title: ptim_mup_r1_s_o_v15

data_processing:
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Assembly: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns.  Those correspond to the NCBI accessions and builds indicated in the Supplementary file.
Assembly: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10).
Supplementary files format and content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

organism: Hoylesella timonensis

source_name: Liquid culture of Prevotella timonesis (DSM 22865)

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.
other: 5PSeq that captures  transcripts with free 5' phospahte (without cap)

value: 65ug/ml Mupirocin incubated for 10 minutes at 37˚C

value: ptim_mup_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.

tag: ribosomal rna depletion strategy

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: Embryo_11 Endoderm [DNA_batch4_sc21]

status: Public on Mar 24 2023

type: SRA

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
Processing of the scChaRM-seq DNA data:Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the monkey reference genome mf5 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Genome_build: mf5
Supplementary_files_format_and_content: bedgraph files；RNAid_DNAid_celltype.csv
Assembly: mf5
Supplementary files format and content: bedgraph files;csv files

molecule: genomic DNA

organism: Macaca fascicularis

source_name: in vitro

growth_protocol: The creation of cynomolgus monkey embryos including oocyte retrieval, intracytoplasmic sperm injection, and pre-implantation embryo culture were performed as described by Yamasaki et al (Nakamura et al., 2016). Briefly, female cynomolgus monkeys 7-10 years old with a successful reproductive history were used for mature oocyte collection by super-ovulation with follicle-stimulation hormone. The day collected oocytes were artificially fertilized by sperm injection was designated as embryonic day (E) 0. When the embryos developed to E6-E7, embryos with an  expanded blastocoel (>75% volume of the embryo) were selected for further culture .

extract_protocol:
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were  dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
Single cells were individually picked into ice-cold lysis buffer under stereoscopic microscope. single cells were picked of each stage and then the subjected to construct scChaRM-seq library. The method of library construction was described in our recently published method (Yan et al., 2021). In brief, in vitro CpG methylation was performed by M.CviPI (New England Biolabs, NEB) supplemented with S-adenosyl-methionine (SAM;NEB) and terminated by adding RLT buffer (QIAGEN). Then the genome DNA and mRNA were separated by capturing mRNA with oligo(dT) primers conjugated beads (Invitrogen), the supernatant containing genomic DNA was transferred into another PCR tube to bisulfite conversion (Zymo Research) and DNA library construction using previously descried TAILS method (Gu et al., 2019). The captured mRNA was subjected correspondingly to cDNA synthesis, PCR amplification and library construction (Gu et al., 2019).

tag: cell line

value: in vitro

tag: cell type

value: Embryo

tag: genotype

value: WT

tag: time


title: Embryo_5 EPI [DNA_batch4_sc2]


title: ptim_mup_r2_s_o_v15

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

library_source: transcriptomic

molecule: total RNA

growth_protocol: Bacteria were grown according to their requirements. Overnight Cultures were diluted to OD600 0.05-0.07, growth was continued and cells were harvested in log-phase by centrifugation. Resulting pellet was shock-frozen in Dry ice/Ethanol bath and stored for RNA analysis

treatment_protocol: As for Chloramphenicol (CAM) treatment, Bacterial cells were incubated with Chloramphenicol (100µg/ml final) for 5 minutes at 37˚C with aeration and harvested at 4˚C on ice supplemented with Chloramphenicol (~100µg/ml final).   Mupirocin (MUP) was added to bacterial culture at a final concentration of 65µg/ml and incubated for 10 minutes at 37˚C with aeration.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Salt stress samples were generated as described in PMID: 28290514 with minor modifications Salt stress was initiated by mixing equal volumes of bacterial growth culture and 2M NaCl (~5.8% NaCl). Bacterial cells were exposed to salt stress for 10 minutes at room temperature and harvested by centrifugation.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Heat shock experiments were setup the following. Lactobacillus plantarum (ATCC 8014) growth culture was harvested by centrifugation and heat shock was induced by resuspending cell pellet in prewarmed broth media following 15-minute incubation at 60˚C.   To generate low nutrient samples, actively growing Lactobacillus plantarum (ATCC 8014) culture was harvested by centrifugation. Low nutrient stress was induced for 15 minutes beginning with excessive washing of the cell pellet with Low nutrient media (0.5x LB broth), followed by centrifugation. Washed cell pellet was resuspended in 0.5x LB broth, incubated at 37˚C for the remaining time.   Polyribosome fractions were generated as described in PMID: 27146487 with minor modifications. For short, exponentially grown bacterial cells were harvested by centrifugation (5 minutes) at 4˚C on ice supplemented with 100µg/ml Chloramphenicol. Lysis was done in 1xTN buffer (50mM TRIS/HCl pH 7.4,150mM NaCl, 1mM DTT, 100μg/ml CAM and Complete EDTA Free Protease inhibitor tablet) using glass beads and of vortexing (2minutes) followed by resting of sample on ice (5 minutes).  Vortexing/resting cycle was repeated two more times. Lysate was cleared by centrifugation at 1500g for 5 minutes at 4˚C. Resulting supernatant was loaded on to a 15-50% sucrose gradient with a 80% cushion and sedimentation was accomplished by ultracentrifugation for 90 minutes at 36,000rpm. Fractions were collected and A254 value was monitored. Subsequently, RNA was extracted from sucrose fractions by adding equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water followed by 2-minute vortexing and centrifugation. Aqueous phase was further cleaned up by the addition of Chloroform, vortexing and centrifugation. Resulting aqueous phase was sodium acetate-ethanol precipitated.

tag: treatment

tag: culture conditions

value: ptim_mup_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.

tag: library protocol


title: Embryo_6 Non-neural ectoderm [DNA_batch4_sc20]


title: ptim_ctr_r1_s_o_v15

value: Untreated

value: ptim_ctr_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.


title: ptim_ctr_r2_s_o_v15

value: ptim_ctr_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.


title: ptim_cam_r2_s_o_v15

value: 100ug/ml Chloramphenicol for 10 minutes at 37˚C

value: ptim_cam_r2 was anaerobically cultured in GAM Broth (HyServe) and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch4_sc25]


title: ptim_cam_r1_s_o_v15

value: ptim_cam_r1 was anaerobically cultured in GAM Broth (HyServe) and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Embryo_3 EVT [DNA_batch4_sc18]


title: Embryo_6 Non-neural ectoderm [DNA_batch4_sc19]


title: Secukinumab.W12.NL.1001008

type: RNA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

organism: Homo sapiens

source_name: psoriasis patient

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: disease state

value: psoriasis

tag: subject

value: Secukinumab

tag: timepoint

tag: tissue

value: NL

tag: specimen

value: Skin


title: Placebo.W52.LS.1001009

value: Placebo

value: LS


title: Placebo.BL.LS.1001006

value: BL


title: Placebo.BL.NL.1001006


title: Placebo.W12.LS.1001006


title: Embryo_7 Mesoderm [DNA_batch4_sc23]

value: in vitro


title: Placebo.W12.NL.1001006


title: pmer_mup_r2_s_o_v15

organism: Parabacteroides merdae

source_name: Liquid culture of Parabacter merdae (DSM 19495)

value: 65ug/ml Mupirocin incubated for 10 minutes at 37˚C

value: pmer_mup_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: Embryo_2 CTB [DNA_batch4_sc16]

value: Embryo

value: WT


title: pmer_mup_r1_s_o_v15

value: pmer_mup_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.


title: Embryo_1 EXMC [DNA_batch4_sc15]


title: Placebo.W52.NL.1001006


title: Embryo_3 EVT [DNA_batch4_sc14]


title: Embryo_6 Non-neural ectoderm [DNA_batch4_sc13]


title: Embryo_1 EXMC [DNA_batch4_sc12]


title: pmer_ctr_r2_s_o_v15

value: Untreated

value: pmer_ctr_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.


title: Embryo_2 CTB [DNA_batch4_sc11]


title: Placebo.W52.LS.1001006


title: pmer_ctr_r1_s_o_v15

value: pmer_ctr_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.


title: Embryo_6 Non-neural ectoderm [DNA_batch4_sc17]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch4_sc10]


title: Placebo.W52.LS.1001005

value: psoriasis


title: pmer_cam_r2_s_o_v15

value: 100ug/ml Chloramphenicol for 10 minutes at 37˚C

value: pmer_cam_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Embryo_2 CTB [DNA_batch4_sc1]


title: Placebo.BL.NL.1001005

value: NL

value: Skin


title: Embryo_2 CTB [DNA_batch4_sc22]


title: Embryo_10 PS and derivative [DNA_batch3_sc91]


title: Embryo_10 PS and derivative [DNA_batch3_sc94]


title: pmer_cam_r1_s_o_v15

value: pmer_cam_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Embryo_10 PS and derivative [DNA_batch3_sc92]


title: pcop_mup_r2_s_o_v15

organism: Segatella copri

source_name: Liquid culture of Prevotella copri (DSM 18205)

value: pcop_mup_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.


title: pcop_mup_r1_s_o_v15

value: pcop_mup_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior treatments and Mupirocin was added to culture for 10 minutes.


title: Embryo_10 PS and derivative [DNA_batch3_sc89]

value: in vitro


title: Embryo_10 PS and derivative [DNA_batch3_sc87]


title: Embryo_10 PS and derivative [DNA_batch3_sc86]


title: Embryo_10 PS and derivative [DNA_batch3_sc85]


title: Embryo_10 PS and derivative [DNA_batch3_sc81]


title: pcop_ctr_r2_s_o_v15

value: pcop_ctr_r2 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.


title: Embryo_10 PS and derivative [DNA_batch3_sc95]


title: pcop_ctr_r1_s_o_v15

value: pcop_ctr_r1 was anaerobically cultured in GAM Broth (HyServe) at 37˚C and split 24 hours prior harvesting.

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: Placebo.W52.NL.1001005

value: Placebo


title: Placebo.BL.LS.1001005

value: BL

value: LS


title: Embryo_10 PS and derivative [DNA_batch3_sc88]

value: Embryo

value: WT


title: pcop_cam_r2_s_o_v15

value: pcop_cam_r2 was anaerobically cultured in GAM Broth (HyServe)  at 37˚Cand split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Secukinumab.BL.NL.1001004

value: psoriasis

value: Secukinumab


title: pcop_cam_r1_s_o_v15

value: 100ug/ml Chloramphenicol for 10 minutes at 37˚C

value: pcop_cam_r1 was anaerobically cultured in GAM Broth (HyServe)  at 37˚Cand split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: Embryo_10 PS and derivative [DNA_batch3_sc75]


title: Placebo.W12.NL.1001005

value: NL

value: Skin


title: Embryo_10 PS and derivative [DNA_batch3_sc79]


title: Embryo_10 PS and derivative [DNA_batch3_sc8]


title: Embryo_10 PS and derivative [DNA_batch3_sc77]


title: Secukinumab.W52.LS.1001004


title: Embryo_10 PS and derivative [DNA_batch3_sc74]


title: Secukinumab.W12.NL.1001004


title: Embryo_10 PS and derivative [DNA_batch3_sc73]


title: Embryo_10 PS and derivative [DNA_batch3_sc76]


title: Embryo_10 PS and derivative [DNA_batch3_sc80]


title: Embryo_10 PS and derivative [DNA_batch3_sc72]


title: Embryo_10 PS and derivative [DNA_batch3_sc71]


title: Embryo_10 PS and derivative [DNA_batch3_sc70]


title: U87MG_siAUP1_2

city: Taipei

first: YAO FENG

last: LI

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Pathology

country: Taiwan

institute: National Defense Medical Center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

molecule: polyA RNA

source_name: U87MG, siAUP1

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using total RNA using TRIzol reagent (Invitrogen) and assessed its quality at 260/280 nm and 260/230 nm, and RIN ranged from 9.7 to 10.0
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics supplemented 100mM metformin with  in humidified atmosphere with 5% CO2 at 37C

value: glioblastoma

value: IDH mutant


title: U87MG_siAUP1_1


title: U87MG_siAUP1_3


title: Placebo.W12.LS.1001005


title: Secukinumab.BL.LS.1001004


title: Secukinumab.BL.LS.1001003


title: U87MG_control_3

source_name: U87MG, control

value: Scramble siRNA


title: Secukinumab.W52.NL.1001004


title: Embryo_10 PS and derivative [DNA_batch3_sc7]

value: in vitro


title: Secukinumab.W12.LS.1001004


title: Embryo_10 PS and derivative [DNA_batch3_sc67]


title: Embryo_10 PS and derivative [DNA_batch3_sc66]


title: U87MG_control_2


title: Embryo_10 PS and derivative [DNA_batch3_sc65]


title: Embryo_10 PS and derivative [DNA_batch3_sc63]


title: Embryo_10 PS and derivative [DNA_batch3_sc62]


title: Embryo_10 PS and derivative [DNA_batch3_sc64]


title: Bronchioalveolar organoids, SARS-CoV-2, cycloheximide 2

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq500 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.17 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: iPS cell-derived bronchioalveolar organoids

growth_protocol: Bronchioalveolar organoids differentiation were performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Thermo Fisher Scientific) supplemented with N2 (FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Thermo Fisher Scientific), ascorbic acid (50 μg/mL, STEMCELL Technologies), 1×Glutamax (Thermo Fisher Scientific), 1% monothioglycerol (FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin , 1×penicillin-streptomycin (Thermo Fisher Scientific). For endoderm induction (day 0-3), the SFD medium supplemented with 10 μM Y-27632 and 100 ng/mL recombinant Activin A (R&D systems),was used for 3 days. For anterior foregut endoderm induction (day 3-5), the SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (FUJIFILM Wako Pure Chemical) was used for 24 h, and then switched to the SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (REPROCELL) for 24 h. For lung progenitors induction (day 5-12), the resulting anterior foregut endoderm was cultured with the SFD medium supplemented with 3 μM CHIR99021 (FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (PeproTech), 10 ng/mL human FGF7 (PeproTech), 10 ng/mL human BMP4 (PeproTech), 20 ng/mL human EGF (peprotech), and all-trans retinoic acid (ATRA, Sigma-Aldrich) for 7 days. For bronchioalveolar organoids maturation (day 12-30), the cells were cultured in the SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA for 8 days. At then, the cells were cultured in the SFD medium containing 50 nM dexamethasone (Selleck), 0.1 mM 8-bromo-cAMP (Sigma-Aldrich), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (FUJIFILM Wako Pure Chemical) for 10 days.

extract_protocol:
Total RNA was isolated from human iPS-bronchioalveolar organoids using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Human iPS-bronchioalveolar organoids were infected with SARS-CoV-2 (0.1 MOI) in the presence or absence of cycloheximide.

value: bronchioalveolar organoids

value: wild type

value: SARS-CoV-2, cycloheximide

value: 4 dpi


title: Bronchioalveolar organoids, SARS-CoV-2, cycloheximide 3

value: iPS cell-derived bronchioalveolar organoids


title: Embryo_10 PS and derivative [DNA_batch3_sc61]

value: Embryo

value: WT


title: Embryo_10 PS and derivative [DNA_batch3_sc60]


title: Secukinumab.W52.LS.1001002

value: psoriasis

value: LS


title: Secukinumab.BL.NL.1001002

value: Secukinumab

value: BL


title: Embryo_10 PS and derivative [DNA_batch3_sc69]


title: Secukinumab.W52.NL.1001002

value: NL


title: Secukinumab.BL.NL.1001003

value: Skin


title: Secukinumab.W12.LS.1001002


title: U87MG_control_1

value: glioblastoma


title: Embryo_10 PS and derivative [DNA_batch3_sc59]


title: Secukinumab.W12.NL.1001002


title: Embryo_10 PS and derivative [DNA_batch3_sc58]


title: Bronchioalveolar organoids, mock, cycloheximide 3

value: mock, cycloheximide


title: Embryo_10 PS and derivative [DNA_batch3_sc57]


title: Embryo_10 PS and derivative [DNA_batch3_sc52]


title: Embryo_10 PS and derivative [DNA_batch3_sc55]


title: Embryo_10 PS and derivative [DNA_batch3_sc5]


title: Secukinumab.W12.LS.1001001


title: Embryo_10 PS and derivative [DNA_batch3_sc49]


title: Embryo_10 PS and derivative [DNA_batch3_sc48]


title: Placebo.BL.NL.1001009

value: Placebo


title: Bronchioalveolar organoids, mock, cycloheximide 1


title: Bronchioalveolar organoids, mock, cycloheximide 2


title: Bronchioalveolar organoids, SARS-CoV-2, no drug 3


title: Bronchioalveolar organoids, SARS-CoV-2, cycloheximide 1


title: Secukinumab.W52.NL.1001001


title: Embryo_10 PS and derivative [DNA_batch3_sc47]

value: in vitro


title: Embryo_10 PS and derivative [DNA_batch3_sc46]


title: Bronchioalveolar organoids, SARS-CoV-2, no drug 2

value: bronchioalveolar organoids


title: Secukinumab.W12.NL.1001001


title: Embryo_10 PS and derivative [DNA_batch3_sc45]


title: Bronchioalveolar organoids, SARS-CoV-2, no drug 1

value: wild type


title: Embryo_10 PS and derivative [DNA_batch3_sc44]


title: Embryo_10 PS and derivative [DNA_batch3_sc42]


title: Embryo_10 PS and derivative [DNA_batch3_sc43]


title: znf7d-3

city: Hangzhou

first: Jing

last: Bao

state: Zhejiang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital of Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000002035.6_GRCz11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GCF_000002035.6_GRCz11

organism: Danio rerio

source_name: whole  larvae

growth_protocol: Zebrafish embryos were collected and maintained in E3 medium in a 28.5 °C incubator

extract_protocol:
Total RNAs were isolated from a pool of 50 whole zebrafish larvae of homozygous mutants or WT at 7dpf using TRIzol Reagent (Invitrogen).
Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China)

value: whole  larvae

tag: development stage


title: znf7d-2


title: znf7d-1


title: Embryo_10 PS and derivative [DNA_batch3_sc40]


title: Secukinumab.BL.NL.1001001


title: Embryo_10 PS and derivative [DNA_batch3_sc4]


title: Bronchioalveolar organoids, mock, no drug 2

value: mock

value: 4 dpi


title: Bronchioalveolar organoids, mock, no drug 1

value: iPS cell-derived bronchioalveolar organoids


title: Embryo_10 PS and derivative [DNA_batch3_sc38]

value: Embryo

value: WT


title: Embryo_10 PS and derivative [DNA_batch3_sc37]


title: wt7d-2

value: wt


title: Embryo_10 PS and derivative [DNA_batch3_sc33]


title: Secukinumab.W52.LS.1001001

value: psoriasis

value: Secukinumab

value: LS


title: Embryo_10 PS and derivative [DNA_batch3_sc32]


title: Bronchioalveolar organoids, mock, no drug 3


title: Embryo_10 PS and derivative [DNA_batch3_sc31]


title: Embryo_10 PS and derivative [DNA_batch3_sc41]


title: Embryo_10 PS and derivative [DNA_batch3_sc29]


title: svtRNA1-2 KO rep3

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: chromatin-associated RNA-seq (ChrRNA-seq)
Reads were mapped to hg38 genome using STAR aligner  with following settings:  --readFilesCommand zcat --outFilterMultimapNmax 1
DESeq2 differential expression analysis (p-adj value < 0.001)
Predicting binding targets for svtRNA1-2 using up-regulated genes in vtRNA1-2KO condition (Miranda tool -sc 150 -en -15 -strict)
Create BigWig files from bam files (deeptools --outFileFormat bigwig --verbose --binSize 1)
Assembly: hg38 (Downloaded from GENCODE)
Supplementary files format and content: BigWig files

source_name: svtRNA1-2 KO

growth_protocol: All cells were grown in DMEM.

extract_protocol:
Cells were harvested from 15 cm dishes and lysed in HLB+N buffer (10mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40), and underlaid with HLB+NS buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10% sucrose), before centrifugation at 420g for 5 minutes. Nuclear pellets were then resuspended in NUN1 buffer (20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, 50% glycerol). Chromatin was extracted by addition of NUN2 buffer (20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% NP-40, 1M urea) on ice for 15 minutes with vortexing. Samples were centrifuged at 17,000g for 10 minutes and chromatin pellets collected. Chromatin was digested by the addition of Proteinase K and Turbo DNase (Thermo Fisher). RNA was extracted from the chromatin samples using TRIzol (Invitrogen) and chloroform extraction, followed by the Monarch® Total RNA Miniprep Kit (NEB) according to the manufacturer's instructions and eluted in water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: vtRNA1-2 knock-out was done using CRISPR-CAS12a

value: Immortalized human embryonic kidney cells

value: svtRNA1-2 KO

tag: molecule type

value: chromatin-associated RNA


title: svtRNA1-2 KO rep2


title: N_LN_KO_AB4193

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
RSEM.genes.expected_count.all_samples.txt
RSEM.genes.TPM.all_samples.txt

data_processing:
demutiplexed paired-end reads with bcl2fastq
Trimming, alignment, gene expression estimates were calculated using a containerized RNA-seek package on the Biowulf HPC.nih.gov
RNA-seek: https://github.com/OpenOmics/RNA-seek.git
rna-seek --mode slurm --genome /data/OpenOmics/references/rna-seek/mm39_M30/mm39_M30.json --star-2-pass-basic
ccbrpipeliner  4.0.6; STAR/2.7.6a;
Assembly: mm39_M30
Supplementary files format and content: raw counts, tab delim text, RSEM.genes.TPM.all_samples.txt
Supplementary files format and content: TPM normalized gene expression, tab delim text, RSEM.genes.expected_count.all_samples.txt

organism: Mus musculus

source_name: Lymph Node

extract_protocol:
RNAeasy kit with gDNA eliminator column
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
Paired-end sequencing was completed on an illumina NextSeq 500 system, running illumina NextSeq Control Software System Suite version 2.1.0 and RTA version 2.4.11.  The final library pool was sequenced via 2 x 76 bp run configuration using the product NextSeq 500/550 High Output Kit v2.5 (150 Cycles

value: Lymph Node

tag: rna sample id

value: CD4 T-cells

tag: genotype of original donor

value: Tnfrsf8 KO

value: Naive


title: N_LN_WT_AB4192


title: N_LN_KO_AB4195


title: Embryo_10 PS and derivative [DNA_batch3_sc27]

value: in vitro


title: wt7d-3

value: whole  larvae


title: Embryo_10 PS and derivative [DNA_batch3_sc35]


title: N_LN_KO_AB4191


title: svtRNA1-2 KO rep1


title: Embryo_10 PS and derivative [DNA_batch3_sc3]


title: N_LN_WT_AB4194


title: Embryo_10 PS and derivative [DNA_batch3_sc25]


title: Embryo_10 PS and derivative [DNA_batch3_sc24]


title: N_LN_WT_AB4190


title: Embryo_10 PS and derivative [DNA_batch3_sc30]


title: wt7d-1


title: Embryo_10 PS and derivative [DNA_batch3_sc26]


title: Embryo_10 PS and derivative [DNA_batch3_sc22]


title: Embryo_10 PS and derivative [DNA_batch3_sc28]


title: HEK293T WT rep2

source_name: HEK293T WT

value: Wild-Type


title: Embryo_10 PS and derivative [DNA_batch3_sc20]


title: N_LN_WT_AB4188


title: N_LN_KO_AB4189


title: HEK293T WT rep1


title: Embryo_10 PS and derivative [DNA_batch3_sc19]


title: Embryo_10 PS and derivative [DNA_batch3_sc2]


title: Embryo_10 PS and derivative [DNA_batch3_sc18]


title: ACT_LUNG_KO_AB4187

source_name: Lung (parenchyma)

value: Lung (parenchyma)

value: Mtb Activated


title: Embryo_5 EPI [DNA_batch3_sc17]

value: Embryo

value: WT


title: ACT_LUNG_WT_AB4186


title: Embryo_10 PS and derivative [DNA_batch3_sc15]


title: ACT_LUNG_KO_AB4185


title: Embryo_10 PS and derivative [DNA_batch3_sc16]


title: HEK293T WT rep3


title: DOXCM-2

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

description: circular RNA

data_processing:
After get the raw fastq files from sequencer, fastp software (v0.20.0) was used for adaptor-trimming and low quality reads removing., Then the clean reads were aligned to the Human reference genome (hg19) with STAR software (v2.5.1b).
DCC software (v0.4.4) was used to detect  circRNAs. circBase database was used to annotate the identified circRNAs.
The junction read counts were normalized by edgeR packages (v3.16.5), and differentially expressed circRNAs were also filtered by edgeR.
Genome_build: ucsc hg19
Supplementary_files_format_and_content: circRNA Expression Profiling

source_name: Left Ventricle

extract_protocol:
Heart were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.The ribo-zero-magnetic-kit (Epicentre) was used to remove ribosomal RNA from the samples. The samples were then incubated for 1 h at 40℃ with RNase R (Epicentre) to remove linear RNA.
CircRNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: developmentak stage

value: adult

tag: cumulative dox dose(mg/m2)


title: DOXCM-3

description: circular RNA


title: ACT_LUNG_KO_AB4183

tag: cell type


title: ACT_LUNG_WT_AB4184


title: control-3

description: circular RNA


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch3_sc12]

tag: cell line

tag: genotype


title: Embryo_10 PS and derivative [DNA_batch3_sc13]

tag: time


title: Embryo_10 PS and derivative [DNA_batch3_sc14]


title: ACT_LUNG_WT_AB4182

tag: treatment


title: Embryo_10 PS and derivative [DNA_batch3_sc10]


title: Embryo_10 PS and derivative [DNA_batch3_sc11]


title: Embryo_10 PS and derivative [DNA_batch3_sc1]


title: Embryo_10 PS and derivative [DNA_batch2_sc94]


title: control-1

description: circular RNA


title: Embryo_10 PS and derivative [DNA_batch2_sc93]


title: Embryo_10 PS and derivative [DNA_batch2_sc91]


title: ACT_LUNG_KO_AB4181


title: EP976

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 6

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq 1.8 software was used for base calling (for samples split between flowcells and later merged per run)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Mmusculus.UCSC.mm9.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse"
Assembly: mm9
Supplementary files format and content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

growth_protocol: Female BALB/cj mice had ovaries removed at 9 weeks of age.  Treatment conditions started 10 weeks after surgery.

extract_protocol:
RNeasy Mini kit
KAPA stranded polyA kit

treatment_protocol: PBDE combination was provided by diet, and 1 µg E2 was provided by injection

tag: mouse model

value: surgical menopausal (ovariectomized)

value: fourth mouse mammary gland without the lymph node


title: ACT_LUNG_WT_AB4180


title: Embryo_10 PS and derivative [DNA_batch2_sc9]


title: Embryo_10 PS and derivative [DNA_batch2_sc90]


title: DOXCM-1

description: circular RNA


title: Embryo_10 PS and derivative [DNA_batch2_sc89]


title: EP984

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 4


title: EP990

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 5


title: Embryo_10 PS and derivative [DNA_batch2_sc88]


title: Embryo_10 PS and derivative [DNA_batch2_sc85]


title: control-2

description: circular RNA


title: NEU_DEL_NI_01

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

description: single cell RNA sequencing analysis of infected or bystander (noninfected) neutrophils during M. marinum infection

data_processing:
Demultipexing and alignment of reads with CellRanger v2.1.1 for replicates 01 and v3.1.0 for replicates 02. Data is paired and pooled on 4 lanes.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Genome_build: mm10 (replicates 01) and mm10-2.1.0 (replicates 02)
Supplementary_files_format_and_content: tsv.gz & mtx.gz

source_name: Neutrophils

growth_protocol: Bacteria (WT and dRD1 M. marinum) were inoculated from frozen stocks and grown at 30°C in 7H9 culture medium until late log phase.

extract_protocol:
Two independent experiments were performed. For each experiment 14 to 15 tails (i.e. infected tissue) per group were collected, pooled and digested at two weeks post infection. Cell surface markers were stained with antibodies. Live infected neutrophils (CD45+Ly6G+CD11b+Wasabi+) or live uninfected neutrophils (CD45+Ly6G+CD11b+Wasabi-) were sorted by FACS in PBS supplemented with 1% BSA using a FACS ARIA Fusion (BD Biosciences).
Single cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223). Library quality control and quantification were performed using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems, KK4873) and the 2100 Bioanalyzer equipped with a High Sensitivity DNA kit (Agilent, 5067-4626).

treatment_protocol: C57Bl/6JRj female 8 weeks old mice were infected via tail vein injections with 5 x 10^7 bacteria per mouse, in a total volume of 200 µL.

tag: infection

value: Not infected

value: dRD1 M. marinum M-strain

tag: strain


title: EP980

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 3


title: Embryo_10 PS and derivative [DNA_batch2_sc84]


title: Embryo_10 PS and derivative [DNA_batch2_sc80]


title: EP971

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 2


title: Embryo_10 PS and derivative [DNA_batch2_sc83]


title: NEU_WT_INF_01

value: Infected

value: Wild-type M. marinum M-strain


title: Embryo_5 EPI [DNA_batch2_sc78]


title: NEU_WT_NI_01


title: Embryo_10 PS and derivative [DNA_batch2_sc8]


title: Embryo_1 EXMC [DNA_batch2_sc79]


title: EP953

description: RNA-Seq data, E2+PBDE treatment in Mouse Model, replicate 1


title: Embryo_10 PS and derivative [DNA_batch2_sc77]


title: Embryo_10 PS and derivative [DNA_batch2_sc75]


title: E966

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 6


title: Embryo_10 PS and derivative [DNA_batch2_sc76]


title: PTM6_scRNA-seq

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
BD Rhapsody WTA Analysis Pipeline (version 1.0) on SevenBridges Genomics online platform (SevenBridges) was used for alignment and sample de-multiplexing
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include UMI counts for each cell barcode and genes

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by a standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen tank until use.
Freshly frozen PBMCs were thawed in a water bath at 37oC for 1 min, transferred to a 50-ml tube, and ten volumes of warm RPMI 1640 medium with 10% FCS and 0.1mg/ml DNase I were added slowly, followed by centrifugation at 300g for 5 min. The cell pellet was collected and cell number and viability were determined using trypan blue on Luna-II automated cell counter (Logos Biosystems). Each PBMC sample was labelled with respective sample multiplexing antibody (Single-Cell multiplex kit - Human; BD Biosciences) and then up to 6 samples were pooled together at equal numbers of 10,000 cells to make up 60,000 cells in total and loaded on a microwell cartridge of the BD Rhapsody Express system (BD Biosciences). Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD, 633802).

tag: cohort

tag: disease state

tag: gender

value: male

tag: group

value: Corticosteroid treated

value: PBMC


title: PTM5c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc74]

value: in vitro


title: Embryo_10 PS and derivative [DNA_batch2_sc73]


title: E959

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 5

tag: tissue


title: PTM5b_scRNA-seq


title: NEU_DEL_INF_01


title: Embryo_10 PS and derivative [DNA_batch2_sc70]


title: Embryo_10 PS and derivative [DNA_batch2_sc7]


title: E970

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 4


title: E982

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 3


title: PTM5a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc69]


title: Embryo_10 PS and derivative [DNA_batch2_sc68]


title: PTM5_scRNA-seq


title: E981.2

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 2


title: Embryo_10 PS and derivative [DNA_batch2_sc67]


title: E957

description: RNA-Seq data, E2 treatment in Mouse Model, replicate 1


title: Embryo_10 PS and derivative [DNA_batch2_sc65]


title: P955

description: RNA-Seq data, PBDE treatment in Mouse Model, replicate 3

value: PBDE


title: Embryo_10 PS and derivative [DNA_batch2_sc63]


title: Embryo_10 PS and derivative [DNA_batch2_sc66]


title: Embryo_5 EPI [DNA_batch2_sc62]


title: PTM4b_scRNA-seq


title: P960

description: RNA-Seq data, PBDE treatment in Mouse Model, replicate 2


title: Embryo_10 PS and derivative [DNA_batch2_sc61]


title: PTM4a_scRNA-seq


title: PTM4c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc6]


title: Embryo_10 PS and derivative [DNA_batch2_sc59]


title: PTM4_scRNA-seq


title: P952

description: RNA-Seq data, PBDE treatment in Mouse Model, replicate 1


title: Embryo_10 PS and derivative [DNA_batch2_sc58]


title: PTM3e_scRNA-seq


title: C989

description: RNA-Seq data, Control treatment in Mouse Model, replicate 3

value: Control


title: C963

description: RNA-Seq data, Control treatment in Mouse Model, replicate 2


title: PTM3d_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc54]


title: Embryo_10 PS and derivative [DNA_batch2_sc57]


title: Embryo_10 PS and derivative [DNA_batch2_sc55]


title: Embryo_10 PS and derivative [DNA_batch2_sc51]


title: Embryo_10 PS and derivative [DNA_batch2_sc50]


title: C975

description: RNA-Seq data, Control treatment in Mouse Model, replicate 1


title: PTM3c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc5]


title: Embryo_10 PS and derivative [DNA_batch2_sc60]


title: PTM3a_scRNA-seq


title: Embryo_5 EPI [DNA_batch2_sc47]


title: PTM3b_scRNA-seq


title: sepcv133T9

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.7) and multiqc (v1.6).
Alignment to the human genome using STAR (v2.6.0a)
Read count assessments using htseq-count (v0.11.0)
Assembly: GRCh38.92
Supplementary files format and content: count files, which are text files with counts per gene for each sample

source_name: Whole Blood

extract_protocol:
2.5mL of whole blood was collected into PAXgene Blood RNA tubes (BD Biosciences; San Jose, CA, USA) and total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen; Germantown, MD, USA). Samples with RNA Integrity Numbers less than 6.5 were discarded. Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Ipswich, USA).
cDNA libraries were prepared using the KAPA Total RNA HyperPrep Kit (Roche; Basel, Switzerland) for Illumina sequencing.

value: Whole Blood

tag: age

tag: Sex

value: M

tag: sequencing run

tag: mortality

value: Survived

tag: covid

value: Negative


title: Embryo_10 PS and derivative [DNA_batch2_sc46]

tag: cell line

tag: cell type

value: Embryo

value: WT


title: PTM3_scRNA-seq


title: sepcv133T1


title: Embryo_10 PS and derivative [DNA_batch2_sc40]

tag: genotype

tag: time


title: sepcv132T9

value: F

value: Positive


title: PTM2c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc4]


title: Embryo_10 PS and derivative [DNA_batch2_sc45]


title: Embryo_10 PS and derivative [DNA_batch2_sc38]


title: PTM2b_scRNA-seq


title: Secukinumab.BL.LS.1001001

value: psoriasis

tag: subject

tag: treatment

value: Secukinumab

tag: timepoint

value: BL

value: LS

tag: specimen

value: Skin


title: Embryo_10 PS and derivative [DNA_batch2_sc39]


title: sepcv132T0


title: Embryo_10 PS and derivative [DNA_batch2_sc48]


title: sepcv127T11


title: Embryo_10 PS and derivative [DNA_batch2_sc35]


title: Embryo_10 PS and derivative [DNA_batch2_sc36]


title: PTM2a_scRNA-seq

tag: cohort

tag: disease state

value: male

value: Corticosteroid treated

value: PBMC


title: sepcv127T1


title: Embryo_10 PS and derivative [DNA_batch2_sc34]

value: in vitro


title: PTM2_scRNA-seq

tag: gender

tag: group


title: PTM1c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc32]


title: PTM1b_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc33]


title: Embryo_10 PS and derivative [DNA_batch2_sc30]


title: Embryo_10 PS and derivative [DNA_batch2_sc3]


title: sepcv118T10

tag: tissue

value: Whole Blood

tag: age


title: Embryo_10 PS and derivative [DNA_batch2_sc31]


title: PTM1a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc28]


title: Embryo_10 PS and derivative [DNA_batch2_sc37]


title: sepcv118T1

tag: Sex

tag: sequencing run


title: Embryo_10 PS and derivative [DNA_batch2_sc27]


title: Embryo_10 PS and derivative [DNA_batch2_sc26]


title: sepcv117T11

value: M

tag: mortality

tag: covid


title: sepcv123T10

value: Survived


title: sepcv117T1

value: Negative


title: PTFnb_scRNA-seq

value: female

tag: cell type


title: Embryo_10 PS and derivative [DNA_batch2_sc22]

tag: cell line

value: Embryo

tag: genotype

value: WT


title: Embryo_10 PS and derivative [DNA_batch2_sc23]

tag: time


title: sepcv116T9

value: Positive


title: Embryo_10 PS and derivative [DNA_batch2_sc25]


title: PTFn_scRNA-seq


title: sepcv123T1


title: PTFna_scRNA-seq


title: Embryo_5 EPI [DNA_batch2_sc2]


title: sepcv116T1


title: Embryo_10 PS and derivative [DNA_batch2_sc21]


title: Embryo_10 PS and derivative [DNA_batch2_sc29]


title: sepcv109T2


title: Embryo_10 PS and derivative [DNA_batch2_sc19]


title: Embryo_10 PS and derivative [DNA_batch2_sc18]


title: Embryo_10 PS and derivative [DNA_batch2_sc15]


title: sepcv109T11


title: Embryo_1 EXMC [DNA_batch2_sc16]


title: PTF6_scRNA-seq


title: PTF5e_scRNA-seq


title: PTM1_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc14]


title: Embryo_1 EXMC [DNA_batch2_sc13]


title: sepcv102T10

value: Deceased


title: PTF5d_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc12]


title: sepcv102T1


title: Embryo_10 PS and derivative [DNA_batch2_sc11]


title: PTF5c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch2_sc20]


title: sepcv101T10

value: F


title: PTF6a_scRNA-seq


title: PTF5b_scRNA-seq


title: PAC-seq U1 AMO Replicate 3

city: Boston

first: Claudia

middle: A

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

description:
220217_M2_SpikeAvg_Norm_PACseq_U1_F.bedGraph
220217_M2_SpikeAvg_Norm_PACseq_U1_R.bedGraph

data_processing:
PAC-seq libraries were processed as described in Routh et al., 2017, with the following modifications: First, trimmed and filtered reads were mapped to the Drosophila genome (dm6) using HISAT2. Reads not mapping to the spike genome were aligned to the mouse genome (mm10) using HISAT2.
For final read processing, a minimum of 5 non-primer/non-template As was required for each unique poly(A) tail and a read count filter per nucleotide position was not applied.
Assembly: mm10
Supplementary files format and content: bedGraph
Library strategy: PAC-seq

source_name: F121-9 wt mESCs

growth_protocol: mESCs were cultured on gelatin in KnockOut DMEM (ThermoFisher, 10829018), supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% b-ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021) mESCs were fed daily and passaged every two days. mESCs were cultured at 37°C with 5% CO2.

extract_protocol:
For SCR and U1 AMO conditions, libraries were constructed from 250 ng of enriched 4sU-labelled RNA (as described under TT-seq extraction protocol). For untreated mESC, siNT and siRRP40 conditions, 1 μg of total RNA (as described under RNA-seq extraction protocol) was used for library construction.
PAC-seq libraries were constructed using the PolyA-ClickSeq Library Kit (ClickSeq Technologies)

treatment_protocol: See individual samples.

value: F121-9 wt mESCs

value: Mouse embryonic stem cells

value: F121-9 mESCs with a fluorescent splicing reporter system as described in Vlaming et al., 2022

tag: treatment

value: 20uM U1 AMO, 4 hours.


title: PAC-seq U1 AMO Replicate 1


title: sepcv101T1


title: Embryo_10 PS and derivative [DNA_batch2_sc1]

source_name: in vitro


title: PTF5a_scRNA-seq

value: Corticosteroid treated


title: PAC-seq SCR AMO Replicate 3

description:
220217_M2_SpikeAvg_Norm_PACseq_SCR_F.bedGraph
220217_M2_SpikeAvg_Norm_PACseq_SCR_R.bedGraph

value: 20uM SCR AMO, 4 hours.


title: PTF5_scRNA-seq

value: PBMC


title: Embryo_1 EXMC [DNA_batch1_sc96]

value: in vitro


title: sepcv099T10

value: Whole Blood

value: M


title: PAC-seq SCR AMO Replicate 1


title: sepcv099T1

value: Survived


title: Embryo_4 STB [DNA_batch1_sc94]


title: Embryo_1 EXMC [DNA_batch1_sc95]


title: sepcv096T10

value: Negative


title: PTF4a_scRNA-seq

value: female


title: sepcv096T0


title: PTF4b_scRNA-seq


title: PAC-seq U1 AMO Replicate 2


title: Embryo_3 EVT [DNA_batch1_sc93]

value: Embryo

value: WT


title: PTF4_scRNA-seq


title: sepcv095T10

value: Positive


title: Embryo_10 PS and derivative [DNA_batch2_sc10]


title: PTF3e_scRNA-seq


title: sepcv095T0

value: F


title: AML S21

city: Prague

first: Michal

last: Hensler

state: Prague 7

address: Jankovcova 1518/2

country: Czech Republic

institute: Sotio Biotech a.s.

data_processing:
All RNA-seq data were mapped onto indexed genome using STAR 2.7.0c
Adaptors were soft-clipped during the mapping procedure
Mapped reads were counted using program featureCounts
Read files were mapped onto human genome version hg38/GRCh38.p13.
Assembly: hg38/GRCh38.p13
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

source_name: BLOOD

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep and NEBNext Poly(A) mRNA magnetic isolation module.

value: AML

value: BLOOD

value: treatment naive patients


title: Embryo_1 EXMC [DNA_batch1_sc91]


title: AML S22


title: AML S23


title: PTF3c_scRNA-seq


title: PTF3d_scRNA-seq


title: PAC-seq SCR AMO Replicate 2

value: F121-9 wt mESCs

value: Mouse embryonic stem cells

value: F121-9 mESCs with a fluorescent splicing reporter system as described in Vlaming et al., 2022


title: AML S20

value: PBMC


title: AML S24


title: sepcv074T7


title: sepcv072T7


title: PTF3b_scRNA-seq

value: Corticosteroid treated


title: AML S19


title: sepcv063T7

value: Whole Blood

value: Deceased


title: PTF3a_scRNA-seq


title: Embryo_6 Non-neural ectoderm [DNA_batch1_sc89]

value: in vitro


title: AML S18


title: sepcv060T7

value: Survived

value: Negative


title: AML S17


title: PTF3_scRNA-seq

value: female


title: Embryo_2 CTB [DNA_batch1_sc88]

value: Embryo

value: WT


title: Embryo_2 CTB [DNA_batch1_sc92]


title: sepcv059T7

value: M

value: Positive


title: sepcv056T7


title: PTF2e_scRNA-seq


title: AML S16

value: AML

value: BLOOD


title: Embryo_4 STB [DNA_batch1_sc90]


title: Embryo_6 Non-neural ectoderm [DNA_batch1_sc86]


title: PTF2d_scRNA-seq


title: sepcv055T7


title: AML S14

value: treatment naive patients


title: Embryo_10 PS and derivative [DNA_batch1_sc9]


title: PTF2c_scRNA-seq


title: Embryo_1 EXMC [DNA_batch1_sc85]


title: sepcv054T7


title: sepcv053T7


title: Embryo_1 EXMC [DNA_batch1_sc84]


title: AML S12


title: AML S13


title: PTF2b_scRNA-seq


title: sepcv050T7


title: Embryo_3 EVT [DNA_batch1_sc83]


title: Embryo_2 CTB [DNA_batch1_sc82]


title: AML S11


title: PTF2_scRNA-seq


title: PTF1e_scRNA-seq


title: Embryo_6 Non-neural ectoderm [DNA_batch1_sc87]


title: sepcv049T7


title: AML S10


title: sepcv048T7

value: F


title: AML S15


title: AML S9


title: Embryo_1 EXMC [DNA_batch1_sc81]


title: Embryo_2 CTB [DNA_batch1_sc80]


title: sepcv047T7


title: AML S8


title: PTF1c_scRNA-seq


title: AML S7


title: PTF1b_scRNA-seq


title: PTF2a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc79]


title: sepcv041T1


title: Embryo_10 PS and derivative [DNA_batch1_sc8]


title: sepcv041T7


title: Embryo_10 PS and derivative [DNA_batch1_sc77]


title: PTF1a_scRNA-seq


title: AML S5


title: Embryo_10 PS and derivative [DNA_batch1_sc78]


title: sepcv039T8


title: PTF1d_scRNA-seq


title: PSM6c_scRNA-seq

value: male

value: critical


title: AML S6

value: PBMC


title: sepcv033T7

value: Whole Blood


title: PSM6b_scRNA-seq


title: sepcv036T7


title: Embryo_10 PS and derivative [DNA_batch1_sc74]


title: AML S3


title: AML S2


title: sepcv032T7


title: Embryo_10 PS and derivative [DNA_batch1_sc75]


title: sepcv024T6


title: Embryo_10 PS and derivative [DNA_batch1_sc73]


title: PSM5b_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc72]


title: sepcv024T0


title: PTF1_scRNA-seq

value: Corticosteroid treated


title: sepcv022T7


title: Embryo_10 PS and derivative [DNA_batch1_sc71]

value: in vitro


title: AML S1


title: PSM5a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc70]


title: PSM4c_scRNA-seq


title: sepcv020T3

value: Survived


title: AML S4


title: Experiment 3, scRNAseq [GEX]

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing .fastq files were used as input into the read mapping and counting software, CellRanger v4.0, developed by 10X Genomics, Inc. (Pleasanton, CA, USA). The output filtered_feature_bc_matrix folder, which contains the barcodes after cell-calling filtration, was used for downstream analyses.
The library Seurat in Bioconductor R and custom code were used for all analyses. Data were pre-processed by removing control cells (hashed with TotalSeq™-B0255 antibody) that were not needed for these analyses. The data-driven thresholds for identifying cells positive for a hashing antibody were identified using the mixture model rule. Bad quality cells were removed based on a large percentage of reads mapping to mitochondria genes. The data-driven thresholds for removal of these cells were identified using the interquartile rule. The remaining data were assessed for the presence of droplets that contained more than one cell, based on presence of more than one hash: TotalSeq™-B0252, TotalSeq™-B0253 and TotalSeq™-B0254. “Cells” with more than one hash called positive by the mixture model rule were removed from the analysis. Cells that did not have any hashes were excluded from the analysis of differential gene expression.
Differentially expressed genes between cells that were negative or positive for HIV RNA were identified using FindMarker function in the library Seurat. This analysis was conducted for each cell subset independently: cells that divided many times (CFSElow and hashed with TotalSeq™-B0252); cells that divide a few times (CFSEmed and hashed with TotalSeq™-B0253), and non-dividing cells (CFSEhigh and hashed with TotalSeq™-B0254). Two populations of HIV-positive cells were detected, which formed two distinct peaks: cells with high levels of HIV RNA and cells with low levels of HIV RNA. The threshold for these populations was identified using the mixture model rule. Analysis of differential gene expression was conducted separately for cells with high levels of HIV RNA and cells with low levels of HIV RNA, compared to HIV-negative cells.
Assembly: The Genome Reference Consortium Human Reference 38 combined with HIV genome reference.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Cells were stained with Aqua live/dead stain (Thermo Fisher, Inc., Waltham, MA, USA), and live cells were sorted using FACS Aria or the Sony MA900 Multi-Application cell sorter to separate live cells with robust (CFSElow), moderate (CFSEmed) and no response (CFSEhigh) to TCR stimulus. CFSElow, CFSEmed and CFSEhigh cells were hashed with TotalSeq™-B0252, TotalSeq™-B0253 and TotalSeq™-B0254 antibodies (Biolegend, Inc., San Diego, CA, USA), respectively. CFSEhigh population was stained for cell maturation markers CD45RA (TotalSeq™-B0063) and CD62L (TotalSeq™-B0147) and an early activation marker CD69 (TotalSeq™-B0146). In experiments 2 and 3, a small aliquot of control cells from CFSEmed population was hashed with TotalSeq™-B0255 antibody and stained with isotype controls TotalSeq™-B0090 and TotalSeq™-B0092. Cell hashing antibodies were diluted 1:8; other antibodies were used undiluted. Antibody staining was performed per Biolegend’s protocols. After antibody staining, the cells were mixed back together, 10,000 from each population, and 12,000 total cells were loaded into the Chromium Controller, aiming to achieve the targeted recovery of 10,000 cells in the scRNA-Seq experiment.
Reverse transcription to generate cDNA and library preparation for scRNA-Seq were conducted per the manufacturer’s instructions (10X Genomics, Inc., Pleasanton, CA, USA). For library preparation, 3’ gene expression and 3’ feature barcoding library kits (v3) were used. Briefly, CD4+ T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reversed transcribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Sequencing files generated from the gene expression libraries were named with an abbreviation GEX; sequencing files generated from the feature barcoding libraries were named with an abbreviation FBC.

value: Primary CD4+ T cells

value: Peripheral blood

tag: subject status

value: HIV-seronegative blood donor

tag: library type

value: gene expression library


title: Experiment 3, scRNAseq [FBC]

description: 10x Genomics

value: feature barcoding library


title: PSM4b_scRNA-seq

tag: cohort


title: sepcv020T10

value: M

value: Positive


title: PSM6a_scRNA-seq

tag: disease state


title: Experiment 2, scRNAseq [GEX]

description: 10x Genomics


title: PSM4a_scRNA-seq

tag: gender


title: sepcv019T7

value: Negative


title: Experiment 2, scRNAseq [FBC]

description: 10x Genomics


title: PSM3c_scRNA-seq

tag: group


title: Embryo_10 PS and derivative [DNA_batch1_sc68]

value: Embryo

value: WT


title: sepcv016T7

tag: tissue

value: Deceased


title: PSM3b_scRNA-seq

value: male

value: critical


title: Experiment 1, scRNAseq [FBC]

description: 10x Genomics


title: PSM3a_scRNA-seq

value: PBMC


title: sepcv013T7

value: Whole Blood

tag: age


title: sepcv012T7

tag: Sex


title: PSM2c_scRNA-seq


title: sepcv009T7

value: F

tag: sequencing run


title: Experiment 1, scRNAseq [GEX]

description: 10x Genomics


title: Embryo_10 PS and derivative [DNA_batch1_sc7]

value: in vitro


title: WT HEK293T PRO-seq Replicate 3

description:
220131_NTC_293T_WT_PROseq_3end_hg38_N4_CAM_F.bedGraph
220131_NTC_293T_WT_PROseq_3end_hg38_N4_CAM_R.bedGraph

data_processing:
mESC libraries were mapped as follows: using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 41 bp per mate and read pairs with a minimum average base quality score of 20 were retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm6) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (mm10, using Bowtie 1.2.2 options -v 2 --best).
For HEK293T libraries, the following mapping pipeline was used: Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools. Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1 --match-read-wildcards -m 26). The UMI length was trimmed off the end of both reads to prevent read-through into the mate’s UMI, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq (https://github.com/lh3/seqtk), to preserve a single mate orientation during alignment.
The paired end reads were then mapped to a combined genome index, including both the spike (dm6) and primary (hg38) genomes, using bowtie2. Properly paired reads were retained. These read pairs were then separated based on the genome (i.e., spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated using UMI-tools.
For all libraries, reads mapping to the reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl) that counts each read once at the exact 3’ end of the nascent RNA. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
BedGraphs were normalized using the normalize_bedGraph custom script. For libraries generated from control mESCs and HEK293Ts, no further normalization was performed. For libraries generated under SCR or U1 AMO conditions, we observed a consistent increase in reads mapping to the fly genome (dm6) after U1 inhibition (Average ratio of U1 AMO / SCR AMO = 1.34), indicating a global decrease in RNAPII transcription in U1 AMO cells compared to SCR AMO control. Accordingly, the average ratio of reads mapping to the spike genome between U1 and SCR AMO conditions was used to generate spike normalization factors
Combined bedGraphs were generated by summing counts per nucleotide across replicates for each condition (bedgraphs2stdBedgraph).
Assembly: mm10 (mESC); hg38 (HEK293T)
Supplementary files format and content: bedGraph
Library strategy: PRO-seq

molecule: nuclear RNA

source_name: embryonic kidney

growth_protocol: mESCs were cultured on gelatin in KnockOut DMEM (ThermoFisher, 10829018), supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% b-ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021) mESCs were fed daily and passaged every two days. HEK293Ts were cultured in DMEM (VWR, 45000-312) with 10% FBS (Thermo, 1600044). mESCs and HEK293Ts were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were permeabilized as in Reimer et al. 2021; run-ons were performed with biotinylated NTPs and then purified.
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

treatment_protocol: See individual samples

value: embryonic kidney


title: PSM2a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc69]


title: WT HEK293T PRO-seq Replicate 4


title: WT HEK293T PRO-seq Replicate 2


title: PSM2b_scRNA-seq


title: WT HEK293T PRO-seq Replicate 1


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch1_sc65]


title: Embryo_10 PS and derivative [DNA_batch1_sc64]


title: Embryo_5 EPI [DNA_batch1_sc66]


title: sepcv002T7

tag: mortality

value: Survived


title: Embryo_10 PS and derivative [DNA_batch1_sc67]


title: Embryo_10 PS and derivative [DNA_batch1_sc62]


title: sepcv001T7

tag: covid


title: Embryo_5 EPI [DNA_batch1_sc61]

tag: cell type


title: PSM1b_scRNA-seq


title: PSM1c_scRNA-seq


title: HSC-3-FIN56

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

institute: National Yang Ming Chiao Tung University

data_processing:
Reads were trimmed and clipped for quality control in AfterQC v0.9.7.
Read quality was checked for each sample using FastQC v0.11.7.
High-quality reads were then imported into STAR v2.6.1a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.1 for expected counts, FPKM and TPM estimation.
Expected counts table was extracted from each RSEM output .gene.results file.
Expected counts table was imported into the DESeq2 v1.26.0 for rlog transformation.
Genome_build: hg38, GRCh38.94
Supplementary_files_format_and_content: Tab-delimited text file for expected counts of sample.  Tab-delimited text file for FPKM of sample.  Tab-delimited text file for TPM of sample.  Tab-delimited text file for rlog of sample.

source_name: HNSCC cell line HSC-3

growth_protocol: DMEM medium with 5% FBS , 1% P/S

extract_protocol:
Assay Method: Qubit fluorometer with Quant-iT RNA BR assay kit
Sample Prep. Kit : Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase

treatment_protocol: Ferroptosis inducer FIN56 1uM treated 48hrs, and collect RNA by Trizol.

tag: cell line

value: FIN56 1uM,48hrs


title: WT HEK293T TT-seq Replicate 4

description:
220203_CAM_293T_WT_TTseq_20min_hg38_N4_F.bedGraph
220203_CAM_293T_WT_TTseq_20min_hg38_N4_R.bedGraph

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 120 bp per mate and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the dm6 version of the Drosophila genome using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mouse (mm10) or human (hg38) using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.  Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.
BedGraphs were normalized using the normalize_bedGraph custom script. For libraries generated from untreated mESCs and HEK293Ts, no further normalization was performed. For libraries generated under SCR or U1 AMO conditions: We observed a consistent increase in reads mapping to the fly genome (dm6) after U1 inhibition (Average ratio of U1 AMO / SCR AMO = 2.1), indicating a global decrease in RNA synthesis in U1 AMO cells compared to the SCR AMO control. Accordingly, the average ratio of reads mapping to the spike genome between U1 and SCR AMO conditions was used to generate spike normalization factors
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
Assembly: mm10 (mESC); hg38 (HEK293T)
Supplementary files format and content: bedGraph
Library strategy: TT-seq

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded total RNA kit using the manufacturer's protocol.

treatment_protocol: See individual samples. Cells were labeled with 4sU for the final 20 minutes.

tag: genotype


title: WT HEK293T TT-seq Replicate 3


title: Embryo_10 PS and derivative [DNA_batch1_sc58]

first: Fan

last: Guo

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Processing of the scChaRM-seq DNA data:Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the monkey reference genome mf5 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Genome_build: mf5
Supplementary_files_format_and_content: bedgraph files；RNAid_DNAid_celltype.csv
Assembly: mf5
Supplementary files format and content: bedgraph files;csv files

extract_protocol:
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were  dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
Single cells were individually picked into ice-cold lysis buffer under stereoscopic microscope. single cells were picked of each stage and then the subjected to construct scChaRM-seq library. The method of library construction was described in our recently published method (Yan et al., 2021). In brief, in vitro CpG methylation was performed by M.CviPI (New England Biolabs, NEB) supplemented with S-adenosyl-methionine (SAM;NEB) and terminated by adding RLT buffer (QIAGEN). Then the genome DNA and mRNA were separated by capturing mRNA with oligo(dT) primers conjugated beads (Invitrogen), the supernatant containing genomic DNA was transferred into another PCR tube to bisulfite conversion (Zymo Research) and DNA library construction using previously descried TAILS method (Gu et al., 2019). The captured mRNA was subjected correspondingly to cDNA synthesis, PCR amplification and library construction (Gu et al., 2019).

tag: time


title: WT HEK293T TT-seq Replicate 2

tag: treatment


title: PSM1a_scRNA-seq


title: HSC-3-DMSO


title: sepcv008T7


title: PSF6b_scRNA-seq

value: female


title: Embryo_10 PS and derivative [DNA_batch1_sc57]


title: spcc-6803_hs_r1_s_r_v2

first: Vicent

last: Pelechano

institute: ScilifeLab - Karolinska Institutet

data_processing:
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Genome_build: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns. Those correspond to the following NCBI accessions and builds: G-bamy (Bacillus amyloliquefaciens: GCF_000196735.1), G-bsub (Bacillus subtilis: GCF_000009045.1), G-cvib (Caulobacter vibrioides/crescentus: GCF_000006905.1), G-ecol (Escherichia coli: GCF_000005845.2), G-spcc (Synechocystis sp. PCC 6803: GCF_000009725.1), G-lpla (Lactobacillus plantarum: GCF_000203855.3), G-lreu (Lactobacillus reuteriGCF_000016825.1), G-zymo (mix of the following genomes [Bacillus subtilis: GCF_000009045.1, Enterococcus faecalis: GCF_000007785.1, Escherichia coli: GCF_000005845.2, Lactobacillus fermentum: GCF_000010145.1, Listeria monocytogenes: GCF_000196035.1, Pseudomonas aeruginosa: GCF_000006765.1, Salmonella enterica: GCF_000006945.2, Staphylococcus aureus: GCF_000013425.1]), G-46genera (genomes from 46 genera listed in the Supplementary file).
Genome_build: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10). See details in the supplementary file "46genera.xls". In Brief: Akkermansia muciniphila ATCC BAA-835 (GCF_000020225.1); Alistipes finegoldii DSM 17242 (GCF_000265365.1); Alistipes obesi (GCF_000311925.1); Alistipes putredinis DSM 17216 (GCF_000154465.1); Alistipes shahii WAL 8301 (GCF_000210575.1); Anaerobutyricum hallii DSM 3353 (GCF_000173975.1); Atopobium vaginae DSM 15829 (GCF_000159235.2); Bacillus amyloliquefaciens DSM 7 = ATCC 23350 (GCF_000196735.1); Bacillus subtilis subsp. subtilis str. 168 (GCF_000009045.1); Bacillus subtilis subsp. subtilis str. 168 (GCF_000009045.1); Bacteroides caccae (GCF_002222615.2); Bacteroides cellulosilyticus (GCF_001318345.1); Bacteroides coprocola DSM 17136 (GCF_000154845.1); Bacteroides coprophilus DSM 18228 = JCM 13818 (GCF_000157915.1); Bacteroides faecichinchillae JCM 17102 (GCF_000614145.1); Bacteroides fluxus YIT 12057 (GCF_000195635.1); Bacteroides fragilis YCH46 (GCF_000009925.1); Bacteroides ovatus (GCF_001314995.1); Bacteroides plebeius DSM 17135 (GCF_000187895.1); Bacteroides salanitronis DSM 18170 (GCF_000190575.1); Bacteroides salyersiae WAL 10018 = DSM 18765 = JCM 12988 (GCF_000381365.1); Bacteroides stercoris ATCC 43183 (GCF_000154525.1); Bacteroides thetaiotaomicron VPI-5482 (GCF_000011065.1); Bacteroides uniformis ATCC 8492 (GCF_000154205.1); Bilophila wadsworthia ATCC 49260 (GCF_000701705.1); Caulobacter vibrioides CB15 (GCF_000006905.1); Clostridium phoceensis (GCF_001244495.1); Collinsella aerofaciens ATCC 25986 (GCF_000169035.1); Coprobacter fastidiosus NSB1 (GCF_000473955.1); Coprococcus comes ATCC 27758 (GCF_000155875.1); Culturomica massiliensis (GCF_900091655.1); Desulfovibrio fairfieldensis (GCF_001553605.1); Dorea formicigenerans ATCC 27755 (GCF_000169235.1); Dorea longicatena DSM 13814 (GCF_000154065.1); Enterococcus faecalis V583 (GCF_000007785.1); [Clostridium] innocuum 2959 (GCF_000371425.1); [Clostridium] saccharogumia DSM 17460 (GCF_000686665.1); Escherichia coli str. K-12 substr. MG1655 (GCF_000005845.2); Escherichia coli str. K-12 substr. MG1655 (GCF_000005845.2); Eubacterium ventriosum ATCC 27560 (GCF_000153885.1); Faecalibacterium prausnitzii A2-165 (GCF_000162015.1); Flavobacterium johnsoniae UW101 (GCF_000016645.1); Flavobacterium saccharophilum (GCF_900142735.1); Fusicatenibacter saccharivorans (GCF_001405555.1); Gardnerella vaginalis 409-05 (GCF_000025205.1); Synechocystis sp. PCC 6803 (cyanobacteria) (GCF_000009725.1); Gemmiger formicilis (GCF_900167555.1); Intestinimonas butyriciproducens (GCF_001454945.1); Lactobacillus plantarum WCFS1 (GCF_000203855.3); Lactobacillus reuteri DSM 20016 (GCF_000016825.1); Lactobacillus crispatus ST1 (GCF_000091765.1); Lactobacillus iners DSM 13335 (GCF_000160875.1); Lactobacillus fermentum IFO 3956 (GCF_000010145.1); Lactococcus lactis subsp. lactis Il140 (GCF_000006865.1); Lacunisphaera limnophila (GCF_001746835.1); Listeria monocytogenes EGD-e (GCF_000196035.1); Mediterranea massiliensis (GCF_900128475.1); Megasphaera genomosp. type_1 str. 28L (GCF_000177555.1); Microbacterium barkeri 2011-R4 (GCF_000299315.2); Mucilaginibacter gossypiicola (GCF_900110105.1); Odoribacter splanchnicus DSM 20712 (GCF_000190535.1); Parabacteroides distasonis ATCC 8503 (GCF_000012845.1); Parabacteroides goldsteinii DSM 19448 = WAL 12034 (GCF_000969835.1); Prevotella amnii DSM 23384 = JCM 14753 (GCF_000378745.1); Prevotella bivia DSM 20514 (GCF_000262545.1); Prevotella buccalis ATCC 35310 (GCF_000177075.1); Prevotella timonensis 4401737 = DSM 22865 = JCM 15640 (GCF_000455445.1); Pseudomonas fluorescens F113 (GCF_000237065.1); Pseudomonas protegens CHA0 (GCF_000397205.1); Pseudomonas aeruginosa PAO1 (GCF_000006765.1); Rhodanobacter fulvus Jip2 (GCF_000264315.1); Romboutsia timonensis (GCF_900106845.1); Roseburia hominis A2-183 (GCF_000225345.1); Roseburia inulinivorans DSM 16841 (GCF_000174195.1); Ruthenibacterium lactatiformans (GCF_000949455.1); Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (GCF_000006945.2); Sneathia sanguinegens (GCF_001517935.1); Staphylococcus aureus subsp. aureus NCTC 8325 (GCF_000013425.1); Streptococcus salivarius (GCF_000785515.1); Streptococcus thermophilus JIM 8232 (GCF_000253395.1); [Eubacterium] rectale ATCC 33656 (GCF_000020605.1); [Eubacterium] siraeum DSM 15702 (GCF_000382085.1) and  Ureaplasma parvum serovar 3 str. ATCC 27815 (GCF_000019345.1).
Supplementary_files_format_and_content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

organism: Synechocystis sp. PCC 6803

source_name: Liquid culture of Synechocystis sp. PCC6803.

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.
5PSeq that captures  transcripts with free 5' phospahte (without cap)

value: Heat shock for 90 minutes at 42C

tag: culture conditions

value: spcc-6803_hs_rep1 was cultured in BG11 Media and heat shocked at exponential growth phase OD730 0.47

tag: library protocol

value: Standard 5PSeq, RNA rP5_RND oligo for RNA ligation

tag: ribosomal rna delpetion strategy

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: Embryo_10 PS and derivative [DNA_batch1_sc56]

value: Embryo


title: WT HEK293T TT-seq Replicate 1

value: WT


title: PSF6a_scRNA-seq

tag: cohort

tag: disease state


title: spcc-6803_ctr_r1_s_r_v2

value: Untreated

value: spcc-6803_ctr_rep1 was cultured in BG11 Media and harvested at exponential growth phase OD730 0.47


title: Embryo_10 PS and derivative [DNA_batch1_sc53]


title: Embryo_10 PS and derivative [DNA_batch1_sc59]


title: WT HEK293T RNA-seq Replicate 2

description:
220106_CAM_293T_WT_RNAseq_hg38_N4_F.bedGraph
220106_CAM_293T_WT_RNAseq_hg38_N4_R.bedGraph

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 120bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the dm6 version of the Drosophila genome using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mm10/hg38 using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.
Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.  For siRNA control and RRP40 KD conditions, bedGraphs were depth normalized using normalize_bedGraph
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
Assembly: mm10 (mESC); hg38 (HEK293T)
Supplementary files format and content: bedGraph

extract_protocol:
RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.


title: WT HEK293T RNA-seq Replicate 4


title: comp_ctr_r1-2_c_o-r_v9

organism: compost metagenome

source_name: Compost collected in Sundbyberg, Stockholm

value: in-house Bacterial rRNA Depletion MIX for Cultures oVP676, Yeast_rRNAdepletion_Mix oVP690, human rRNA depletion mix oVP613


title: Embryo_10 PS and derivative [DNA_batch1_sc5]


title: comp_ctr_r1-1_c_o-r_v9

value: in-house Bacterial rRNADepletion MIX for Complex samples oVP676 , Yeast RNAdepletion Mix oVP690, human rRNA depletion mix oVP613


title: WT HEK293T RNA-seq Replicate 3


title: PSF5b_scRNA-seq

tag: gender

tag: group

value: critical

value: PBMC


title: Embryo_10 PS and derivative [DNA_batch1_sc49]

value: in vitro


title: WT HEK293T RNA-seq Replicate 1

value: embryonic kidney


title: PSF4b_scRNA-seq


title: Embryo_11 Endoderm [DNA_batch1_sc47]


title: PSF4a_scRNA-seq


title: PSF3b_scRNA-seq


title: donorH, CD36intMac

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using Salmon
Assembly: hg38
Supplementary files format and content: Table count matrix (raw counts), comma-separated file.

source_name: tonsil

extract_protocol:
Tonsil macrophages were selected after tissue digestion by density gradient, enriched by negative selection, and isolated by cell sorting on a FACS Aria instrument.
Total RNA was extracted using the Total RNA purification kit (Norgen) according to the manufacturer’s protocol. cDNA was generated using the SMART-Seq v4 kit (Takara) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit (Illumina). 10 ng of DNA was used for each sample. Sequencing was performed in 1 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end).

tag: individual

value: donorH

tag: tissue

value: tonsil

value: macrophage

tag: cell subset


title: Embryo_10 PS and derivative [DNA_batch1_sc45]

address: 1 Beichen West Road, Chaoyang District


title: donorH, CD36loMac


title: donorH, CD36hiMac


title: Embryo_10 PS and derivative [DNA_batch1_sc43]


title: PSF3a_scRNA-seq

value: female


title: PSF5a_scRNA-seq


title: Embryo_5 EPI [DNA_batch1_sc42]


title: Embryo_10 PS and derivative [DNA_batch1_sc40]


title: donorF, CD36intMac

value: donorF


title: PSF2b_scRNA-seq


title: PSF2c_scRNA-seq


title: PSF2a_scRNA-seq


title: donorE, CD36loMac

value: donorE


title: PSF1c_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc38]


title: Embryo_10 PS and derivative [DNA_batch1_sc37]


title: PSF1b_scRNA-seq


title: donorE, CD36hiMac


title: Embryo_10 PS and derivative [DNA_batch1_sc39]


title: dLNs_HA_24h_rep8

city: Gothenburg

first: Ali

last: Harandi

address: Box 435

department: Department of Microbiology and Immunology

institute: University of Gothenburg

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to mouse whole genome microarrays (Agilent Technologies).

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies)

data_processing: Data were processed, quantile normalized and analyzed using the R package Limma (Ritchie et al (2015). Nucleic Acids Research, 43(7), pp. e47)

source_name: dLNs, HA, 24h

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was extracted from lymph nodes using the RNeasy Mini QIAcube kit (Qiagen).

treatment_protocol: Anesthesized neonate mice were injected subcutaneously with 100 microliter antigen alone or together with adjuvant.

value: dLNs

tag: timepoint

value: HA


title: donorG, CD36loMac

value: donorG


title: dLNs_HA_7d_rep5

source_name: dLNs, HA, 7d


title: dLNs_HA/CAF01_7d_rep7

source_name: dLNs, HA/CAF01, 7d


title: Embryo_10 PS and derivative [DNA_batch1_sc35]

city: Beijing

value: Embryo

value: WT


title: dLNs_HA/GLA-SE_24h_rep7

source_name: dLNs, HA/GLA-SE, 24h

value: HA/GLA-SE


title: dLNs_HA/GLA-SE_24h_rep6


title: donorD, CD36loMac

value: donorD


title: dLNs_HA/CAF01_24h_rep8

source_name: dLNs, HA/CAF01, 24h


title: dLNs_HA/GLA-SE_7d_rep7

source_name: dLNs, HA/GLA-SE, 7d


title: dLNs_HA/GLA-SE_7d_rep8


title: PMM8_scRNA-seq

source_name: PBMC

value: male

value: mild/moderate


title: donorD, CD36hiMac


title: Embryo_10 PS and derivative [DNA_batch1_sc34]

value: in vitro


title: donorE, CD36intMac


title: PMM7_scRNA-seq

value: PBMC


title: dLNs_HA_24h_rep7


title: donorC, CD36intMac

value: donorC


title: Embryo_10 PS and derivative [DNA_batch1_sc33]


title: Embryo_7 Mesoderm [DNA_batch1_sc32]


title: PSF1a_scRNA-seq

value: critical


title: PMM6_scRNA-seq


title: donorC, CD36hiMac

value: tonsil

value: macrophage


title: PMM5_scRNA-seq


title: dLNs_HA/CAF01_7d_rep6


title: Embryo_10 PS and derivative [DNA_batch1_sc31]


title: dLNs_HA/CAF01_7d_rep5


title: donorB, CD36intMac

value: donorB


title: PMM4_scRNA-seq


title: donorB, CD36loMac


title: Embryo_10 PS and derivative [DNA_batch1_sc28]


title: PMM3_scRNA-seq


title: dLNs_HA/CAF01_24h_rep7


title: dLNs_HA/GLA-SE_24h_rep5


title: Embryo_10 PS and derivative [DNA_batch1_sc3]


title: donorA, CD36intMac

value: donorA


title: PMM2_scRNA-seq


title: PMM1_scRNA-seq


title: Embryo_3 EVT [DNA_batch1_sc26]


title: Embryo_10 PS and derivative [DNA_batch1_sc23]


title: PMF8_scRNA-seq

value: female


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch1_sc27]


title: donorA, CD36loMac


title: donorA, CD36hiMac


title: PMF7_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc21]


title: dLNs_HA/GLA-SE_7d_rep6

value: dLNs


title: dLNs_HA/CAF01_24h_rep6


title: donorB, CD36hiMac


title: PMF6_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc20]


title: dLNs_HA/CAF01_7d_rep4


title: Embryo_10 PS and derivative [DNA_batch1_sc2]


title: dLNs_HA/GLA-SE_7d_rep4


title: PMF5_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc15]


title: PMF4_scRNA-seq


title: dLNs_HA/GLA-SE_24h_rep4


title: RT112_siF-1_siZ-1_rep2 [D763T44]

city: paris

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

description:
Sample 23
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 1 replicate 2

data_processing:
Sequencer: NovaSeq - S1
Read length: 100bp
STAR: STAR_2.6.1a_08-27
GTF Annotation: gencode.v29.annotation.gtf
Index Adapters: Lexogen-Unique Dual index (96 Indexes)
Genome_build: human hg38
Supplementary_files_format_and_content: FOXA1_ZBED2_KD_tablecounts_raw.csv: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: FOXA1_ZBED2_KD_tablecounts_tpm.csv: Matrix table with TPM normalized counts for all samples and all genes.
Supplementary_files_format_and_content: pipeline_config.txt
Supplementary_files_format_and_content: adapter_list.txt
Supplementary_files_format_and_content: index_list.txt

growth_protocol: RT112 were cultured in RPMI +10% FBS, SCaBER in DMEM + 10% FBS. See paper for more details.

extract_protocol:
RNA extraction was performed using RNeasy kit (Qiagen). See paper for more details.
3' mRNA-Seq library Prep Kit - FWD-Lexogen.

treatment_protocol: Cells were transfected using Lipfectamine RNAi Max. See paper for more details.

value: siFOXA1.1 and siZBED2.1

tag: experiment batch replicate


title: RT112_siZBED2-2_rep2 [D763T42]

description:
Sample 21
RT112 Bladder Cancer Cell line treated with siZBED2 number 2 replicate 2


title: Embryo_10 PS and derivative [DNA_batch1_sc14]

tag: cell type

value: Embryo


title: RT112_siZBED2-1_rep2 [D763T41]

description:
Sample 20
RT112 Bladder Cancer Cell line treated with siZBED2 number 1 replicate 2

tag: cell line


title: RT112_siF-1_siZ-2_rep2 [D763T45]

description:
Sample 24
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 2 replicate 2

value: siFOXA1.1 and siZBED2.2


title: Embryo_10 PS and derivative [DNA_batch1_sc13]

tag: genotype

value: WT


title: PMF2_scRNA-seq


title: RT112_siCt2_rep2 [D763T40]

description:
Sample 19
RT112 Bladder Cancer Cell line treated with siControl number 2 replicate 2


title: dLNs_HA/GLA-SE_7d_rep5

value: HA/GLA-SE


title: Embryo_10 PS and derivative [DNA_batch1_sc12]

tag: time


title: dLNs_HA_7d_rep4

value: HA


title: RT112_siF-1_siZ-2_rep1 [D763T39]

description:
Sample 18
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 2 replicate 1

tag: treatment


title: PMF1_scRNA-seq

value: mild/moderate


title: dLNs_HA_7d_rep3


title: dLNs_HA/CAF01_7d_rep3


title: RT112_siFOXA1-1_rep2 [D763T43]

description:
Sample 22
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 replicate 2


title: dLNs_HA/CAF01_24h_rep5