal_Tb_ssGFP_piRNA_2

value: 66A6 single reporter insertion


title: 20A-X_Paternal_Tb_ssGFP_piRNA_1


title: Fwt_M20A-X_TM3_piRNA_2


title: dsGPP_66A6_oxidized_piRNA_2


title: dsGPP_66A6_oxidized_piRNA_1


title: female_T1_male_DB_piRNA_1


title: 20A-X_G0_degradome-seq_2

source_name: adult fly ovaries total RNA


title: 20A-X_Rhino_ChIP_Input, rep1

data_processing:
ChIP-seq reads were trimmed by Trimmomatic (version 0.33) and cutadapt (version 1.15) and filter out those shorter than 50 bp after trimming
The first 50bp of reads were mapped to dm3 genome and vectors sequence respectively, using Bowtie (version 1.0.1, parameters: -v 2 -k 1 -m 1 -t --best -y --strata)
Aligned reads were then used to generate piled-up RPM signals and enrichment profiles by our customized scripts and deepTools
Read counts over equal-sized bins were calculated using deepTools2 and BEDOPS, and plus, minus strand of genome regions and vectors were separate, figures were made by Matlab
smRNA-seq reads were trimmed by Cutadapt to rRNA and filter out those shorter than 15 bp after trimming
Select reads size 21-22bp (siRNA) and 23-29bp (piRNA) and 21-30bp (small RNA)
mapped to dm6 genome and extracted regions 20A cluster(20A) and 42AB cluster(42A), mapped to vector maps, Ubi-GFP(UBIG), non-RMCE Ubi-GFP(originalUBIG), double-stranded GFP reporter(UBIGasG) (parameters: -v 0 -a -m 1 -t --best --strata), and plus, minus strand of genome regions and vectors were separate.
smRNA profilings were generated by Matlab after mapping
Genome_build: dm3(ChIP-seq) and dm6(smRNA-seq)
Supplementary_files_format_and_content: bg4

source_name: adult fly ovaries gDNA (ChIP)

extract_protocol:
Total smRNA from ovary was isolated with Ribozol reagent and do size selection from 19nt to 30nt. For ChIP, ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1.8% in PBS  for 10min at RT. Samples were quenched by 125mM glycine for 5 min at RT and washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM NaCl; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.35% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Lysates were sonicated using Bioruptor (Diagenode, 30 cycles of 30sec ON, 30sec OFF) then add IP diluted buffer (20mM Tris pH7.4; 150mM NaCl; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Supernatants were pre-cleared for 2h at 4°C using Dynabeads Protein G (Invitrogen) beads. 5% of samples were saved for inputs. The rest of the lysates were incubated with antibodies for 2h to overnight at 4°C, then added BSA and DNA blocked Dynabeads Protein G beads and incubated for 3h at 4°C beads The beads were washed 5 times at 4°C with LiCl IP wash buffer (10mM  Tris pH 7.4;  500mM  LiCL;  1%NP40/Igepal;  1%  Sodium  Deoxycholate) and once with TE. Protein was digested with proteinase K for 3hrs at 55°C and reverse-crosslinked by incubation at 65°C overnight. DNA was extracted by phenol:chloroform standard protocol.
smRNA-seq libraries were made by using NEBNext® Small RNA Library Prep Set for Illumina®. Libraries were sequenced on the Illumina HiSeq 2000 platform. ChIP-seq library construction was carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set (E6240) with minor modifications. After adaptor ligation and PCR amplification, size selections were done with  AMPure beads to select the 200bp-600bp size window. Libraries were sequenced on the Illumina HiSeq 2000 platform.
smRNA-seq follow NEBNext® Small RNA Library Prep Set for Illumina®, ChIP-seq follow NEBNext ChIP-Seq Library Prep Master Mix Set

tag: developmental stage

value: adult

value: ovaries

tag: chip antibody

tag: fraction

value: gDNA (ChIP)


title: 20A-X_Rhino_ChIP_Input, rep2


title: M20-X_FAgo2414_dsGFP_TM3_piRNA_2


title: 20A-X_Rhino_ChIP_IP, rep1

value: Rhino (From Julius Brennecke lab)


title: 20A_minus_single_Rhino_ChIP_IP, rep2

value: 20A cluster single reporter insertion minus orientation


title: 20A_minus_single_Rhino_ChIP_Input, rep2


title: 20A_plus_single_Rhino_ChIP_IP, rep1

value: 20A cluster single reporter insertion plus orientation


title: 20A_minus_single_Rhino_ChIP_Input, rep1


title: 20A_plus_single_Rhino_ChIP_Input, rep2


title: 20A_plus_single_Rhino_ChIP_IP, rep2


title: no_dsGFP_66A6_20A-X_smRNA, rep2

value: Maternal 66A6 double-stranded GFP insertion and 20A-X 20A cluster reporter


title: 20A_plus_single_Rhino_ChIP_Input, rep1


title: no_dsGFP_plus_20A-X_smRNA, rep2

value: Maternal 20A cluster double-stranded GFP insertion plus orientation and 20A-X 20A cluster reporter


title: no_dsGFP_plus_20A-X_smRNA, rep1


title: no_dsGFP_minus_20A-X_smRNA, rep1

value: Maternal 20A cluster double-stranded GFP insertion minus orientation and 20A-X 20A cluster reporter


title: no_dsGFP_minus_20A-X_smRNA, rep2


title: dsGFP_66A6_20A-X_smRNA, rep2

value: 66A6 double-stranded GFP insertion and 20A-X 20A cluster reporter


title: no_dsGFP_66A6_20A-X_smRNA, rep1


title: dsGFP_66A6_20A-X_smRNA, rep1


title: dsGFP_plus_20A-X_smRNA, rep2

value: 20A cluster double-stranded GFP insertion plus orientation and 20A-X 20A cluster reporter


title: 20A-X_G8_smRNA, rep1

value: 20A-X 20A cluster reporter G8


title: dsGFP_minus_20A-X_smRNA, rep1

value: 20A cluster double-stranded GFP insertion minus orientation and 20A-X 20A cluster reporter


title: 20A-X_Rhino_ChIP_IP, rep2


title: 20A-X_G3_silenced_smRNA, rep2

value: 20A-X 20A cluster reporter G3 GFP silenced

value: total small RNA


title: 20A-X_G8_smRNA, rep2


title: dsGFP_minus_20A-X_smRNA, rep2


title: 20A-X_G3_silenced_smRNA, rep1


title: 20A-X_G3_mixed_smRNA, rep2

value: 20A-X 20A cluster reporter G3 GFP mixed


title: 20A_minus_single_Rhino_ChIP_IP, rep1


title: 20A-X_G0_degradome-seq_1

value: adult fly ovaries

value: 20A-X 20A cluster reporter


title: 20A-X_G3_active_smRNA, rep1

value: adult

value: ovaries

value: 20A-X 20A cluster reporter G3 GFP active


title: 20A-X_G3_mixed_smRNA, rep1


title: 20A-X_G3_active_smRNA, rep2


title: 20A-X_G0_smRNA, rep1

value: 20A-X 20A cluster reporter G0


title: 20A-X_G0_smRNA, rep2


title: 20A-X_maternal_only_smRNA, rep1

value: Maternal 20A-X smRNA only


title: 20A-X_maternal_only_smRNA, rep2


title: 20A-X_3months_smRNA, rep1

value: 20A-X 20A cluster reporter 3 months


title: 20A-X_3months_smRNA, rep2


title: 20A-X_paternal_smRNA, rep2

value: Paternal 20A-X smRNA


title: 20A-X_paternal_smRNA, rep1


title: 20A-X_maternal_smRNA, rep2

value: Maternal 20A-X smRNA


title: dsGFP_plus_20A-X_smRNA, rep1


title: dsGFP_66A6_smRNA, rep2

value: 66A6 double-stranded GFP insertion


title: dsGFP_66A6_smRNA, rep1


title: 20A-X_maternal_smRNA, rep1


title: dsGFP_plus_smRNA, rep1

value: 20A cluster double-stranded GFP insertion plus orientation


title: 20A-X_control_GLKD_smRNA, rep2


title: 20A-X_Zuc_GLKD_smRNA, rep1


title: dsGFP_minus_smRNA, rep2

value: 20A cluster double-stranded GFP insertion minus orientation


title: 20A-X_Zuc_GLKD_smRNA, rep2


title: 42AB_control_GLKD_smRNA, rep2

value: 42AB cluster single reporter insertion minus orientation


title: 20A-X_control_GLKD_smRNA, rep1


title: 20A-X_Rhino_GLKD_smRNA, rep2


title: 20A-X_11months_smRNA, rep1

value: 20A-X 20A cluster reporter 11 months


title: 42AB_Zuc_GLKD_smRNA, rep2

value: total small RNA


title: 42AB_Zuc_GLKD_smRNA, rep1


title: 42AB_Rhino_GLKD_smRNA, rep2


title: 20A-X_11months_smRNA, rep2


title: 42AB_control_GLKD_smRNA, rep1


title: 66A6_smRNA, rep2

value: 66A6 single reporter insertion


title: 42AB_Rhino_GLKD_smRNA, rep1


title: 20A_minus_single_smRNA, rep2

value: 20A cluster single reporter insertion minus orientation


title: 42AB_minus_smRNA, rep1


title: 42AB_minus_smRNA, rep2


title: 66A6_smRNA, rep1


title: 20A_minus_single_smRNA, rep1


title: 20A_plus_single_smRNA, rep1

value: 20A cluster single reporter insertion plus orientation


title: Wild_type_smRNA, rep2

value: adult

value: Wild type


title: 20A_plus_single_smRNA, rep2

value: ovaries


title: 20A-X_Rhino_GLKD_smRNA, rep1

value: 20A-X 20A cluster reporter


title: dsGFP_plus_smRNA, rep2

value: 20A clusterdouble-stranded GFP insertion plus orientation


title: dsGFP_minus_smRNA, rep1


title: control female F2 25d rep04

city: New Delhi

first: Abhay

last: Sharma

state: New Delhi

address: Sukhdev vihar

department: Molecular medicine

country: India

institute: CSIR Institute of genomics and integrative biology

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_control_25d_4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The CEL files were read using the affy package (version 1.74.0).  The raw data were normalized in sets using the gcrma package (version 2.68.0). 1. The F1 set contained the following samples:  The F1 set contained the following samples: F1_test_25_1, F1_test_25_2, F1_test_25_3, F1_test_25_4 F1_control_25_1, F1_control_25_2, F1_control_25_3, F1_control_25_4, . 3. The F2 set contained the following samples:  F2_test_25_1, F2_test_25_2, F2_test_25_3, F2_test_25_4, F2_control_25_1, F2_control_25_2, F2_control_25_3, F2_control_25_4. The processed data were analyzed using the limma package (version 3.52.4).

source_name: whole body

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3’ IVT plus reagent Kit).

growth_protocol: 30 adult unmated female flies per vial fed respective diet for 7 days at 25degree C  temperature.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Microarray Tissue Handbook) .

treatment_protocol: At the end of treatment, flies were anesthetized using CO2 and collected in Trizol.

value: whole body

tag: generation

tag: diet fed

value: high sugar

tag: gender

value: female


title: Wild_type_smRNA, rep1


title: control F1 female 25d rep04

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_control_25d_4


title: control female F2 25d rep03

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_control_25d_3


title: test female F2 25d rep01

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_test_25d_1


title: test F1 female 25d rep04

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_test_25d_4


title: test female F2 25d rep03

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_test_25d_3


title: test F1 female 25d rep01

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_test_25d_1


title: test F1 female 25d rep02

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_test_25d_2


title: test F1 female 25d rep03

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_test_25d_3


title: test female F2 25d rep04

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_test_25d_4


title: control F1 female 25d rep03

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_control_25d_3


title: control female F2 25d rep02

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_control_25d_2


title: control F1 female 25d rep01

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_control_25d_1


title: control F1 female 25d rep02

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F1_control_25d_2


title: control female F2 25d rep01

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_control_25d_1


title: test female F2 25d rep02

description:
Gene expression data using Affymetrix Drosophila Genome 2.0 array
F2_test_25d_2


title: test male F2 25d rep01

description: Gene expression data using Affymetrix Drosophila Genome 2.0 array

data_processing: The CEL files were read using the affy package (version 1.74.0).  The raw data were normalized in sets using the gcrma package (version 2.68.0). 1. The F0 set contained the following samples: F0_control_25d_1, F0_control_25d_2, F0_control_25d_3, F0_control_25d_4, F0_test_25d_1, F0_test_25d_2, F0_test_25d_3, F0_test_25d_4, F0_control_16d_2, F0_control_16d_3, F0_control_16d_4, F0_test_16d_1, F0_test_16d_2, F0_test_16d_3, F0_test_16d_4 2. The F1 set contained the following samples: F1_control_25d_1, F1_control_25d_2, F1_control_25d_3, F1_control_25d_4, F1_test_25d_1, F1_test_25d_3, F1_test_25d_4. 3. The F2 set contained the following samples: F2_control_25d_1, F2_control_25d_2, F2_control_25d_3, F2_control_25d_4, F2_control_25d_5, F2_test_25d_1, F2_test_25d_2, F2_test_25d_3, F2_test_25d_4, F2_test_25d_5. The processed data were analyzed using the limma package (version 3.52.4).

growth_protocol: 30 adult unmated male flies per vial fed respective diet for 7 days at 16degree C, and or25degree C  temperature.

value: male


title: control male F2 25d rep05


title: test male F2 25d rep04


title: control male F2 25d rep01


title: control male F2 25d rep02


title: control male F2 25d rep03


title: test male F2 25d rep03


title: test male F2 25d rep05


title: test male F2 25d rep02


title: control male F2 25d rep04


title: test F1 male 25d rep04


title: test F1 male 25d rep01


title: control F1 male 25d rep01


title: test F0 male 16d rep04

value: normal

value: actin-Gal4/Pin; UASRNAi-mts/+


title: control F1 male 25d rep04


title: control F1 male 25d rep03


title: control F0 male 16d rep03


title: test F1 male 25d rep03


title: test F0 male 16d rep02


title: control F0 male 16d rep04


title: test F0 male 16d rep01


title: test F0 male 25d rep03


title: test F0 male 25d rep02


title: test F0 male 25d rep01


title: control F0 male 25d rep04


title: HCC1569 FC + DAPT 72h

city: Stockholm

first: Eike-Benjamin

last: Braune

address: Nobels väg 6

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using None from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Data have been processed following NGI-RNAseq BP 2.0 pipeline used by the National Genomics Infrastructure/SciLife , Sweden
TrimGalore was used for  removal of adapter contamination and trimming of low quality regions. Cutadapt was used for adapter trimming and runs FastQC after it finishes.
Reads were aligned using STAR (Spliced Transcripts Alignment to a Reference)
Genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations have been counted using featureCounts v 1.51 from the Subread package and StringTie was used to assess gene expression levels  (see pipeline description above).
Assembly: Homo sapiens, GRCh37
Supplementary files format and content: feature count files

molecule: polyA RNA

source_name: Cell line

growth_protocol: The  breast cancer cell lines used to generate this data set were maintained as described (Brunner et al., 2020). Accutase (cat # A6964-100ML, Sigma-Aldrich) was used to detach the cells prior to seeding on coated plates and during maintenance.

extract_protocol:
RNA was isolated as described in Brunner et al., 2020 (RNeasy Mini Kit (Qiagen)
default Illumina TruSeq Stranded mRNA, Poly-A selection

treatment_protocol: Activation of Notch signaling in the cell lines used for validation of the signature was achieved as previously described (Sahlgren et al., 2008) with minor modifications: 1µg rat Jagged1-Fc (cat #599-JG, R&D systems) or ChromPure Human IgG, Fc (cat #009-000-008, Jackson ImmunoResearch) was used instead of 2 µg. Blockage of Notch signaling was in both cases achieved by adding 10 µM DAPT (InSolution™ γ-Secretase Inhibitor IX, cat #565784, MerckMillipore) directly to the cell culture medium and cells were incubated with DAPT for 8h and 72h. Non-GSI treated cells (Fc control, Jagged1-Fc) were treated with equimolar volumes of carrier control (DMSO, cat #D8418-50ML, Sigma-Aldrich). Transcriptimes were harvested after 8h and 72h of treatment.

value: Cell line

tag: cell line

value: breast cancer

tag: treatment time

value: DAPT (GSI)

tag: mreads


title: HCC1569 FC + DAPT 8h

tag: tissue


title: HCC1187 Jagged1 + DAPT 72h

tag: cell type

value: JAG1 + DAPT


title: HCC1187 Jagged1 72h

value: JAG1  (ligand)


title: control F0 male 25d rep03

tag: genotype


title: HCC1569 FC 8h

value: FC


title: test F0 male 25d rep04


title: control F0 male 16d rep02


title: test F0 male 16d rep03


title: HCC1569 Jagged1 + DAPT 8h


title: control F1 male 25d rep02


title: HCC1187 FC + DAPT 72h


title: HCC1187 FC 72h


title: control F0 male 25d rep01


title: HCC1187 Jagged1 + DAPT 8h


title: HCC1187 Jagged1 8h


title: HCC1187 FC + DAPT 8h


title: HCC1187 FC 8h


title: MDAMB468 Jagged1 + DAPT 72h


title: HCC1569 FC 72h


title: HCC1569 Jagged1 8h


title: MDAMB468 Jagged1 72h


title: MDAMB468 FC 72h


title: HCC1428 Jagged1 8h


title: HCC1428 Jagged1 + DAPT 8h


title: HCC1419 Jagged1 8h


title: HCC1419 Jagged1 + DAPT 8h


title: control F0 male 25d rep02


title: HCC1428 FC 8h


title: T47D Jagged1 + DAPT 8h


title: T47D Jagged1 8h


title: T47D FC + DAPT 8h


title: HCC70 FC + DAPT 72h


title: HCC70 Jagged1 72h


title: T47D FC 8h


title: HCC70 FC 72h


title: HCC70 FC + DAPT 8h


title: HCC70 FC 8h


title: BT20 Jagged1 72h


title: BT20 Jagged1 + DAPT 72h


title: BT20 FC + DAPT 72h


title: BT20 Jagged1 + DAPT 8h


title: MDAMB468 FC + DAPT 72h


title: BT20 FC + DAPT 8h


title: BT20 Jagged1 8h


title: MDAMB157 Jagged1 + DAPT 72h


title: MDAMB157 Jagged1 72h


title: MDAMB157 FC + DAPT 72h


title: HCC1428 FC + DAPT 8h


title: MDAMB157 FC 72h


title: HCC70 Jagged1 + DAPT 72h


title: MDAMB157 FC 8h


title: MCF-7 FC 72h


title: MCF-7 FC + DAPT 72h


title: MCF-7 Jagged1 + DAPT 8h


title: MDAMB157 FC + DAPT 8h


title: MCF-7 FC 8h


title: KPL4 FC + DAPT 72h


title: MCF-7 FC + DAPT 8h


title: KPL4 Jagged1 + DAPT 72h


title: KPL4 Jagged1 72h


title: KPL4 Jagged1 + DAPT 8h


title: KPL4 FC 72h


title: KPL4 Jagged1 8h


title: KPL4 FC + DAPT 8h


title: KPL4 FC 8h


title: BT20 FC 8h


title: BT20 FC 72h


title: SKBR3 FC + DAPT 72h


title: SKBR3 FC 8h


title: MDAMB157 Jagged1 + DAPT 8h


title: SKBR3 Jagged1 + DAPT 8h


title: SKBR3 Jagged1 8h


title: SKBR3 FC + DAPT 8h


title: SKBR3 Jagged1 + DAPT 72h


title: MDAMB157 Jagged1 8h


title: HCC38 Jagged1 + DAPT 72h


title: HCC38 FC 72h


title: HCC38 FC 8h


title: HS578t Jagged1 72h


title: HCC38 Jagged1 8h


title: HCC38 FC + DAPT 8h


title: HCC38 FC + DAPT 72h


title: HS578t FC + DAPT 8h


title: HCC38 Jagged1 + DAPT 8h


title: HS578t Jagged1 + DAPT 72h


title: HCC38 Jagged1 72h


title: HS578t Jagged1 8h


title: BT549 FC + DAPT 8h


title: HS578t FC 72h


title: BT549 Jagged1 + DAPT 8h


title: MCF-7 Jagged1 8h


title: SKBR3 FC 72h


title: SKBR3 Jagged1 72h


title: HS578t Jagged1 + DAPT 8h


title: BT549 Jagged1 8h


title: MDAMB231 Jagged1 + DAPT 8h


title: MDAMB231 Jagged1 72h


title: MDAMB231 FC + DAPT 8h


title: MDAMB231 FC 8h


title: BT549 FC 8h


title: HS578t FC 8h


title: HCC1419 Jagged1 + DAPT 72h


title: MDAMB231 FC 72h


title: MDAMB231 Jagged1 8h


title: MDAMB231 Jagged1 + DAPT 72h


title: HCC1143 Jagged1 + DAPT 72h


title: HCC1419 FC 8h


title: HCC1419 FC + DAPT 8h


title: HCC1143 FC 72h


title: HCC1143 Jagged1 72h


title: HCC1419 FC 72h


title: HCC1419 FC + DAPT 72h


title: HCC1419 Jagged1 72h


title: HCC1143 Jagged1 8h


title: HCC1143 FC 8h


title: HCC1143 FC + DAPT 8h


title: HCC1143 Jagged1 + DAPT 8h


title: BT474 Jagged1 72h


title: HCC1143 FC + DAPT 72h


title: MDAMB231 FC + DAPT 72h


title: BT474 Jagged1 + DAPT 8h


title: BT474 FC + DAPT 72h


title: PCLS_MY47_Ctrl_young

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

description: Gene expression data from young mouse PCLS  treated with medium control

hyb_protocol: Following fragmentation, 5.2 µg fragmented and labeled ss-cDNA were hybridized 16 hr at 45°C on mouse Clariom S Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0, ThermoFischer Scientific), using Affymetrix default settings and RMA normalization

source_name: precision cut lung slices (PCLS)

label_protocol: Fragmented and biotinylated ss-cDNA (5.5 µg) were prepared according to the GeneChip WT PLUS Reagent Kit Manual (Target Preparation for Gene Chip Whole Transcript (WT) Expression Arrays, ThermoFisher Scientific

growth_protocol: Two PCLS per well were incubated in 500 µL of DMEM/F-12 at 37°C, 5% CO2

extract_protocol: RNA was isolated according to an optimized protocol for RNA isolation from PCLS from different species established by Niehof et al. 2017 [BMC Res Notes 10:121]. The protocol is based on a homogenisation and phenol extraction procedure coupled with a MagMax™ magnetic beads cleaning procedure.

treatment_protocol: Bacteria were added to two PCLS/well. One hour post infection (p.i.), the inoculum was discarded and PCLS were washed once with warm Dulbecco's phosphate-buffered saline and transferred into new plates containing DMEM/F-12. Tissue cultures were post-incubated for 7 h at normal cell culture conditions

tag: sample

value: Mouse_PCLS_medium Ctrl_young

tag: strain

tag: age

value: 10-15 weeks

value: lung

tag: treatment_pseudomonas (strains)

value: medium


title: PCLS_MY46_Ctrl_young


title: BT474 Jagged1 8h

tag: treatment


title: HCC1954 Jagged1 + DAPT 72h


title: HCC1954 Jagged1 72h


title: HCC1954 FC + DAPT 72h


title: BT474 FC + DAPT 8h


title: BT474 FC 8h


title: HCC1954 FC 72h


title: HCC1954 Jagged1 8h


title: PCLS_MY38_Ctrl_young


title: PCLS_MY43_Ctrl_young


title: HCC1954 FC 8h


title: PCLS_MY39_Ctrl_young


title: JIMT1 FC + DAPT 72h


title: BT474 FC 72h


title: PCLS_MY37_Ctrl_young


title: PCLS_MY33_Ctrl_young


title: PCLS_MO45_Ctrl_old

description: Gene expression data from old mouse PCLS  treated with medium control

value: Mouse_PCLS_medium Ctrl_old

value: 18- 21 months


title: JIMT1 FC 72h


title: PCLS_MY42_Ctrl_young


title: JIMT1 Jagged1 + DAPT 8h


title: PCLS_MO32_Ctrl_old


title: HCC1954 Jagged1 + DAPT 8h


title: PCLS_MO40_Ctrl_old


title: PCLS_MO36_Ctrl_old


title: PCLS_MY42_D61_young

description: Gene expression data from young mouse PCLS treated with Pseudomonas aeruginosa strain, D61


title: HCC1954 FC + DAPT 8h


title: PCLS_MO41_Ctrl_old


title: HS578t FC + DAPT 72h


title: PCLS_MO31_Ctrl_old


title: JIMT1 Jagged1 8h


title: JIMT1 Jagged1 72h


title: PCLS_MY47_D61_young


title: JIMT1 Jagged1 + DAPT 72h


title: PCLS_MO44_Ctrl_old


title: JIMT1 FC + DAPT 8h


title: PCLS_MY46_D61_young


title: PCLS_MY43_D61_young


title: PCLS_MY33_D61_young


title: HCC1937 Jagged1 + DAPT 72h


title: HCC1937 FC + DAPT 72h


title: HCC1937 FC 72h


title: PCLS_MY37_D61_young


title: JIMT1 FC 8h


title: MCF-7 Jagged1 + DAPT 72h


title: HCC1937 Jagged1 72h


title: PCLS_MO44_D61_old

description: Gene expression data from old mouse PCLS treated with Pseudomonas aeruginosa strain, D61

value: Mouse PCLS_D61_old


title: MCF-7 Jagged1 72h


title: T47D Jagged1 + DAPT 72h


title: HCC70 Jagged1 + DAPT 8h


title: HCC70 Jagged1 8h


title: PCLS_MY38_D61_young


title: PCLS_MO41_D61_old


title: T47D Jagged1 72h


title: PCLS_MO45_D61_old


title: PCLS_MY42_PAO1_young

description: Gene expression data from young mouse PCLS treated with Pseudomonas aeruginosa strain, PAO1

value: Mouse PCLS_PAO1_young


title: PCLS_MO32_D61_old

value: male


title: PCLS_MY47_PAO1_young


title: PCLS_MY38_PAO1_young


title: PCLS_MO36_D61_old


title: PCLS_MY39_PAO1_young


title: T47D FC 72h


title: PCLS_MO40_D61_old


title: PCLS_MY33_PAO1_young


title: PCLS_MO45_PAO1_old

description: Gene expression data from old mouse PCLS treated with Pseudomonas aeruginosa strain, PAO1

value: Mouse PCLS_PAO1_old


title: HCC1428 Jagged1 + DAPT 72h


title: PCLS_MY37_PAO1_young


title: HCC1569 Jagged1 72h


title: PCLS_MO44_PAO1_old


title: HCC1428 Jagged1 72h


title: HCC1428 FC + DAPT 72h


title: HCC1428 FC 72h


title: PCLS_MO41_PAO1_old


title: PCLS_MO40_PAO1_old


title: suprachiasmatic nucleus, control, 00, replicate 3, female, read 1

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

country: United Kingdom

institute: University of Manchester

data_processing:
The Galaxy server was used for all pipelines excepted DryR and CompareRhythms. Raw reads were QCed and trimmed using Trimmomatic (Sliding window trimming, 4 bases average, average quality required 20) before being aligned to the mouse genome (Release M33 GRCm39) using HISAT2 using default options. Transcripts were assembled and counted using Stringtie with GENCODE annotations for M33 (GRCm39), using default options and keeping all annotated genes including all predicted genes, pseudogenes and non-coding RNAs (for a total of 56,884 genes). Gene counts output from Stringtie were then used as input from DryR or compareRhythms, pre-filtered based on Cook’s distance and the mean of normalized counts by DESEq2 to remove genes with too low expression values and high residuals. The resulting pre-filtered count tables are provided as precessed data files (total number of genes from liver, 22,823; SCN, 15,759). Stringtie raw gene counts tables were also used for DESEq2 pairwise comparisons of transcriptome signatures between MCD- and control-fed animals at each time points, also applying DESeq2’s pre-filters.
DEXseq on Galaxy was used for differential exon usage analysis. First, exons were counted from the bam files output by HISAT2 using GENCODE annotations for M33 (GRCm39) prepared for counting by the DEXseq-Count function. Differential exon usage was then analysed from count tables (counte tables for each sample are provided as processed datafiles).
Assembly: Gencode Release M33 (GRCm39)
Supplementary files format and content: Two pre-filtered gene count tables, for the liver and SCN samples, used for downstream analyses, provided as comma-separated text files.
Supplementary files format and content: Exon count tables for each sample, provided as txt files (72 files in total).

source_name: suprachiasmatic nucleus

growth_protocol: Animal experiments were licensed under the Animals (Scientific Procedures) Act of 1986 (UK) and were approved by the animal welfare committees at the University of Manchester. Eight- to twelve-weeks old C57BL/6J male mice were purchased from Charles River (UK) and acclimatized to the local animal unit for 1 week before the experiment. Mice were then provided with the MCD diet (TD.220158) or its isocaloric control (TD.220157) ad libitum and single-housed under a 12:12 h light/dark cycle at ~350 lux during the light phase and 0 lux during the dark phase for 10 days before being exposed to constant darkness (DD) for the 11th day. Ambient temperature was kept at 21 ± 5 °C, the humidity was ~51 ± 8%, with water available ad libitum.

extract_protocol:
RNA was extracted form liver samples using standard Trizol procedure (Invitrogen). Brains were cryosectionned (Leica CM3050, head at -15°C chamber -20°C), first by coarsely trimming the anterior brain until the start of the SCN, then by cutting 23 sequential 25-micrometer coronal sections, each immediately mounted onto a single PEN Membrane Glass Slide (LCM0522, ThermoFisher) and allowed to dry for a few seconds. Slides with mounted sections were warmed at room temperature for a few seconds, then fixed for 3 min in ethanol:acetic acid (19:1), rinsed briefly by immersion in water, stained by immersion in water with 0.2% toluidine blue followed by two washes by immersion in water. All solutions were ice-cold and RNase-free. After the last wash, excess water was flicked off from the slide and slide was placed (sections face up!) onto a plate heater at 50°C for a few minutes until dry. On the same day, SCN were microdissected using a laser dissection microscope (Leica LMD7000; 10× magnification), using 350 microliter RLT buffer with 1% b-mercaptoethanol as a collection/lysis buffer (RNeasy micro kit, Qiagen). RNA was extracted following manufacturer’s instructions (RNeasy micro kit, Qiagen).
Total RNA was submitted to the Genomic Technologies Core Facility (GTCF). Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

treatment_protocol: From CT0 on the 11th day and every 4 hours until CT20, under dim red light mice were killed humanely by cervical dislocation followed by cessation of circulation, and the eyes were removed. Then, under normal room lighting, liver ( ~40 mg from the centre of the left lobe) and whole brains were immediately dissected and flash frozen in liquid nitrogen or on dry ice, respectively.

value: suprachiasmatic nucleus

tag: circadian time

tag: Sex

value: female

value: control


title: PCLS_MO36_PAO1_old


title: suprachiasmatic nucleus, MCD, 00, replicate 3, female, read 1

value: MCD


title: 5TR_6194DP_S16

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

data_processing:
FlipJump-seq reads were trimmed using cutadapt and mapped using bowtie2, all the BAM files were merged to find all the peaks on all files and count tables were made for each BAM files using BEDTools
bowtie2 -x ${Ref_DIR} -1 ${R1} -2 ${R2} --end-to-end -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 -X 1000 | samtools view -Sb - > BAMs/${File_Name}.bam
bedtools coverage -counts -b BAMtoBED.bed -a Peaks.bed > CounTable.bed. CountTable contains all 3TR and 5TR samples' counts for all barcodes.
The count table loaded into R (v.4.1.2) and was segregated by sample, with 3TR and 5TR samples for a given mouse/population paired. Read filters were applied to each 3TR and 5TR sample independently.
Assembly: mm10
Supplementary files format and content: .csv, 8-populations-filt0: 8-population,  barcode x population binary matrix
Supplementary files format and content: .csv, 8-populations-filt10: 8-population,  barcode x population binary matrix with only those barcodes that have 10 reads for 3TR and 5TR samples
Supplementary files format and content: .csv, 8-populations-filt10-ng2: 8-population,  barcode x population binary matrix with only those barcodes that have 10 reads for 3TR and 5TR samples and are present in >= 2 populations
Supplementary files format and content: .csv, 5-populations-filt10: 5-population,  barcode x population binary matrix with only those barcodes that have 10 reads for 3TR and 5TR samples
Supplementary files format and content: .csv, 5-populations-filt10-ng2: 8-population,  barcode x population binary matrix with only those barcodes that have 10 reads for 3TR and 5TR samples and are present in >= 2 populations
Library strategy: Flip-Jump-Seq

source_name: Thymus

extract_protocol:
NA
DNA  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flip-Jump-Seq (MiSeq): Genomic DNA was extracted by NucleoSpin Tissue XS (Takara). Extracted DNA was further amplified with REPLI-g Mini Kit (Qiagen) for whole genome amplification (WGA). Three-arm LM-PCR-based method was optimized and adapted to clone FlipJump transposon integration sites from both 3TR and 5TR ends. Amplified DNA was quantified using Qubit 2.0 fluorometer (Thermo Fisher), and 1 ug was digested separately with MspI, HindIII or HaeIII for 5TR cloning, and MspI, DpnII or HaeIII for 3TR cloning. The digested DNA was purified using QIAquick PCR Purification Kit. To prepare the individual LM-PCR linker mix, the equal volume of 50 uM linker common (long strand)(5’ GACCCGGGAGATCTGAATTCAGTGGCACAGCAGTTAGGGGGCTGGTCG 3’) and 50 uM restriction enzyme (RE)-digested end-specific linker (Blunt end linker /5Phos/CGACCAGCCC/3AmMO/ for HaeIII or CG end linker /5Phos/CGCGACCAGCCC/3AmMO/ for MspI or GATC end linker/5Phos/GATCCGACCAGCCC/3AmMO/ for DpnII or AGCT end linker/5Phos/AGCTCGACCAGCCC/3AmMO/ for HindIII were mixed in a PCR tube. The linker mix was then denatured and annealed by heating it to 95° C for 5 mins and cooling slowly to room temperature. One third of purified digested DNA was ligated with the individual LM-PCR linker mix using PfuTurbo Hotstart DNA Polymerase (Agilent Technologies). The ligation reaction was then digested with EcoRV (internal RE site of PB at 5TR direction) or MluI (internal RE site of PB at 3TR direction) to remove any linker that has ligated onto the 5TR or 3TR end of DNA, respectively. The remaining DNA containing MspI, HindIII and HaeIII linkers were pooled for 5TR sampling and the remaining DNA containing MspI, DpnII and HaeIII were pooled for 3TR processing. The pooled DNA was set up for PCR amplification using linker primer 1 (5’ GACCCGGGAGATCTGAATTC3’) and TR-specific biotinylated primers (LM_5TR_inver_A2: /5Biosg/AGATAATCATGCGTCATTTTGACTCAC or LM_3TR_inverA: /5Biosg/TCGATATACAGACCGATAAAACACATG). Biotinylated PCR products were pulled down using Dynabeads kilobaseBINDER kit at room temperature for 4 hours. Further nested PCR amplification was conducted using a primer that was specific for 5TR (LM_5TR_inver_B2: AGCGGCGACTGAGATGTCC) or 3TR (LM_3TR_inverB: ATGCGTCAATTTTACGCATGATTATC), and a Miseq sequencing index primer containing individual sample barcode. The PCR products were tagged with modified P5 and P7 primers for sequencing.

value: Thymus

value: double-positive T cell


title: suprachiasmatic nucleus, control, 00, replicate 2, male, read 1


title: 3TR_6194DP_S16


title: 3TR_5672DP_3TR_46_S14


title: suprachiasmatic nucleus, control, 20, replicate 3, female, read 1


title: suprachiasmatic nucleus, MCD, 00, replicate 2, male, read 1


title: suprachiasmatic nucleus, MCD, 00, replicate 1, male, read 1


title: suprachiasmatic nucleus, control, 20, replicate 2, male, read 1


title: 5TR_6192DP_S8


title: Neural differentiation of mESCs (Control)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression analysis post differentiation with scrambled shRNA

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

source_name: R1 mESCs

label_protocol: The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000

extract_protocol: RNA was prepared by using RNA isolation kit (Takara Bioscience) and total RNA was isolated according to the manufacturer’s protocol. RNA was quantified by Nanodrop (ThermoScientific Corporation)

value: Control

tag: shRNA

value: Harbors scrambled shRNA


title: suprachiasmatic nucleus, MCD, 20, replicate 2, male, read 1


title: suprachiasmatic nucleus, MCD, 20, replicate 1, male, read 1


title: suprachiasmatic nucleus, control, 00, replicate 1, male, read 1


title: suprachiasmatic nucleus, control, 20, replicate 1, male, read 1


title: Control mouse

description: Control

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0424). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5325)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX using the control genes present in the array.

source_name: Olfactory bulb

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0424). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-2000.

value: Neurons of olfactory bulb in control mouse

tag: condition

value: Standard odor perception conditions


title: HCC1569 Jagged1 + DAPT 72h

value: Cell line

value: breast cancer

value: JAG1 + DAPT


title: PCLS_MO31_D61_old

value: Mouse PCLS_D61_old

value: 18- 21 months

value: lung


title: Neural differentiation of mESCs (Zic3 shRNA)

description: Gene expression analysis post differentiation with Zic3 shRNA

value: Gene manipulated

value: Harbors Zic3 shRNA


title: PCLS_MO32_PAO1_old

value: Mouse PCLS_PAO1_old

value: male


title: Mouse subjected to odor stimulation

description: Odor enriched

value: Neurons of olfactory bulb in test mouse

value: Odor enriched conditions


title: 3TR_6192DP_S8

value: Thymus

value: double-positive T cell


title: suprachiasmatic nucleus, MCD, 16, replicate 3, female, read 1

value: suprachiasmatic nucleus

value: female

value: MCD


title: 3TR_4916DP_3TR_62_S14


title: suprachiasmatic nucleus, MCD, 20, replicate 3, female, read 1


title: 5TR_3990DP_S24


title: 5TR_5672DP_5TR_46_S14


title: 5TR_6194DN_S15

value: double-negative T cell


title: 3TR_6194DN_S15


title: suprachiasmatic nucleus, MCD, 16, replicate 2, male, read 1


title: 5TR_4916DP_5TR_62_S14


title: 5TR_6192DN_S7


title: 3TR_3990DP_S24


title: 5TR_5672DN2-3_5TR_45_S13


title: 3TR_6192DN_S7


title: suprachiasmatic nucleus, MCD, 12, replicate 3, female, read 1


title: 3TR_4916DN2-3_3TR_61_S13


title: suprachiasmatic nucleus, MCD, 16, replicate 1, male, read 1


title: suprachiasmatic nucleus, control, 16, replicate 2, male, read 1

value: control


title: 3TR_5672DN2-3_3TR_45_S13


title: suprachiasmatic nucleus, control, 16, replicate 1, male, read 1


title: suprachiasmatic nucleus, control, 16, replicate 3, female, read 1


title: suprachiasmatic nucleus, control, 12, replicate 2, male, read 1


title: 3TR_6192ImmB_S6

source_name: Bone marrow

value: Bone marrow

value: immature B cell


title: suprachiasmatic nucleus, MCD, 8, replicate 3, female, read 1


title: suprachiasmatic nucleus, control, 8, replicate 2, male, read 1


title: 5TR_3990DN_S23


title: 5TR_6194ImmB_S14


title: suprachiasmatic nucleus, MCD, 12, replicate 2, male, read 1


title: suprachiasmatic nucleus, control, 8, replicate 3, female, read 1


title: 3TR_6194ImmB_S14


title: suprachiasmatic nucleus, MCD, 8, replicate 1, male, read 1


title: 5TR_6192ImmB_S6


title: 3TR_5672ImmB_3TR_39_S7


title: 5TR_4916DN2-3_5TR_61_S13


title: 3TR_4916ImmB_3TR_55_S7


title: suprachiasmatic nucleus, control, 12, replicate 3, female, read 1


title: suprachiasmatic nucleus, MCD, 12, replicate 1, male, read 1


title: 3TR_3990ImmB_S22


title: 5TR_5672ImmB_5TR_39_S7


title: suprachiasmatic nucleus, control, 8, replicate 1, male, read 1


title: suprachiasmatic nucleus, MCD, 4, replicate 2, male, read 1


title: suprachiasmatic nucleus, control, 4, replicate 3, female, read 1


title: suprachiasmatic nucleus, control, 12, replicate 1, male, read 1


title: 5TR_4916ImmB_5TR_55_S7


title: 5TR_3990ImmB_S22


title: 5TR_6194Mono_S12

value: monocyte


title: suprachiasmatic nucleus, MCD, 8, replicate 2, male, read 1


title: suprachiasmatic nucleus, MCD, 4, replicate 1, male, read 1


title: 3TR_6192Mono_S4


title: 3TR_5672Mono_3TR_38_S6


title: 5TR_6192Mono_S4


title: 3TR_3990DN_S23


title: liver, MCD, 00, replicate 3, female, read 1

source_name: liver

value: liver


title: suprachiasmatic nucleus, control, 4, replicate 1, male, read 1


title: suprachiasmatic nucleus, MCD, 4, replicate 3, female, read 1


title: 3TR_4916Mono_3TR_54_S6


title: liver, MCD, 00, replicate 2, male, read 1


title: 5TR_5672Mono_5TR_38_S6


title: liver, MCD, 00, replicate 1, male, read 1


title: liver, MCD, 20, replicate 3, female, read 1


title: 5TR_3990Mono_S20


title: 5TR_6194Gran_S13

value: granulocyte


title: 3TR_3990Mono_S20


title: liver, control, 20, replicate 3, female, read 1


title: liver, control, 00, replicate 2, male, read 1


title: suprachiasmatic nucleus, control, 4, replicate 2, male, read 1


title: 3TR_6194Gran_S13


title: liver, MCD, 20, replicate 2, male, read 1


title: liver, control, 00, replicate 1, male, read 1


title: liver, control, 20, replicate 2, male, read 1


title: liver, MCD, 20, replicate 1, male, read 1


title: 3TR_5672Gran_3TR_37_S5


title: 3TR_6192Gran_S5


title: 5TR_5672Gran_5TR_37_S5


title: liver, control, 00, replicate 3, female, read 1


title: liver, control, 20, replicate 1, male, read 1


title: liver, MCD, 16, replicate 3, female, read 1


title: liver, control, 16, replicate 3, female, read 1


title: 5TR_3990Gran_S21


title: 5TR_4916Mono_5TR_54_S6


title: liver, control, 16, replicate 2, male, read 1


title: liver, MCD, 16, replicate 2, male, read 1


title: 3TR_3990Gran_S21


title: 3TR_6194MPP_S9

value: MPP


title: 5TR_6194MPP_S9


title: liver, control, 12, replicate 3, female, read 1


title: 5TR_6192MPP_S1


title: PCLS_MO31_PAO1_old

value: Mouse PCLS_PAO1_old

value: 18- 21 months

value: lung


title: liver, MCD, 12, replicate 3, female, read 1


title: liver, control, 16, replicate 1, male, read 1

value: male


title: 5TR_6192Gran_S5


title: liver, control, 12, replicate 2, male, read 1


title: 3TR_5672MPP_3TR_34_S2


title: 3TR_6192MPP_S1


title: 5TR_5672MPP_5TR_34_S2


title: 5TR_4916Gran_5TR_53_S5


title: liver, control, 12, replicate 1, male, read 1


title: 3TR_4916Gran_3TR_53_S5


title: 3TR_4916MPP_3TR_50_S2


title: 3TR_6194Mono_S12


title: liver, MCD, 8, replicate 3, female, read 1


title: 5TR_3990MPP_S17


title: 5TR_4916MPP_5TR_50_S2


title: liver, control, 8, replicate 3, female, read 1


title: liver, MCD, 12, replicate 1, male, read 1


title: liver, MCD, 16, replicate 1, male, read 1


title: 3TR_3990MPP_S17


title: liver, MCD, 8, replicate 2, male, read 1


title: liver, control, 8, replicate 2, male, read 1


title: 5TR_6194Mkp_S11

value: MkP


title: liver, MCD, 12, replicate 2, male, read 1


title: liver, MCD, 8, replicate 1, male, read 1


title: liver, control, 8, replicate 1, male, read 1


title: 5TR_6192Mkp_S3


title: 3TR_5672Mkp_3TR_35_S3


title: 3TR_6192Mkp_S3


title: 3TR_6194Mkp_S11


title: 5TR_5672Mkp_5TR_35_S3


title: liver, control, 4, replicate 2, male, read 1


title: liver, MCD, 4, replicate 3, female, read 1


title: liver, MCD, 4, replicate 1, male, read 1


title: 5TR_4916Mkp_5TR_51_S3


title: 16wks HFD Exo 4

city: La Jolla

first: Wei

last: Ying

state: CA

address: 9500 Gilman Dr, Stein Clinical Research Building, Room 225

institute: UC San Deigo

data_processing:
Adapter trimming:  cutadapt (v1.13)
polyA removal
QC:  R-3.3
DEG:  edgeR (version 3.16.5)
GO
Genome_build: mm10
Supplementary_files_format_and_content: unique-mouse-QUANTIFIED-miRNA_CPM_continuous.xlsx

source_name: primary hepatocytes

growth_protocol: Williams’ E Medium +10%FBS+1% glutamax

extract_protocol:
Zymo RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary hepatocyte

tag: passage

value: 16wks HFD


title: 5TR_6194Eryp_S10

value: EryP


title: 3TR_6194Eryp_S10


title: 16wks HFD Exo 3


title: 5TR_6192Eryp_S2


title: T47D FC + DAPT 72h

value: Cell line

value: breast cancer

value: DAPT (GSI)


title: 16wks HFD Exo 2


title: 4wks HFD Exo 4

value: 4wks HFD


title: 16wks HFD Exo 1


title: 3TR_6192Eryp_S2

value: Bone marrow


title: 3TR_3990Mkp_S19


title: 4wks HFD Exo 3


title: 3TR_5672Eryp_3TR_36_S4


title: 5TR_5672Eryp_5TR_36_S4


title: 4wks HFD Exo 1


title: 3TR_4916Mkp_3TR_51_S3


title: 5TR_3990Eryp_S18


title: lean Exo 4

value: control


title: 3TR_3990Eryp_S18


title: lean Exo 3


title: 5TR_3990Mkp_S19


title: 3TR_4916Eryp_3TR_52_S4


title: liver, control, 4, replicate 3, female, read 1

value: liver

value: female


title: 4wks HFD Exo 2


title: lean Exo 2


title: 5TR_4916Eryp_5TR_52_S4


title: ATAC_bcl7a_bcl7b_bio_2

city: Guangzhou

first: Yawen

last: Lei

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

description: chromatin accessibility assay of 14-day-old seedlings, chromatin digested using Tn5

data_processing:
ATAC-seq raw data was trimmed by fastp set adapter sequence with parameter “-a CTGTCTCTTATACACATCT”.
The clean data was mapped to the A. thaliana reference genome (TAIR10) using Bowtie 2 with the default settings.
The online tool Filter BAM datasets was used with parameter “mapping quality ≥30,! Mt,! Pt” to removed unmapped and organelle reads. The online tool MarkDuplicates was used with the default settings to remove duplicated reads.
The peak calling, peak annotation, bamCoverage, and IGV visualization were performed according to the methods used for ChIP-seq data analyses.
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
About 1 g of 14-day-old Arabidopsis seedlings grown under short-day conditions were collected and extract the nuclei.
The purified nuclei were then incubated with Tn5 transposome and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, Cat. No. TD501). After the tagmentation, the DNA was purified using MinElute PCR purification kit (Qiagen, Cat. No. 28004) and then amplified using TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme Biotech, Cat. No. TD501) for 9 cycles.

value: seedlings


title: ATAC_bcl7a_bcl7b_bio_1


title: ATAC_brip1_brip2_bio_2


title: ATAC_brip1_brip2_bio_1


title: ATAC_brm-3_bio_2


title: ATAC_brm-1_bio_2


title: ATAC_brm-1_bio_1


title: G1E-ER4 24h - rnaseq_rep2

city: Cambridge

first: Jonathan

last: Li

state: Massachusetts

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

data_processing:
Alignment done using TopHat2 and Bowtie
mm9
rna abudnance

growth_protocol: G1ER4 cells were cultured in Isocove’s modified Dulbecco’s medium (IMDM) supplemented with 15%  fetal calf serum (FCS), 100 units (U) /mL penicillin and 100 g/mL streptomycin (PS), 2 U/mL recombinant human erythropoietin (EPO), and 50 ng/ml mouse recombinant SCF or 1% conditioned medium from murine SCF producer cell line

extract_protocol: isolated total RNA, depleted ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina cat: MRZH11124), and added ERCC RNA Spike-In Mix 1 (ThermoFisher: cat: 4456740) based on cell number

treatment_protocol: Differentiation was induced by adding beta-estradiol (Sigma, cat: E8875) at a final concentration of 10 nM for 24 hrs or as otherwise indicated

value: 10 nM beta-estradiol for 24h


title: ATAC_WT_bio_2

value: WT


title: G1E-ER4 0h - rnaseq_rep2

value: 10 nM beta-estradiol for 0h


title: lean Exo 1


title: G1E-ER4 0h - rnaseq_rep1


title: ATAC_WT_bio_1


title: G1E-ER4 24h - rnaseq_rep1


title: G1E-ER4 24h - chipseq-SMC3_rep1

data_processing:
Libraries were aligned using Bowtie
Peaks called using MACS with pval=1e-9 and default parameters for the rest
mm9
bed files; regions of peaks for ChIPseq experiments

extract_protocol: As described in Yu et al., Molecular Cell., 2021

tag: chip antibody

value: SMC3 (abcam, cat:ab9263)


title: PBMC_Cont_Day7pc_rep4

city: Salvador

first: Almiro

middle: Pires

last: Neto

state: Bahia

address: Waldemar Falcão Street

department: Immunology

country: Brazil

institute: Gonçalo Muniz Institute

description: Gene expression (mice PBMC) of control group collected in parallel to Day 7pc

hyb_protocol: Sample hybridizations were performed on Agilent slides for 16 h at 65°C. After gentle washing in accordance with Agilent’s protocol, microarrays were scanned on a C scanner (Agilent)

scan_protocol: Slides were scanned immediately after washing on a Agilent G2565CA DNA Microarray Scanner using one color scan setting for SurePrint G3 Mouse GE 8x60K array slides

data_processing: Agilent Feature Extraction software (v10.7) was used to read and process microarray image files. The software determined feature intensities and background, rejected outliers, and generated validated data files for further analyses. Each array was validated via the analysis of additive error, spatial distribution of outliers in the array, a histogram of signal plots, background sub-signal value and linear range spike-in statistics.

source_name: PBMC, Cont, Day7pc, rep4

label_protocol: To produce Cy3-labeled cRNA, total RNA was amplified and labeled using an Agilent Low Input Quick Amplification Labeling Kit in strict accordance with manufacturer instructions. Briefly, 100 ng of template RNA was used for cDNA synthesis, and T7 RNA polymerase was then used for cRNA amplification and Cy3 labeling. After purification, yield and dye incorporation was measured using a Nanodrop spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was extracted using TRizol® Reagent (Ambion RNA, Life Technologies), with a precipitation step incorporating glycogen (5mg/mL, Ambion, USA) plus 3M sodium acetate (Ambion, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 mice were distributed into five groups: control (C), non-treated animals; vaccinated once (V1) with 500 attenuated cercariae and challenged with 120 normal cercariae; vaccinated three times (V3) with 500 attenuated cercariae (4-week intervals) and challenged with 120 normal cercariae; only challenged with 120 normal cercariae (Chc); and  infected with 500 normal cercariae (Inf) in parallel with the 1V group. Blood was drawn from the same groups of mice in a time-course manner at Days 7 and 17 after imunization/infection, and Day 7 post-challenge and the PBMC was purified.

value: Peripheral blood mononuclear cells

tag: gender

value: Female


title: G1E-ER4 0h - chipseq-SMC3_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2020


title: PBMC_Cont_Day7pc_rep3

source_name: PBMC, Cont, Day7pc, rep3


title: scRNA-seq (10X) of Spontaneous blastoids upon removal of BRAF/MEK signaling inhibition

first: Jinyi

last: Wu

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou Laboratory

library_source: transcriptomic single cell

data_processing:
For bulk RNA-seq data, raw reads of fastq format from this study were first processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw reads. Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. For single cell RNA-seq data, data of day 6 blastoids was pre-processed through Trimmomatic software to remove adapters and to drop low quality reads or short reads below 26 bps. Other single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq and scRNAseq (Smartseq2) count table: gene by cell expression matrix generated with STAR; scRNAseq (10X) count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: blastoids

extract_protocol:
For bulk RNA-seq, total RNAs were collected and isolated from cells using RNAiso Plus (Takara). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina following manufacturer’s recommendations. For scRNA-seq, CI-hnESCs and day 2 aggregates were dissociated and sorted by flow cytometer for Smart-seq2 library construction and the libraries were sequenced on MGISEQ2000 (MGI Tech) platform to generate 100-bp paired-end reads. Day 3, day6 blastoids and the blastoids upon removing MEK/BRAF inhibition from Aggrewell were manually picked and polled with a mouth pipette, washed once with DPBS and then dissociated with 0.25% trypsin-EDTA (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Attached cultured bE14 blastoids were first rinsed once with DPBS and then treated with cold DPBS and incubated in 4°C for 10-20min to allow breaking of the matrix. When the samples became mobile under a microscope upon gentle shaking, the bE14 blastoids were transferred to a clean tube using a cut-tip and dissociated with 0.25% trypsin-EDTA at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cell

value: blastoids


title: PBMC_Cont_Day7pc_rep1

source_name: PBMC, Cont, Day7pc, rep1


title: PBMC_Cont_Day17_rep4

description: Gene expression (mice PBMC) of control group collected in parallel to Day 17

source_name: PBMC, Cont, Day17, rep4


title: PBMC_Cont_Day7_rep8

description: Gene expression (mice PBMC) of control group collected in parallel to Day 7

source_name: PBMC, Cont, Day7, rep8


title: ATAC_brm-3_bio_1


title: G1E-ER4 24h - chipseq-SMC1A_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2019

value: anti-SMC1 (Bethyl, cat:A300-055A)


title: PBMC_Cont_Day7_rep7

source_name: PBMC, Cont, Day7, rep7


title: G1E-ER4 0h - chipseq-SMC1A_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2018


title: PBMC_Cont_Day17_rep2

source_name: PBMC, Cont, Day17, rep2


title: liver, MCD, 4, replicate 2, male, read 1

value: male

value: MCD


title: scRNA-seq (10X) of bE14-blastoids (Spontaneous blastoids undergoing post-implantation development)


title: PBMC_Cont_Day7pc_rep2

source_name: PBMC, Cont, Day7pc, rep2


title: PBMC_Cont_Day17_rep3

source_name: PBMC, Cont, Day17, rep3


title: PBMC_Cont_Day17_rep1

source_name: PBMC, Cont, Day17, rep1


title: G1E-ER4 24h - chipseq-INPUT_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2017


title: PBMC_Cont_Day7_rep6

source_name: PBMC, Cont, Day7, rep6


title: G1E-ER4 24h - chipseq-GATA2_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2015

value: anti-GATA2 (Santa Cruz, cat:sc-9008)


title: scRNA-seq (10X) of D3 Spontaneous Blastoids


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 73

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-73


title: G1E-ER4 0h - chipseq-INPUT_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2016


title: G1E-ER4 0h - chipseq-GATA2_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2014


title: G1E-ER4 24h - chipseq-GATA1_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2013

value: anti-GATA1-N6 (Santa Cruz cat. no. sc-265) pre-incubated with rabbit anti-rat IgG (AffiniPure Rabbit anti-Rat IgG H+L, Jackson ImmunoResearch, cat:312-005-003)


title: PBMC_Cont_Day7_rep4

source_name: PBMC, Cont, Day7, rep4


title: G1E-ER4 0h - chipseq-GATA1_rep1

extract_protocol: As described in Yu et al., Molecular Cell., 2012


title: RNA-seq of TJ 1# CI-hnESC replicate 2

description:
TJ1_nESC_count.csv
nESCs-IM-2

source_name: TJ 1# CI-hnESC

tag: cell line

value: TJ 1# CI-hnESC

value: cultured with IM-12


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 72

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-72


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 71

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-71


title: RNA-seq of TJ 1# CI-hnESC replicate 1

description:
TJ1_nESC_count.csv
nESCs-IM-1


title: scRNA-seq (10X) of D6 Spounateneous Blastoids


title: RNA-seq of TJ 1# C-hnESC replicate 1

description:
TJ1_nESC_count.csv
nESCs-Chir-3

source_name: TJ 1# C-hnESC

value: TJ 1# C-hnESC

value: cultured with Chir99021


title: RNA-seq of TJ 1# C-hnESC replicate 2

description:
TJ1_nESC_count.csv
nESCs-Chir-4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 69

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-69


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 68

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-68


title: Jurkat cells, lnc-CEBPB-13 overexpression

city: Yantai

first: Xicheng

last: Song

address: No.20, Yuhuangding East Road, Zhifu District, Yantai City, Shandong Province

department: Department of Otorhinolaryngology, Head and Neck Surgery

institute: Qingdao University Affiliated Yantai Yuhuangding Hospital

data_processing:
The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using the Personalbio company's self-developed script, clean data was obtained by removing adapter and Low quality sequence. Filter Clean Reads from 18 nt to 36 nt in length and perform deduplication to obtain Unique Reads for subsequent analysis.
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: XLSX  and DESeq

source_name: blood

extract_protocol:
Total RNA was extracted from the Jurkat cells using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter_x0002_ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, the library preparations were sequenced on an Illumina Novaseq 6000 (or MGISEQ-T7) and 150 bp paired-end reads were generated

value: blood

value: Jurkat

value: lnc-CEBPB-13 overexpression


title: Jurkat cells, lnc-CEBPB-13 control

value: control


title: A549, H2AK119ub, ChIP

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Quality control was performed using Fastqc (v 0.11.9) for sequencing clean data.
The reference genome (UCSC hg38) was utilized for mapping clean reads to the human genome using Bowtie2 (v 2.4.5)
Mapped reads with high confidence were sorted, indexed, and transformed to bam format using SAMtools (v1.6).
Removal of duplicates was carried out using Sambamba (v0.8.2).
The bigwig files were calculated and normalized with counts per million (CPM) using bamCompare from Deeptools (v3.5.1). Macs2 (v2.2.7.1) was employed for peak calling.
Assembly: hg38
Supplementary files format and content: H2AK119ub_CPM.bw,H2AK119ub_peaks.broadPeak: bigWig and broadPeak files for H2AK119ub
Supplementary files format and content: Input_CPM.bw: The bigwig file for Input in A549 cells.

source_name: lung

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
A549 cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was subsequently quenched with 0.125 mol/L glycine. Cells were then resuspended in SDS buffer. The resulting cell pellets were resuspended in ice-cold immunoprecipitation (IP) buffer, and then subjected to sonication. The supernatant post-centrifugation was incubated overnight at 4°C with H2AK119ub antibodies. Protein A/G beads were then added at 4℃ for 4 hours. After thorough washes, samples were incubated at 65°C for 6 hours, and DNA was extracted.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific.

value: lung

value: Human lung adenocarcinoma cell


title: PBMC_Cont_Day7_rep3

source_name: PBMC, Cont, Day7, rep3

value: Peripheral blood mononuclear cells

value: Female


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 67

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-67

value: pluripotent stem cell

value: blastoids


title: PBMC_CHC_Day7pc_rep4

description: Gene expression (mice PBMC) of challenge control at Day 7 after infection (120 normal cercariae)

source_name: PBMC, CHC, Day7pc, rep4


title: A549, H2AK119ub, Input

description: Raw data: The original sequencing file of Input is at https://ngdc.cncb.ac.cn/gsa/browse/CRA001102/CRR033172.


title: A549, shc

data_processing:
Adapters and low quality sequences using Trimmomatic (0.36).
Trimmed reads were aligned to the human genome (UCSC hg38) using STAR (2.6.1d) with the following parameters: --outSAMtype BAM SortedByCoordinate --outSAMattributes All --chimSegmentMin 10 --outSAMattrIHstart 0 --outWigStrand Stranded --outSAMstrandField intronMotif --quantMode GeneCounts
Gene expression levels were quantified as read counts and FPKM. Unstranded read counts was directly collected from STAR output. FPKM was calculated by dividing read count by the gene length and the total number of reads mapped to protein-coding genes, according to the formula in GDC mRNA Analysis Pipeline.
Differential gene analysis using edgeR (3.22.5)
Assembly: hg38
Supplementary files format and content: edgeR_count: gene counts for every gene and every sample.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The lentiviruses expressing control or shCBX4 shRNA were employed to infect A549 cells to obtain stable expression cells.

value: human lung adenocarcinoma cell


title: A549, sh4-2

value: CBX4 shRNA2


title: PBMC_Cont_Day7_rep1

source_name: PBMC, Cont, Day7, rep1


title: PBMC_Cont_Day7_rep2

source_name: PBMC, Cont, Day7, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 66

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-66

source_name: blastoids


title: PBMC_Cont_Day7_rep5

source_name: PBMC, Cont, Day7, rep5


title: PBMC_CHC_Day7pc_rep2

source_name: PBMC, CHC, Day7pc, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 65

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-65


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 70

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-70


title: 293T, WT, 5

first: Zbigniew

last: Warkocki

address: ul. Z. Noskowskiego 12/14

institute: Institute of Bioorganic Chemistry PAS

data_processing:
From 3'RACE-Seq raw reads, adapters were removed with cutadapt (v4.0) and sequences shorter than 20 nt were discarded. Low-quality nucleotides from 3’ end of reads were removed using ConDeTri (v2.3) with the following settings hq=37, ml=1, mh=5 and minlen=40.
For further analyses only reads containing a unique molecular identifier (UMI) in length 15 nt and delimiter (GTCAG) on 5’ end of read R2 were kept.
UMI and delimiter sequences were removed from read sequences and moved to the read name with the extract mode of UMI-tools (v1.1.2).
Reads were mapped to reference using STAR (v2.7.9a) with soft-clipping allowed (with the following settings outFilterMatchNmin 20, outFilterScoreMinOverLread 0.1 and outFilterMatchNminOverLread 0.1). Mapped reads were deduplicated with UMIcollapse.
For pair of reads in which both reads mapped non-templated tails and their nucleotide compositions were retrieved from the sam file from the soft-clipped fragments of read R2 using the previously published script (get_softclipped_reads_from_sam.pl) [Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022)]. For pair of reads in which only R1 mapped due to presence of long homopolymeric sequence in the read R2 length sequence of tails were extracted directly from the read R2.
Statistical analyses were performed in R (v4.2). In these analyses were included reads with no tails and those with the following composition: tails containing only A (A tails), only U (U tails), A with U on their 3’ (AU tails). In AU tails were allowed tails with U between A but not at the beginning of the tail. All operations on bam and sam files were performed with samtools (v1.13).
Assembly: LINE-1 sequence
Supplementary files format and content: tails_LINE1_3KOs.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_LINE1_PA1cells.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_LINE1_293Tcells.txt; tab-delimited text file containing tails sequences and lengths
Library strategy: 3' RACE-seq to assess non-templated 3' ends

extract_protocol:
RNA was isolated by using extraction with TRI (Chomczynski and Sacchi, 1987), followed by extraction with chloroform. After precipitation samples were dilluted in TNES with 20ng/µl proteinase K (USB), incubated at 37C for ~15mins, and purified again by phenol/chloroform/isoamly alc. (PCIA), followed by chloroform extractions, and precipitated with isopropanol in the presence of 100mM NaOAc 5.2. Nucleic acids were centrifuged and treated with TURBO DNAse in 0,5x buffer in 100µl for 15mins, followed by another round of extractions with PCIA, chlorofom, and precipitation. Such RNA was measured (for all A260/280 >1,85, A260/230 >2), analyzed for quality by electrophoresis in agarose gels, staining and photographing followed by quantitation of 28S RNA to 18S rRNA ratios. Good quality RNA was used for 3' RACE-seq library preparations, RT-qPCR, and Northern blots (all with same preparations of RNA). Endogenous L1 were amplified by nested PCR to prepare libraries for Illumina 100+100 paired-end sequencing
For the 12 home-made 293T cell lines (this paper) including the wild-type and the XRN1 KO each biological replicate was a single technical replicate (one index per cell line). For the PA-1 cells, 2 sets of RNAi-induced knock-downs were prepared and analyzed: including control kd, XRN1 kd, DCP2 kd, and DIS3L2 kd (only 1 set). Set 1 = 1 transfection with siRNA, 48h between transfection and harvest for RNA, 3 biological replicates for each condition, each a different siRNA, but for DIS3L2 for which only 1 siRNA was transfected into 3 independent wells of a multiwell plate. Set 2 = 2 transfections with siRNA, 1st transfection (siRNA silencer select for each of two duplicates for each condition), 72h, 2nd transfection (same siRNA), 54h, harvest; each well was considered as an independednt biological replicate. Each biological replicate were performed and marked with a different index. For all libraries after index installation during RT, libraries from a single conditions were pooled (e.g. WT or XRN1 KO), and PCR1 and PCR2 were performed on pools of each of the conditions (e.g. 6 indexes for 293T Wt were RT separately, but amplified in a common pool). Libraries were prepared as described in (10.1016/j.cell.2018.07.022) with modifications. Briefly, 2µg total RNA after DNase treatment were ligated with 100pmole RA3_15N 5’ preadenylated adapter comprising a 15-nucleotide unique molecular identifier (UMI) in 20µl of 1x enzyme-supplied buffer, 15% PEG 8000 by T4 RNA ligase 2 truncated (NEB, M0242) for 18h at 18˚C. Nucleic acids of each reaction were purified using 20µl Ampure XP magnetic beads, eluted in and used for reverse transcription in 20µl with 100pmoles RPI primer (containing an 6-nucleotide index) using Superscript III (ThermoScientific) enzyme according to the manufacturer’s protocol (2mins at 50˚C, 30mins at 45˚C, 15mins at 85˚C), followed by purification on 1,25 volume of Ampure XP magnetic beads. Nested PCR was performed with PrimeSTAR GLX polymerase (TaKaRa, R050B) since it proofed best at elongating long poly(A) tracts (as compared to Phusion of ThermoScientific and Q5 polymerases of NEB; not shown). First round PCR were performed in 25µl with an equivalent of 500ng input total RNA (input to RT step) per reaction. Primers at 0,35µM were 3UNP1f for L1, universal reverse primer, RP_uni, was added at 0,4µM. Reactions were carried out: 98˚C 2mins, [98˚C 12sec, 52˚C 15sec, 70˚C 40sec]x30 (set 1 PA-1)/33 (set 2 PA-1 & 293T), 68˚C 1min, 1/10 of each reaction was used without purification as template for second round PCR in 50µl (set 1) or 2x50µl (total 100µl; set 2 & 293T) with 0,36µM transcript-specific forward primer: L-1rep_NGS1, and 0,4µM universal reverse primer RP_uni. PCRs were carried out: 98˚C 2mins, [98˚C 12sec, 55˚C 15sec, 70˚C 30sec]x30 (set 1 PA-1)/33 (set 2 PA-1 & 293T), 70˚C 1min. The reactions of set 1 PA-1 (48h RNAi) were purified on 1,3 volume Ampure XP magnetic beads, and eluted. The reactions of set 2 PA-1 (126h) and 293T: duplicate 50µl were pooled and precipitated, separated on 5% non-denaturing PAA in 1x TBE for 45min @ 500V, stained with SYBR Gold (Thermo Fisher Scientific) 1:2000 in 1x TBE, cut within a range from 180 to 500bp (as assessed by comparison with migration ladders), eluted in 1x TNES (10mM Tris 8.0/100mM NaCl/2mM EDTA/0,1% SDS), precipitated with 1,2vol isopropanol in the presence of 1µl glycoblue co-precipitant and 100mM NaOAc 5,2, sedimented overnight, washed 2x with 70% ethanol, air-dried and suspended in 14µl. Set 1 libraries were measured and diluted to ~5ng/µl, set 2 & 293T libraries were analysed by electrophoresis in agarose gels. All libraries were analysed on TapeStation (Agilent). The set 2 and 293T were 'overamplified' as suggested by smearing in PAA and on Tapestation but not in agarose gels. On the other hand performing less cycles did not yield any interpretable signal on the gels and preculded size-based separation on PAA gels, which was performed to exclude libraries of sizes of lenghts matching just forward and reverse primers (160bp). Before running on Illumina Novaseq libraries were quantitated by qPCR to adjust the number of reads to ~3-5 MRds for each transcript for each biological/technical replicate (each index).

value: WT


title: PBMC_VC_Day35_rep4

description: Gene expression (mice PBMC) of VC group at Day 35 after infection with 500 normal cercariae

source_name: PBMC, VC, Day35, rep4


title: PBMC_CHC_Day7pc_rep3

source_name: PBMC, CHC, Day7pc, rep3


title: 293T, WT, 3


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 64

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-64


title: A549, sh4-1

value: CBX4 shRNA1


title: 293T, WT, 2


title: PBMC_VC_Day35_rep2

source_name: PBMC, VC, Day35, rep2


title: 293T, XRN1 KO, 6

value: XRN1 kd


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 63

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-63


title: 293T, WT, 1


title: 293T, XRN1 KO, 4


title: 293T, XRN1 KO, 5


title: PBMC_CHC_Day7pc_rep1

source_name: PBMC, CHC, Day7pc, rep1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 61

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-61


title: PBMC_VC_Day35_rep1

source_name: PBMC, VC, Day35, rep1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 62

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-62


title: PA-1 126h XRN1 kd, 2


title: 293T, WT, 6


title: PBMC_VC_Day35_rep3

source_name: PBMC, VC, Day35, rep3


title: 293T, XRN1 KO, 2


title: 293T, XRN1 KO, 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 60

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-60


title: 293T, XRN1 KO, 3


title: PBMC_V3_Day7pc_rep5

description: Gene expression (mice PBMC) of V3 group at Day 7 post-challenge with 120 normal cercariae

source_name: PBMC, V3, Day7pc, rep5


title: PA-1 126h XRN1 kd, 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 59

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-59


title: PBMC_V3_Day7pc_rep4

source_name: PBMC, V3, Day7pc, rep4


title: PA-1 126h DCP2 kd, 2

value: DCP2 kd


title: PBMC_V3_Day7pc_rep3

source_name: PBMC, V3, Day7pc, rep3


title: PBMC_V3_Day7pc_rep2

source_name: PBMC, V3, Day7pc, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 58

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-58


title: PA-1 126h CNT kd, 2


title: PA-1 126h DCP2 kd, 1


title: PA-1 126h CNT kd, 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 57

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-57


title: PBMC_V3_Day7pc_rep1

source_name: PBMC, V3, Day7pc, rep1


title: PA-1 48h XRN1 kd, 3


title: PA-1 48h XRN1 kd, 2


title: PA-1 48h XRN1 kd, 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 56

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-56


title: PA-1 48h DCP2 kd, 2


title: PBMC_V1_Day7pc_rep4

description: Gene expression (mice PBMC) of V1 group at Day 7 post-challenge with 120 normal cercariae

source_name: PBMC, V1, Day7pc, rep4


title: PA-1 48h DCP2 kd, 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 55

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-55


title: PBMC_V1_Day7pc_rep3

source_name: PBMC, V1, Day7pc, rep3


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 53

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-53


title: PA-1 48h DCP2 kd, 3


title: PA-1 48h DIS3L2 kd, 3

value: DIS3L2 kd


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 54

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-54


title: PA-1 48h DIS3L2 kd, 2


title: PA-1 48h DIS3L2 kd, 1


title: PA-1 48h CNT kd, 2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 52

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-52


title: Pt18_Z2, scRNAseq

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University First Affiliated Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver adjacent tissue

extract_protocol:
Tissue samples were processed with mechanical chopping with blades, followed by Tumor Dissociation Kit (Miltenyi Biotec) and DNaseI (DN25-100MG, Sigma Aldrich) digestion in medium (RPMI1640 with 5% FBS) for 30 min at 37°C. The cell suspension was passed through a 70-um filter (Miiltenyi Biotec), followed by 1×RBC lysis buffer (eBioscience) treatment.
Single cells were processed with the GemCode Single Cell Platform using the Gemcode Gel Bead, Chip and Libraray Kits (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol with modifications. Briefly, samples were processed using kits pertaining to the Chromium 5' immune profling v2 barcoding chemistry of 10x Genomics. Libraries were constructed according to the standard 10x Genomics protocol (Single Cell 5’Reagent Kits v5.2 User Guide) with modifications and performed the paired-end 2×150bp (PE150) sequencing on Novaseq 6000 (llumina, San Diego, CA).

value: liver adjacent tissue


title: PA-1 48h CNT kd, 3


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 51

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-51

source_name: blastoids


title: PA-1 48h CNT kd, 1


title: PBMC_V1_Day7pc_rep1

source_name: PBMC, V1, Day7pc, rep1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 50

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-50


title: liver, control, 4, replicate 1, male, read 1

source_name: liver

extract_protocol:
RNA was extracted form liver samples using standard Trizol procedure (Invitrogen). Brains were cryosectionned (Leica CM3050, head at -15°C chamber -20°C), first by coarsely trimming the anterior brain until the start of the SCN, then by cutting 23 sequential 25-micrometer coronal sections, each immediately mounted onto a single PEN Membrane Glass Slide (LCM0522, ThermoFisher) and allowed to dry for a few seconds. Slides with mounted sections were warmed at room temperature for a few seconds, then fixed for 3 min in ethanol:acetic acid (19:1), rinsed briefly by immersion in water, stained by immersion in water with 0.2% toluidine blue followed by two washes by immersion in water. All solutions were ice-cold and RNase-free. After the last wash, excess water was flicked off from the slide and slide was placed (sections face up!) onto a plate heater at 50°C for a few minutes until dry. On the same day, SCN were microdissected using a laser dissection microscope (Leica LMD7000; 10× magnification), using 350 microliter RLT buffer with 1% b-mercaptoethanol as a collection/lysis buffer (RNeasy micro kit, Qiagen). RNA was extracted following manufacturer’s instructions (RNeasy micro kit, Qiagen).
Total RNA was submitted to the Genomic Technologies Core Facility (GTCF). Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

value: liver

value: male


title: PBMC_VC_Day17_rep2

description: Gene expression (mice PBMC) at Day 17 after infection (500 normal cercariae)

source_name: PBMC, VC, Day17, rep2

extract_protocol: Total RNA was extracted using TRizol® Reagent (Ambion RNA, Life Technologies), with a precipitation step incorporating glycogen (5mg/mL, Ambion, USA) plus 3M sodium acetate (Ambion, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: Pt18_Z1, scRNAseq

description: 10x Genomics

source_name: colon adjacent tissue

value: colon adjacent tissue


title: PBMC_VC_Day17_rep3

source_name: PBMC, VC, Day17, rep3


title: PBMC_VC_Day17_rep1

source_name: PBMC, VC, Day17, rep1


title: PBMC_V1_Day7pc_rep2

source_name: PBMC, V1, Day7pc, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 49

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-49


title: Pt18_T1, scRNAseq

description: 10x Genomics

source_name: primary tumor

value: primary tumor