title: HUVECs EXO-treated rep2

city: Singapore

first: Chwee Teck

last: Lim

state: Singapore

address: T-Lab, #08-03, 5A Engineering Drive 1

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

data_processing:
Reads were filtered by Software SOAPnuke (v1.5.2) with parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G. The removed reads are those with 1) adaptors; 2) more than 0.1% unknown bases; 3) more than 40% low quantility base.
Clean reads were mapped to hg38 whole genome using HISAT2 v2.0.4 with parameters --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Raw gene counts were calculated using HTSeq v0.11.1 with parameters -r name -s no -a 10
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human umbilical vein endothelial cells

growth_protocol: HUVECs were seeded in 24-well plate and cultured in EGM-2 till 70-80% conflucency

extract_protocol:
Cell lysates were harvested and RNAs were extracted with Qiagen RNeasy kit (Cat#74104)
RNA libraries were prepared for sequencing by BGI Genomics (Shenzhen, China)

treatment_protocol: Confluent HUVECs were incubated in basal medium EBM-2 only or treated with 50μg/mL exosomes derived from hypoxia (1% O2 for 24 h)-induced MDA-MB-231 cells

value: endothelial

value: umbilical vein/vascular endothelium

value: Treated with hypoxia-induced MDA-MB-231 cell-derived exosomes for 24 h


title: HUVECs EXO-treated rep1

status: Public on May 19 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue

tag: treatment


title: HUVECs WT rep2

value: untreated


title: Empty_Ctrl_H727_2_S6_L004_R1_001

city: Kingston

first: Neil

last: Renwick

state: ON

address: 88 Stuart Street

country: Canada

institute: Queen's University

data_processing:
Raw sequence reads were assessed for quality using FastQC (v.0.11.8)
Low-quality reads removed using Trimmomatic (v.0.36)
Reads were annotated against the human reference transcriptome GRCh38 (release 97) using an established alignment and quantification tool (Kallisto v.0.46.0)
Genome_build: hg38
Supplementary_files_format_and_content: expression spreadsheet files

source_name: Lung carcinoid cells (H727)

growth_protocol: H727 cells were grown in ATCC-formulated RPMI-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS). Cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from miR-375-depleted, YAP overexpression, and control cells using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and the NEBNext rRNA depletion kit (NEB, E6310) according to the manufacturer’s instructions; RNA fragmentation was performed for 10 min.

treatment_protocol: Stable miR-375-depleted H727 or doxycycline (Dox)-inducible YAP overexpression H727 (H727-YAP-S127A) cells were established by infection with lentivirus and subsequent antibiotic selection. Briefly, H727 cells were grown to 30-50% confluence in 6-well plates prior to replacement of the complete growth medium (ATCC-formulated RPMI-1640 containing 10% FBS) with virus solution containing 8 mg/ml Polybrene (Sigma Aldrich). Following an incubation period of 12 h at 37°C, virus-containing medium was refreshed and cells further cultured for 24 h. Stable miR-375-depleted H727 or H727-YAP-S127A cells were respectively selected with 2 mg/ml puromycin or 800 mg/ml hygromycin over a period of 8-9 days. Once established, stable cells were used for molecular characterization or in functional assays below; H727-YAP-S127A cells were treated with 1 µg/ml doxycycline hyclate (Bioshop Canada) for 48 h prior to use.

tag: experiment

value: miR-375 Ctrl


title: FGF2 Early MOLM14 DMSO Day 21 R2 [LIB200527JT_M14_FGF2e_D21_DMSO2_Ln1S8_L001]

city: Portland

first: Sunil

middle: Kumar

last: Joshi

state: OR

address: 3181 SW Sam Jackson Park Rd. Mail Code: KR-HEM

department: Knight Cancer Institute

country: USA

institute: Oregon Health & Science University

description: LIB200527JT_M14_FGF2e_D21_DMSO2_Ln1S8_S8_L001

library_source: genomic

data_processing:
library strategy: PCR library sequencing
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Genome_build: Custom reference created from CRISPR library
Supplementary_files_format_and_content: Read counts per sgRNA for each sample

molecule: genomic DNA

source_name: FGF2 Early Gilteritinib Resistant MOLM14 cells infected with library

growth_protocol: Early and late gilteritinib resistant MOLM14 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone. Early cell lines were also supplemented with 10 ng/mL  or FGF2 or FL.

extract_protocol:
30 million cells were collected from gilteritinib-treated flasks on day 14 (late resistance screens) and 21 (early resistance screens). DNA was extracted by desalting method
100 micrograms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/mL concentration for 7 days. 100 nM of  gilteritinib was applied to 30 million cells in a single flask

tag: cell line/type

tag: genotype/variation

value: infected with CRISPR/Cas9 library

value: day 21 post puromycin selection, DMSO


title: Empty_Ctrl_H727_1_S3_L004_R1_001


title: N001

city: Seoul

first: Hee Doo

last: Hee Doo

address: Banpo-Dong Seocho-Gu

country: South Korea

institute: The Catholic Univ. of Korea

description: Sample 1

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 hg19 whole genome using star method.
Transcript per million (TPM) were calculated. In short, all small RNAs 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.

source_name: liver tissue

extract_protocol:
Liver tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Normal


title: IHBD-KRAS-3D-from 6weeks primary tumor

type: RNA

city: Shinjuku-ku

first: Akiyoshi

last: Kasuga

state: Tokyo

address: 35, Shinanomachi

country: Japan

institute: Keio University

description: Gene expression data from secondary IHBD tumor initiating cells from 6 weeks primary tumor under organoid culture

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The raw data for each spot were normalized by subtraction of the mean background signal intensity determined from the intensities of all blank spots with 95% confidence intervals.

organism: Mus musculus

source_name: IHBD, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under 3D culture

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

extract_protocol: RNA was extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

value: secondary IHBD, from 6 weeks primary tumor

tag: culture

value: organoid culture


title: FGF2 Early MOLM14 Gilteritinib Day 21 R1 [LIB200527JT_M14_FGF2e_D21_GILT1_Ln1S9_L001]

description: LIB200527JT_M14_FGF2e_D21_GILT1_Ln1S9_S9_L001

value: FGF2 Early Gilteritinib Resistant MOLM14 cells

value: day 21 post puromycin selection, Gilteritinib


title: EHBD-GFP

description: Gene expression data from EHBD GFP cells.

source_name: EHBD, transduction of GFP

value: EHBD, non-tumor


title: IHBD-KRAS

description: Gene expression data from primaty IHBD tumor initiating cells

source_name: IHBD, transduction of KRAS

value: IHBD, KRAS


title: FGF2 Early MOLM14 DMSO Day 21 R1 [LIB200527JT_M14_FGF2e_D21_DMSO1_Ln1S7_L001]

description: LIB200527JT_M14_FGF2e_D21_DMSO1_Ln1S7_S7_L001


title: HUVECs WT rep1


title: Sample_A

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: GRCm38
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

molecule: polyA RNA

source_name: Ventromedial hypothalamus

growth_protocol: Chow with ad libitum food

extract_protocol:
Mice were euthanized, the VMH was dissected, nuclei were isolated, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression

value: Ventromedial hypothalamus


title: N005

description: Sample 5


title: GB-GFP

description: Gene expression data from GB GFP cells.

source_name: GB, transduction of GFP

value: GB, non-tumor


title: FGF2 Early MOLM14 Gilteritinib Day 21 R2 [LIB200527JT_M14_FGF2e_D21_GILT2_Ln1S10_L001]

description: LIB200527JT_M14_FGF2e_D21_GILT2_Ln1S10_S10_L001


title: IHBD-GFP

description: Gene expression data from IHBD GFP cells.

source_name: IHBD, transduction of GFP

value: IHBD, non-tumor


title: VHH_3

status: Public on May 18 2021

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: VHH sequencing

data_processing:
base calling: illumina CASAVA 1.8.2
nanobody diversity analysis: trim : sickle (v1.33) with  “pe -t sanger -q 30 -l 180-188 –no-fiveprime” option
nanobody diversity analysis: merge : flash (v1.2.11) with  “-m 20 -M 200 -x 0.1” option
nanobody diversity analysis: unique nucleotide and protein sequence extracted by in-house perl script
nanobody diversity analysis: IMGT numbering on VHH genes: ANARCI unix version
nanobody diversity analysis: CDR3 clustering: cd-hit (v4.6.8) with "-c 0.7" option
VHH usage analysis: merge: Ngmerge program with default setting
VHH usage analysis: trim pMES4 vector seqeunce: pTrimmer
VHH usage analysis: clean: remove reads with undtermined nucleotide N, low quality or less than 300nt with fastp with " -n 0 -q 30 -u 10 -l 300 -A" option
VHH usage analysis: fastq to fasta: sed -n '2~4p' - | sed = | sed '1-2s/^/>vhh_1_/'.
VHH usage analysis: BLAST database with 30 VHH genes with BLAST+
VHH usage analysis: alignment: igblast -germline_db_V to 30 VHH genes
VHH usage analysis: usage calculation by in-house python script
Genome_build: NA
Supplementary_files_format_and_content: nanobody diversity analysis: fasta file for protein sequences
Supplementary_files_format_and_content: VHH usage analysis: text file for VHH gene identification

source_name: spleen

growth_protocol: Two modified ESCs clones that have 40 normal chromosomes determined by karyotyping, negative for both mycoplasma and virus infection (mouse antibody production test) were injected into blastocysts from C57BL/6 strain by standard procedures. Injected blastocysts were transferred to the uteri of pseudopregnant female C56BL/6 recipients. High percentage chimeras were mated with C57BL/6 mice and offspring were genotyped for VHH minigene knock-in and Cuand Cgamma1 exon deletion. One out of three chimeras produced germline transmitted F1 offspring. Three F1 male mice with all three loci in Igh gene modified were backcrossed with C57BL/6 mice. F2 heterozygous mice were inbred to produce mice homozygous for all three loci modifications. Homozygous offspring were inbred to establish the mouse strain named as “nanomouse”. Two F1 offspring from the same chimera founder mouse were genotyped to only have CH1 exon of Cu deleted, while VH and CH1 exon of Cgamm1 awere intact. The two F1 mice were backcrossed with C57BL/6 miceand F2 heterozygous mice were inbred to produce mice homozygous for CH1 exon of Cu deletion. This stain was named “IguCh1-/-".

extract_protocol:
Diversity: Llama nanobody phage library was constructed as described before (PMID:24577359) with some modifications. Briefly, 300 ml of whole blood was collected from llama and peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Paque plus (GE Healthcare, 17-1440-03) according to manufacturer’s instruction. Total RNA e  xtracted from PBMC was used as starting material for RT-PCR to amplify the variable domains of immunoglobulin heavy chain (VHH) by two steps of PCR reactions. 50ug of RNA was reverse transcribed to cDNA with random hexamers and 2.5ul of cDNA (corresponding to about 0.9ug of original RNA) was used for first round PCR with gene-specific primers CALL001 and CALL002. The PCR reaction was repeated in 12 individual tubes with cDNA added into reactions separately. PCR fragment of about 700 bp long was gel purified and used as template (30 ng for each reaction, repeated in 12 individual tubes) for second round PCR with nested primers VHH-Back and VHH-For to amplify nanobody-encoding genes. PCR product from individual reactions werepooled, gel purified. Nanobody fragments and pMES4 phagmid were digested with PstI-HF and BstEII-HF restriction enzymes (NEB R3140L, R3162L) and ligated (1ug and 2ug respectively) with T4 ligase at 16 °C overnight. Ligation product was column purified (into 12ul of H2O) and electroporated into 360ul of TG1 cells. After 1 hour of recovery in 37 °C in shaker incubator, cells were plated on 6 of 245mm x 245mm dish (Thermo Fisher Scientific,431301) containing 2-YT Agar supplemented with 100ug/ml carbenicillin and 2% (wt/vol) glucose. Plates were placed in 37 °C bacteria incubator overnight and then bacteria scaped off plates. Cells were infected with VSCM13 helper phage (Agilent Technologies, 200251) and nanobody phage library preprepared as described before (PMID: 24577359). Nanomouse nanobody phage libraries were constructed the same way as nanomouse VHH(D)J region phagemid library construction with some modifications. Briefly, total RNA was extracted from splenic cells, bone marrow (femur and tibia) cells and PBMC of immunized mice and processed separately until TG1 cell electroporation step. RNA from splenic cells, bone marrow and PBMC (50ug, 50ug and all respectively) were reversed transcribed to cDNA with Ighg1 CH2-specific primer in separate tubes. 2ul of cDNA was used as template for BCR variable domains amplification (12 reactions each), using unmodified  TSO and Ighg1 CH2-specific oligonucleotide as primers. Second PCR was repeated in 12 reactions with 30 ng of the first-step PCR product as template 30 FR1 and 4 JH oligonucleotide mix as primers. PCR products were gel purified, digested with SfiI and ligated with pMES4 (200 ng and 400 ng respectively). Ligation products from splenic cells, bone marrow and PBMC samples were pooled and column purified (into 12ul of H2O) and electroporated into 360ul of TG1 cells and phage libraries prepared as described above.  VHH usage analysis: BCR VHH(D)J region phage library of unimmunized nanomouse was constructed and deep sequenced by Illumina Miseq for VHH usage analysis. Briefly, total RNA was extracted from nanomouse splenic cells by Trizol Reagent (Thermo Fisher Scientific,15596026) and reverse transcribed to cDNA with SuperScript™ III First-Strand Synthesis SuperMix (Thermo Fisher Scientific, 18080400) according to manufacturer’s instructions with some modifications.10ug of total RNA was denatured and annealed with gene specific primer corresponding to CH2 of Ighm gene. After elongation at 50 °C for 50 minutes, template switching oligonucleotide (TSO, 3’-propyl modified) linker was added to the 3’ end of the first strand cDNA with 90 minutes incubation at 42 °C as described before (Fernando Lopes Pinto et al. 2010, Anal Biochem. PMID: 19837043). Reaction was inactivated at 85 °C for 5 minutes and 2ul of cDNA was used as template for BCR variable domains amplification by two-step PCR with CloneAmp HiFi PCR Premix (Takara, 639298). For the first-step PCR, unmodified TSO and Ighm CH2-specific oligonucleotide were used as primers. 30 ng of the first-step PCR product was used as template for second-step nested PCR with a primer mix of 30 forward primers corresponding to framework (FR1) of 30 VHH genes and 4 reverse primers corresponding to JH1~JH4 of Igh gene. pMES4 phagemid was amplified with primers to introduce two different SfiI sites on two ends. Both VHH(D)J and pMES4 fragments were digested with restriction enzyme SfiI (NEB, R0123L) and ligated (100 and 200 ng respectively) with T4 ligase (NEB, M0202L) at 16 °C overnight. Ligation product was purified with DNA Clean & Concentrator (Zymo Research, D4014) and eluted into 12ul of H2O. 3ul of DNA was electroporated into 60ul of TG1 cells (Lucigen, 60502-2) in 1.0 mm cuvette (HARVARD Apparatus, 450134) with BTX electroporation system ECM 630 at the setting of 25uF, 200 Ohms, 1600 Volts. After 1 hour of recovery in 37 °C in shaker incubator, TG1 cells were plated on 5 of 10-cm LB Agar plates supplemented with 100ug/ml carbenicillin (KD Medical, BPL-2400). Plates were placed in 37 °C bacteria incubator overnight and then bacteria scaped off plates and phagemid library DNA extracted with Zymo Plasmid Miniprep kit (Zymo Research, D4054).
Phagemid DNA extracted from TG1 cell libraries was used as starting material for constructing MiSeq libraries for both VHH usage and nanobody diversity analysis. Briefly, 1.2 ug of phagemid DNA was used as template and VHH(D)J inserts were amplified by two primers recognizing pMES4 backbone with CloneAmp HiFi PCR Premix (Takara, 639298) in 50 ul reaction volume (9 cycles). To avoid MiSeq failure due to low complexity at initial cycles and to enable multiplex sequencing, 1-9 nt long staggers were introduced into forward primers. Without purification, 5 ul of the first PCR product was used as template for a second PCR (9 cycles) to add Illumina P5 and P7 primers on DNA ends. PCR product was then loaded onto 2% agarose gel and ~580 bp size band was purified with Zymoclean Gel DNA Recovery Kit (Zymo Research, D4002). DNA concentration was determined by Qubit 4  Fluorometer (Thermo Fisher Scientific, Q33238) and average DNA size was determined by TapeStation 4150 (Agilent). DNA was then adjusted to 2 nM in elution buffer containing 0.1% Tween-20. For unimmunized nanomice VHH(D)J library, DNA (2nM) from 3 mice were mix at 1:1:1 ratio and loaded for MiSeq run. For immunized llama and nanomice nanobody diversity analysis, DNA (2nM) of pre-selection and post-selection library were mixed at 10:1 ratio first and then samples from individual animals were pooled at 1:1 ratio before loading for MiSeq Sequencing (Illumina). 270 cycles of paired-end sequencing data were acquired  for VHH usage analysis and 300 cycles of paired-end sequencing data were acquired for nanobody diversity analysis.

treatment_protocol: One llama was immunized subcutaneously with SARS-CoV-2 virus antigens (recombinant protein of RBD and Spike) in the presence of Freund’s adjuvant according to the scheme described in the table below. Day 0 Bleed for test serumImmu. 1 Day 01 mg RBD, CFAImmu. 2 Day 140.5 mg RBD, IFADay 24Bleed for test serumImmu. 3 Day 280.5 mg RBD, IFADay 38Bleed for test serumImmu. 4 Day 420.5 mg RBD, IFADay 52Bleed for test serumImmu. 5 Day 560.5 mg Spike, IFADay 66Bleed for test serumImmu. 6 Day 700.5 mg Spike, IFADay 80500 ml bloodTwo groups of Nanomice (5 mice in group1, 6 mice in group2) were immunized with SARS-CoV-2 virus antigens (recombinant protein of RBD and Spike) in the presence of Freund’s adjuvant according to the scheme described in the table below.   Group1.  Day 0.   Bleed for test serum  Immu. 1  Day 0    50 ug RBD, CFA, i.p.  Immu. 2. Day 14. 25 ug RBD, IFA, i.p.                   Day 21. Bleed for test serum  Immu. 3.  Day 28. 25 ug RBD, IFA, i.p.                    Day 35. Bleed for test serum  Immu. 4   Day 42.  25 ug RBD, IFA, i.p.                   Day 49.  Bleed for test serum  Immu. 5.  Day 56.  25 ug Spike in PBS, i.p.  Immu. 6.  Day 59.  25 ug Spike in PBS, i.v.                    Day 62.  Harvest Experiment  Group 2    Day 0.    Bleed for test serum  Immu. 1.    Day 0.   50 ug Spike, CFA, i.p.  Immu. 2.   Day 14.  25 ug Spike, IFA, i.p.                    Day 21   Bleed for test serum  Immu. 3.   Day 28.  25 ug Spike, IFA, i.p.                    Day 35.  Bleed for test serum  Immu. 4.   Day 42. 25 ug Spike, IFA, i.p.                    Day 49.  Bleed for test serum  Immu. 5.   Day 56.  25 ug Spike in PBS, i.p.  Immu. 6.   Day 59.  25 ug Spike in PBS, i.v.                    Day 62.  Harvest Experiment.

value: Bone marrow cells, splenic cells and peripheral blood mononuclear cells

tag: genotype

value: IgVH-/VHH+

value: spleen


title: 808 2020

city: Barcelona

first: Laudanna

last: Carmelo

state: Barcelona

address: Baldiri i Reixac, 10

department: Aging and Metabolism

country: Spain

institute: Institute for Research in Biomedicine (IRB-Barcelona)

hyb_protocol: cDNA was hybridized to the Clariom S Mouse Array (901570, Thermo Scientific).

scan_protocol: The arrays were scanned on a GeneAtlas Imaging station (Affymetrix).

data_processing: After RMA normalisation and batch correction using the ComBat function of the SVA package in R, differentially expressed genes were determined using the limma package (version 3.32.10) in R and a FDR < 0.05.

label: biotin

source_name: mammary epithelium

label_protocol: Standard Affymetrix protocol

extract_protocol: For RNA amounts of 25 or 50 ng, as used initially and in the 10,000 cell analysis, library preparation and amplification for 17 cycles were performed following the distributor's (Sigma-Aldrich) recommendations.

value: basal


title: ESCs, Jun-12h.RNA-seq

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

country: China

institute: westlake University

description: Jun.timecourse.RNA-seq.merge.csv

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode  (mm10 vM13) transcriptome using Bowtie2  (v2.2.5) and RSEM  (v1.3.0)
Gene expression level was calculated using EDASeq  (v2.4.1) GC-normalized method
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value file containing GC-normalized RNA-seq data

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium  (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: Treated with 2µg/ml doxycycline

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

tag: strain

value: treated with doxycycline for 12h

tag: passage


title: nanoMouse3_Spike_after

description: VHH sequencing

value: SARS-CoV-2 Spike infection selection


title: nanoMouse3_Spike_before

description: VHH sequencing

value: SARS-CoV-2 Spike infection


title: ESCs, Jun-24h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: treated with doxycycline for 24h


title: VHH_1

description: VHH sequencing


title: 804 2020


title: nanoMouse1_RBD_before

description: VHH sequencing

value: SARS-CoV-2 RBD + Spike infection


title: nanoMouse2_Spike_before

description: VHH sequencing


title: 795 2020

value: luminal


title: 800 2020


title: 799 2020


title: nanoMouse2_Spike_after

description: VHH sequencing

value: SARS-CoV-2 Spike infection, selection


title: 796 2020


title: 801 2020


title: 794 2020


title: 798 2020


title: nanoMouse1_RBD_after

description: VHH sequencing

value: SARS-CoV-2 RBD + Spike infection, selection


title: 793 2020


title: 805 2020


title: 802 2020


title: 807 2020


title: 803 2020


title: 806 2020


title: VHH_2

description: VHH sequencing


title: N012

description: Sample 12

value: Normal


title: 797 2020


title: ESCs, Jun-8h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: treated with doxycycline for 8h


title: ESCs, Jun-4h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: treated with doxycycline for 4h


title: ESCs, Jun-1h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: treated with doxycycline for 1h


title: ESCs, Jun-0h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: no doxycycline


title: SM014

city: New York

first: Job

last: de Jong

address: 1051 Riverside Drive

department: Psychiatry

institute: Columbia University

data_processing:
Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center. Multiplex samples with unique barcodes were mixed in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. RTA software (Illumina) was used for base calling, and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference human genome (hg19) using Tophat2.0 (version 2.0.4) with four mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Genome_build: hg19
Supplementary_files_format_and_content: rawcounts

source_name: patient derived iPSC

growth_protocol: hiPSCs were dissociated with 0.5 mM EDTA in PBS and triturated to generate a single cell suspension. A total of 10,000 cells were then plated into each well of an ultra-low-attachment 96-well plate (Nunc) to form embryoid bodies (EBs) in medium containing mTesR1, 1 µg/ml heparin and Penicillin-Streptomycin antibiotics. EBs were exposed to medium containing the ROCK inhibitor Y27632 (50 µM) for the first 24h, followed by 5 days without interference in 96-well plates. On day 5, the medium was switched to medium containing DMEM/F12 (1:1) (Gibco; 11330), N-2 supplement (Gibco; 17502-048), MEM-NEAA (Invitrogen), Glutamax (Invitrogen 35050-061), Penicillin-Streptomycin and 0.1 mM ®-Mercaptoethanol, Dorsomorphin (2 µM), SB431542 (10 µM) and IWR1e (3 µM). On day 25, 0.2% Chemically Defined Lipid Concentrate was added to this medium until day 39. On day 40, EBs were transferred to ultra-low attachment 24 well plates with 1 ml of medium per organoid/well. Between day 40 and 80, 1 ml of medium containing DMEM/F12 (1:1) (N-2 supplement MEM-NEAA, Glutamax, Penicillin-Streptomycin and 0.1 mM ®-Mercaptoethanol, 10% fetal bovine serum (FBS) and 1% Matrigel (Corning) was replaced weekly. After day 80 medium was replaced once per week. Matrigel was added bi-weekly to prevent excess Matrigel deposition on the outer shell of the organoid.

extract_protocol:
Ten forebrain organoids per line (i.e., 3 control-derived lines, 3 patient-derived lines) were collected at 8 weeks in vitro. Total RNA was isolated from hiPSC-derived cortical neurons using miRNeasy kit (Qiagen, USA) according to instructions of the manufacturer.A poly-A pull-down step was performed to enrich mRNAs from total RNA samples (200 ng to 1 µg per sample, RIN > 8 required)
library preparation was done using Illumina TruSeq RNA prep kit
Libraries were sequenced using Illumina HiSeq2000 at the Columbia Genome Center. Multiplex samples with unique barcodes were mixed in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. RTA software (Illumina) was used for base calling, and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. The reads were mapped to a reference human genome (hg19) using Tophat2.0 (version 2.0.4) with four mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).

treatment_protocol: growth and treatment described in growth protocol

value: wildtype (rescue)

tag: cell line

value: P2 CRISPR Rescue

value: forebrain organoids from patient derived iPSC

tag: batch

value: Batch 2 Rescue_batch


title: CNT004

value: wildtype

value: Batch 1_case_control


title: SM011

value: mutant

value: P2 (mock)


title: CNT003


title: CNT006


title: SM013


title: SM015


title: CNT001


title: SM012


title: CNT005


title: SM016


title: EM.28.10

city: Southampton

first: Michaela

last: Reichmann

address: Tremona Road

country: United Kingdom

institute: University of Southampton

data_processing:
GENEWIZ sequencing facilities performed base calling using Illumina software
After quality control for adapter contamination by FastQC software, fastq files were mapped to the  human genome transcriptome (Homo_sapiens.GRCh38.cdna) using kallisto software (version 0.43.1).
Reads were imported by tximport (version 1.10.1, R), and annotated to gene level with ensembldb program (version 2.6.8, R)
Inter-sample normalisation with TMM normalisation using edgeR (version 3.24.3, R).
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

growth_protocol: PBMCs were infected overnight with Mtb in a 250cm2 flask.  The PBMCs were then detached, pelleted and mixed with 1.5% sterile alginate (Pronova UP MVG alginate, Nova Matrix, Norway), with or without 1mg/mL collagen (Advanced BioMatrix, USA), at a final concentration of 5 x 106 cells/ml. The cell-alginate suspension was injected into the electrostatic generator where microspheres formed in an ionotropic gelling bath of 100mM CaCl2 in HBSS.  After twice washing with HBSS with Ca2+/Mg2+, microspheres were incubated at 37oC in RPMI 1640 medium containing L-glutamine, ampicillin, kanamycin and 10% human AB serum. Microspheres were then placed into Eppendorf tubes and randomly allocated to different experimental conditions.

extract_protocol:
Samples were thawed on ice, and 200µl Chloroform added per 1ml of sample.  Samples were shaken for 15 seconds, incubated for 3 minutes at room temperature, then centrifuged at 12000g for 15 minutes at 4OC.   The upper aqueous layer was extracted.  Then manufacturer’s instructions were followed (RNeasy® Midi Kit, QIAGEN), adding 70% ethanol, shaking, and then samples added to RNeasy Midi columns, and washed with Buffer RW1 and Buffer RPE.  Total RNA was eluted with RNase-free H2O.
GENEWIZ sequencing facilities performed RNA library preparation with polyA selection and sequencing of thirty-six samples using Illumina HiSeq with standard Illumina protocols, with twelve samples per lane.   A configuration of 2 x 150 base pairs per lane was used, and a mean average of 31 million paired end reads.

treatment_protocol: Bioluminescent H37Rv was cultured in Middlebrook 7H9 medium supplemented with 10% ADC, 0.2% glycerol and 0.02% Tween 80 (BD Biosciences, Oxford) with kanamycin 25 μg/ml. Cultures at 1×108 CFU/ml Mtb (Optical Density = 0.6) were used for all experiments at MOI of 0.1.  Decapsulation solution was 55mM sodium citrate and 5mM EDTA with HBSS, with pH adjusted to 7.4 by adding 5M HCl.  The decapsulation solution was warmed to 37°C and on day 4 applied to microspheres after washing with HBSS.  Once decapsulated, the cells were centrifuged at 2000 xg for 8 minutes at 4°C.  The same centrifugation was used to pellet PBMCs in 2D culture on day 4.  After centrifugation, cell pellets were resuspended in QIAzol Lysis Reagent (QIAGEN) and stored at -80°C.

tag: donor

value: F

tag: condition

value: Alginate

value: Mtb


title: EM.28.7

value: Control


title: EM.28.6

value: E

value: Collagen


title: EM.28.5


title: EM.28.8


title: EM.28.4


title: EM.28.3


title: EM.28.1


title: EM.28.12


title: ESCs, Jun-2h.RNA-seq

description: Jun.timecourse.RNA-seq.merge.csv

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

value: treated with doxycycline for 2h


title: EM.28.11


title: EM.28.9


title: EM.28.2


title: EM.23.10

value: D


title: CNT002


title: EM.23.5

value: C


title: EM.23.6


title: EM.23.4


title: EM.23.2


title: EM.23.3


title: EM.23.9


title: EM.23.1


title: EM.23.7


title: EM.21.11

value: B


title: EM.21.10


title: EM.23.8


title: EM.21.9


title: EM.21.4

value: A


title: EM.21.5


title: EM.23.12


title: EM.21.7


title: EM.21.12


title: EM.23.11


title: Quiescent Melanoma Q1

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

country: Australia

institute: UON

data_processing:
HiSeq sequencing (TruSeq SBS kit v4-HS)
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling and preliminary quality analysis.
The Illumina built-in software determines whether to keep or discard each of the sequencing fragments (namely reads) based on the quality of the first 25 bases.
The raw data (Pass Filter Data) obtained from this step is stored in FASTQ format, which contains the base sequence (the second line of a FASTQ record) and the corresponding sequencing quality information (the fourth line of a FASTQ record).
low-quality reads and contaminations were filtered out before data analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Human meanoma cells

extract_protocol:
Total RNA were extracted by ISOLATE II RNA Mini Kit (Bioline)
Library construction: NEBNext Ultra Directional RNA library prep kit (E7420L); Library purification: AxyPrep Mag PCR (Clean-up)

treatment_protocol: Serum starvation was used to arrest more quiescent cells.

value: skin

value: melanoma

tag: cell population


title: Quiescent Melanoma Q2


title: EM.21.1


title: EM.21.6


title: Cycling Melanoma C2


title: EM.21.3


title: Cycling Melanoma C1


title: GB-KRAS-adherent-from 6weeks primary tumor

description: Gene expression data from secondary GB tumor initiating cells from 6 weeks primary tumor under adherent culture

source_name: GB, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under adherent culture

value: secondary GB, from 6 weeks primary tumor

value: adherent culture


title: RPE1-hTERT Torin1 treated cells rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-Seq reads were aligned to the human transcriptome prepared with an ensembl version 89 annotation using STAR version 2.5.3a and gene expression was summarized using RSEM version 1.3.0
Genome_build: hg38 with and ensembl version 89 annotation
Supplementary_files_format_and_content: rxwang022221_intCt.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: rxwang022221_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

source_name: RPE1-hTERT cells

growth_protocol: All samples were derived from the RPE1-hTERT cell line (ATCC Cat# CRL-4000). Cells were cultured in Dulbecco’s modified Eagle’s medium supplied with 10% FBS and penicillin/streptomycin (100 U/ml) and L-Glutamine (2 mM) at 37 °C with 5% CO2 in a humidified environment.

extract_protocol:
Qiagen RNEasy Kit
Roche KAPA stranded RNA-Seq

tag: population

value: bulk culture

tag: treatment protocol

value: Treated with 1 uM Torin1 for 7 days


title: RPE1-hTERT Torin1 treated cells rep2

tag: cell type


title: RPE1-hTERT Torin1 treated cells rep1


title: RPE-1 hTERT control cells rep9

value: Untreated


title: ArCK STAT1 KO single cell clone 3

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-Seq reads were aligned to the human transcriptome prepared with an ensembl version 89 annotation using STAR version 2.5.3a and gene expression was summarized using RSEM version 1.3.0
Genome_build: hg38 with and ensembl version 89 annotation
Supplementary_files_format_and_content: rxwang_intCt.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: rxwang_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

treatment_protocol: Cells were synchronized in 5mM of thymidine for 24hrs, treated with 500nM reversine for 18hrs after thymidine release, and the mitotic cells were removed ~72h after chromosome mis-segregation. Cells were collected ~156 hours after the faulty mitosis.

value: STAT1 single cells clone 3


title: EHBD-KRAS-adherent-from 3weeks primary tumor

description: Gene expression data from secondary EHBD tumor initiating cells from 3 weeks primary tumor under adherent culture

source_name: EHBD, KRAS, secondary tumor initiating cells from 3 weeks primary tumor under adherent culture

value: secondary EHBD, from 3 weeks primary tumor


title: RPE-1 hTERT control cells rep8


title: ArCK STAT1 KO single cell clone 1

value: STAT1 single cells clone 1


title: ArCK KO control single cell clone 2

value: control single cell clone 2


title: EM.21.8

tag: treatment

value: Mtb


title: Cycling STAT1 KO single cell clone 3

treatment_protocol: Untreated


title: EM.21.2


title: Cycling STAT1 KO single cell clone 2

value: STAT1 single cells clone 2


title: Cycling KO control single cell clone 2


title: ArCK KO control single cell clone 1

value: control single cell clone 1


title: RPE-1 hTERT control cells rep7


title: RPE1-hTERT doxorubicin treated cells rep2

treatment_protocol: Treated with 100ng/mL doxorubicin for 7 days.


title: Cycling KO control single cell clone 1


title: RPE1-hTERT control cells rep1


title: RPE1-hTERT nutlin3 treated cells rep2

treatment_protocol: Treated with 10μM nutlin3 for 7 days.


title: RPE1-hTERT nutlin3 treated cells rep3


title: RPE1-hTERT nutlin3 treated cells rep1


title: RPE1-hTERT palbociclib treated cells rep2

treatment_protocol: Treated with 5μM palbociclib for 7 days.


title: RPE1-hTERT palbociclib treated cells rep1


title: RPE1-hTERT palbociclib treated cells rep3


title: RPE1-hTERT doxorubicin treated cells rep3


title: RPE1-hTERT doxorubicin treated cells rep1


title: RPE1-hTERT control cells rep3


title: RPE1-hTERT control cells rep2


title: ArCK STAT1 KO single cell clone 2


title: RPE1-hTERT ArCK cells rep2


title: RPE1-hTERT ArCK cells rep3


title: RPE1-hTERT ArCK cells rep1


title: Cycling STAT1 KO single cell clone 1


title: SKBR3_CBP30_1

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

data_processing:
RNA-seq processing:
RNA-seq analysis was performed with the nextpresso pipeline v1.9, using the following tools:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19

source_name: SKBR3 cells

growth_protocol: SKBR3 cells were grown in RPMI+10%FBS, MDA-MB-453 and MDA-MB-231 cells were grown in DMEM+10%FBS

extract_protocol:
Cells were trypsinized and total RNA was extracted using the RNeasy kit (Qiagen).
From 1 µg of total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit. Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced for 50 bases in a single-read format (Illumina HiSeq 2000).

treatment_protocol: cells were treated for 48 hours with with 2 µM CBP30, 150 nM JQ1 or vehicle (DMSO). Two biological replicates were used per condition.

value: 2 μM CBP30


title: MDA_MB_453_CBP30_1

source_name: MDA_MB_453 cells


title: SKBR3_JQ1_2

value: 150 nM JQ1


title: MDA_MB_453_JQ1_1


title: SKBR3_DMSO_2

value: DMSO


title: SKBR3_CBP30_2


title: MDA_MB_453_DMSO_2


title: MDA_MB_231_CBP30_2

source_name: MDA-MB-231 cells


title: SKBR3_JQ1_1


title: MDA_MB_453_CBP30_2


title: MDA_MB_453_DMSO_1


title: MDA_MB_231_JQ1_2


title: MDA_MB_453_JQ1_2


title: MDA_MB_231_CBP30_1


title: SKBR3_DMSO_1


title: MDA_MB_231_DMSO_1


title: PD1_5575 L

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

data_processing:
Fastq files were aligned with STAR to the mouse reference genome and featureCounts was used to quantified read count. Gene expressions are calculated in FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Myc-CaP tumor

growth_protocol: Myc-CaP cells were injected into FVB male mice subcutaneously on both flanks.

extract_protocol:
Tumors were collected after 3 weeks of treatment, and total RNA was extracted by QIAGEN RNA extraction kit.
Library was prepared by RiboErase selection kit.

treatment_protocol: When tumors reached 50 mm3, mice were randomized and treated with 15 mg/kg ESK981 or vehicle at 5 days per week by oral gavage, while anti-PD-1 or isotype control were given at 200 µg per mouse 3 times per week by intraperitoneal injection.

tag: tissue

value: Myc-CaP tumor

value: FVB

tag: ear tag


title: PD1_5575 R


title: PD1_5574 L


title: PD1_5574 R


title: PD1_5573 R


title: PD1_5572 R


title: ESK981 15mg/kg+PD1_5571 R


title: MDA_MB_231_JQ1_1


title: ESK981 15mg/kg+PD1_5570 R


title: ESK981 15mg/kg+PD1_5569 R


title: ESK981 15mg/kg+PD1_5567 L


title: PD1_5576 L


title: ESK981 15mg/kg+PD1_5569 L


title: ESK981 15mg/kg_5581 R


title: ESK981 15mg/kg_5581 L


title: ESK981 15mg/kg+PD1_5567 R


title: ESK981 15mg/kg+PD1_5568 R


title: ESK981 15mg/kg_5578 R


title: Vehicle_3505 R

value: Vehicle


title: ESK981 15mg/kg_5579 R


title: ESK981 15mg/kg_5577 R


title: ESK981 15mg/kg_5579 L


title: Ba/F3, SPAG9-JAK2(-), rep3

city: Kyoto

first: Azusa

last: Mayumi

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Pediatrics

institute: Kyoto Prefectural University of Medicine

description: Gene expression data from non-induced Ba/F3 cells not expressing SPAG9-JAK2 (mock Ba/F3)

hyb_protocol: Biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) following the standard protocols.

scan_protocol: Hybridized arrays were stained and scanned with a Genechip 3000 7G Scanner (Thermo Fisher Scientific) at the default settings.

data_processing: Data were analyzed using Affymetrix Expression Console Software 1.4.1.

label_protocol: cRNA target synthesis was carried out using a GeneChip 3’IVT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Ba/F3 cells transduced with SPAG9-JAK2 fusion protein by the Retro-X Tet-on Advanced Inducible System (Takara Bio) were washed twice with phosphate-buffered saline and seeded in triplicate with or without 500 ng/ml doxycycline.

extract_protocol: Total RNA was extracted 48 hours later from Ba/F3 cells with or without expression of SPAG9-JAK2 using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and the quality was checked on a NanoDrop 2000 (Thermo Fisher Scientific) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: Ba/F3 cells expressing SPAG9-JAK2 under doxycycline dependent manner were established, and SPAG9-JAK2 protein expression was induced using 500 ng/ml doxycycline.

value: interleukin-3-dependent murine pro-B cell line


title: Vehicle_3505 L


title: Vehicle_3504 R


title: Ba/F3, SPAG9-JAK2(+), rep1

description: Gene expression data from SPAG9-JAK2-expressing Ba/F3 cells induced by doxycycline (Ba/F3-SPAG9-JAK2)


title: Vehicle_3504 L


title: Vehicle_3503 R


title: Ba/F3, SPAG9-JAK2(-), rep1

source_name: non-induced Ba/F3 cells not expressing SPAG9-JAK2 (mock Ba/F3)


title: Vehicle_3502 R


title: ESK981 15mg/kg+PD1_5570 L


title: Vehicle_3502 L


title: ESK981 15mg/kg_5580 R


title: Vehicle_3501 L


title: ESK981 15mg/kg_5577 L


title: Vehicle_3501 R


title: Ba/F3, SPAG9-JAK2(-), rep2


title: SSMs_2 [RNA191014FP_TD2_minus_S3_L004]

first: Ferdinando

last: Pucci

address: 2720 S Moody ave

department: Otolaryngology

institute: Oregon Health&Science University

data_processing:
Fastq files were generated using Bcl2Fastq2 (Illumina), trimmed with trimmomatic, and aligned using STAR aligner bcl2fastq v2.20.0.422 STAR_2.5.3a trimmomatic-0.36
genome build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Count matrix

source_name: Tumor-draining lymph node 2

growth_protocol: The chemically-induced squamous cell carcinoma model MOC2 was purchased from Kerafast. For tumor formation, 5•105 cells in 50ul of PBS were implanted in the flank of C57B/6 male mice (Charles River Labs) intradermally, near the inguinal lymph node, as previously described . After 2 weeks, we selected mice with similar tumor size for tdLN and ndLN collection. All procedures were in accordance with OHSU IACUC.

extract_protocol:
Flow sorting and RNA extraction. All antibodies (and Fc Block) were from Biolegend, and were used at 2ul per 100ul of cell suspension, with the exception of CD45-PC7 and Ly6G-PE, which were used at 1ul per 100ul of cell suspension. Single stain controls were made by pooling a small amount from all samples. Flow sorting was done on a BD Aria and recovered ~10,000 LN macrophages from each group. LN macrophages were then pelleted and lysed in RLT with B-mercapto-ethanol for RNA extraction (RNeasy micro kit), with on column DNAse treatment.
RNA sequencing. RNA integrity was determined using the 2100 Bioanalyzer (Agilent). RNA was converted to cDNA with the SMART-Seq v4 Ultra Low Input RNA kit (Takara) and converted into sequencing libraries using the DNA Nano Kit (Illumina). Libraries were profiled on the 4200 TapeStation (Agilent) and quantified using the Kapa Library Quantification Kit (Roche) on a StepOnePlus Real Time PCR Workstation (Thermo). Sequencing was done on a HiSeq 2500 (Illumina).

treatment_protocol: Enzymatic dissociation of lymph nodes. LNs from 2 different mice were pooled: 2 tdLN and 6 ndLN (contralateral inguinal, axillary, brachial). Dissociation buffer was prepared by dissolving 3mg/ml of Collagenase IV (Worthington), 0.1 U/ml of DNase I (Roche), 2% FBS, pen/strep and L-glutamine in IMDM. Whole LNs were incubated in 5ml of dissociation buffer at 37ºC and 225rpm agitation. After 15 minutes, LNs were mechanically dissociated by passing them through an 18G needle syringe at 2ml/second (LNs burst immediately) and put back at 37ºC in same dissociation buffer, at 225rpm agitation. After 15 more minutes, the LN cell suspensions were mechanically dissociated by passing them through an 27G needle syringe at 0.5ml/second for 10 times. The LN cell suspension was then filtered on a 100um cell strainer and washed in 50ml of MACS buffer (2mM EDTA, 2.5% BSA in PBS). All centrifugation steps were performed at 500g for 10 minutes and supernatants were checked at the microscope for absence of cells. If significant cell numbers were observed (>0.1•106/ml), supernatants were diluted 1:1 in MACS buffer and centrifuged again. LN cells were resuspended at ~108/ml for staining (~1.5ml) in MACS buffer.

tag: tumor

value: Lymph node


title: SSMs_1 [RNA191014FP_TD_minus_S1_L003]

source_name: Tumor-draining lymph node 1


title: MSMs_1 [RNA191014FP_TD2_plus_S4_L003]


title: MSMs_2 [RNA191014FP_TD2_plus_S4_L004]


title: SSMs_1 [RNA191014FP_ND2_minus_S7_L003]

source_name: Non-draining lymph node 2


title: MSMs_2 [RNA191014FP_ND1_plus_S6_L004]

source_name: Non-draining lymph node 1


title: MSMs_1 [RNA191014FP_TD1_plus_S2_L003]


title: SSMs_2 [RNA191014FP_ND2_minus_S7_L004]


title: MSMs_1 [RNA191014FP_ND2_plus_S8_L003]


title: SSMs_1 [RNA191014FP_TD2_minus_S3_L003]


title: Vehicle_3503 L


title: SSMs_2 [RNA191014FP_ND1_minus_S5_L004]


title: RNA-seq on EMPTY NRAS murine leukemia cells_replicate 3

first: Sarah

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

institute: OHSU

data_processing:
Raw reads were trimmed with BBDuk and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered gene counts table provided as a .txt file

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen).
Takarak SmartSeq for Ultra Low Input

treatment_protocol: [retroviral protocol]  Retrovirus was generated by transfecting SETBP1 or NRAS or control vector plasmids and the EcoPac plasmid (provided by Dr. Rick Van Etten) into 293T17 cells using FuGENE 6 (Promega). The supernatant from these cells at 48 and 72h was used to transduce using murine bone marrow isolated from 6 to 10-week old female C57BL/6J mice.

value: Bone marrow

tag: retroviral transduction

value: EMPTY + NRAS (G12D)


title: RNA-seq on SETBP1 NRAS murine leukemia cells_replicate 1

value: SETBP1 (D868N) + NRAS (G12D)


title: SSMs_1 [RNA191014FP_ND1_minus_S5_L003]


title: RNA-seq on EMPTY NRAS murine leukemia cells_replicate 2


title: SSMs_2 [RNA191014FP_TD_minus_S1_L004]


title: MSMs_1 [RNA191014FP_ND1_plus_S6_L003]


title: RNA-seq on SETBP1 EMPTY murine leukemia cells_replicate 1

value: SETBP1 (D868N) + EMPTY


title: MSMs_2 [RNA191014FP_TD1_plus_S2_L004]


title: RNA-seq on SETBP1 EMPTY murine leukemia cells_replicate 2


title: RNA-seq on EMPTY EMPTY murine leukemia cells_replicate 2

value: EMPTY + EMPTY


title: RNA-seq on EMPTY EMPTY murine leukemia cells_replicate 3


title: MSMs_2 [RNA191014FP_ND2_plus_S8_L004]


title: RNA-seq on EMPTY NRAS murine leukemia cells_replicate 1


title: RNA-seq on EMPTY EMPTY murine leukemia cells_replicate 1


title: RNA-seq on SETBP1 EMPTY murine leukemia cells_replicate 3


title: MG_4

data_processing:
Samples were sequenced on a HiSeq2500 sequencer (Illumina) using V4 chemistry, generating 50-bp paired-end reads.
After adapter-cleaning and quality correction using Trimmomatic (version 0.36), paired-end reads were aligned to the mm10 genome (UCSC) using Bowtie 2 Aligner (version 0.3.3.1). Duplicate reads were removed using SAMtools (version 1.3.1).
Peaks were called using MACS2 (version 2.0.10) and an FDR < 0.05. Differential peaks were determined using the DiffBind package (version 2.4.8) in R (version 3.5.2) and an FDR < 0.05.   The distribution of the differential regions within genomic features was conducted with HOMER (version 2015-03-22).
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using bedGraphToBigWig tool from ENCODE

source_name: Mammary gland cells

extract_protocol: Library preparation for ATAC (assay for transposase-accessible chromatin) sequencing used 5x104 luminal or basal cells FACS-sorted from four wild-type and three G9caKO independent mice as previously described (Buenrostro et al., 2013).

value: Luminal cells

value: Ctrl

tag: replicate


title: MG_12

value: Basal cells

tag: genotype


title: MG_8


title: RNA-seq on SETBP1 NRAS murine leukemia cells_replicate 3

tag: strain


title: MG_10


title: M_94


title: RNA-seq on SETBP1 NRAS murine leukemia cells_replicate 2


title: M_82


title: M_80


title: MG_1


title: L_95


title: L_82


title: L_80


title: L_94


title: M_669_29523_GTGAAA

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.36)
Reads were aligned to the mm10 genome (UCSC) using TopHat Aligner (version 2.1.1)
For differentially expressed genes (DEGs), read count was performed using featureCounts (version 1.6.0) and DEGs were called using DESeq2 (version 1.26.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.

extract_protocol:
RNA was extracted following the manufacturer´s recommendations and treated with TURBO DNA-free Kit (AM1907, Thermo Fisher)
Libraries were prepared with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Kit (RS-122-2201/2202, Illumina). Samples were sequenced on a HiSeq2500 sequencer (Illumina) using V4 chemistry, generating 125-bp single reads.

value: Basal


title: L_669_29529_ACTGAT

value: Luminal


title: L_668_29528_GTCCGC

value: WildType


title: M_668_29522_ACAGTG


title: L_252_29526_GGCTAC


title: L_258_29527_GATCAG


title: M_258_29521_TTAGGC


title: M_252_29520_CTTGTA


title: M_250_29518_ATCACG


title: M_251_29519_GCCAAT


title: L_251_29525_TAGCTT


title: MG_2


title: P0_TOM_VPM4

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av Ramon y Cajal s/n, Campus de San Juan

department: Instituto Neurociencias CSIC-UMH

institute: Universidad Miguel Hernández (UMH)

data_processing:
Quality control of the raw data was performed with FastQC (v.0.11.7) and all sequenced dataset adapters were trimmed using Trim Galore (0.6.1) and Cutadapt (2.3)
RNA-seq reads were mapped to the Mouse genome (GRCm.38.p6/mm10 Ensembl release 95, Jan 2019) using STAR (v2.7.0d) (Dobin et al., 2013) and SAM/BAM files were further processed using SAMtools v1.9. (Li et al., 2009).
Aligned reads were counted and assigned to genes using Ensembl release 95 gene annotation and FeatureCounts, Subread (v1.6.4) (Liao et al., 2014).
Genome_build: GRCm.38.p6/mm10 Ensembl release 95, Jan 2019
Supplementary_files_format_and_content: Tab-delimited text files include Gene Counts values for each Sample.

source_name: Thalamus, Ventral Posteriomedial Nucleus

extract_protocol:
Total RNA extraction was done using the RNeasy® Micro Kit (Qiagen, #74004).
cDNA libraries were preparared using SMARTer TM Ultra Low RNA Kit v4 and Nextera XT kit Ultra DNA Library Prep for Illumina according to the manufacturer’s instructions. Then the libraries were sequenced for 50pb single-read and performed on an Illumina HiSeq2500 V4 using 1x50 sequencing to read depth of > 25 million reads per sample at CNAG-CRG facility at Barcelona (Spain).

treatment_protocol: Brains of P0 Gbx2CreER-IRES-EGFP/+::R26lsl-tdTomato/+ mice were selected by their red fluorescence and were combined in each experiment. Four brains were pooled for each sample. The brains were extracted in ice-cold KREBS solution and cut in the vibratome in 300 micrometer slices and cells were dissociated as in a previous publication (Gezelius et al., 2016).

value: Neurons

tag: age

value: Post natal day 0


title: M_95


title: P0_TOM_VPM3

value: Thalamus, Ventral Posteriomedial Nucleus


title: P0_TOM_VPM1


title: L_250_29524_ACTTGA


title: P0_TOM_VPM2


title: P0_TOM_MGV3

source_name: Thalamus, Medial Geniculate Nucleus, ventral division


title: P0_TOM_DLG4

source_name: Thalamus, dorsolateral Geniculate Nucleus


title: P0_TOM_DLG2

value: Thalamus, dorsolateral Geniculate Nucleus


title: P0_TOM_MGV2

value: Thalamus, Medial Geniculate Nucleus, ventral division


title: P0_TOM_DLG3


title: P0_TOM_DLG1


title: VPMd

data_processing:
Quality control of the raw data was performed with FastQC (v.0.11.7).
RNA-seq reads were mapped to the Mouse genome (GRCm.38.p6/mm10 Ensembl release 95, Jan 2019) using STAR (v2.7.0d) (Dobin et al., 2013) and SAM/BAM files were further processed using SAMtools v1.9. (Li et al., 2009).
Aligned reads were counted and assigned to genes using Ensembl release 95 gene annotation and FeatureCounts, Subread (v1.6.4) (Liao et al., 2014).
Genome_build: GRCm.38.p6/mm10 Ensembl release 95, Jan 2019
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include Gene Counts values for each Sample.

extract_protocol:
Total RNA extraction was done using the RNeasy® Micro Kit (Qiagen, #74004).
cDNA libraries were prepared using SMARTer TM Ultra Low RNA Kit v4 and NEBNext Ultra DNA Library Prep for Illumina according to the manufacturer’s instructions. Then the libraries were sequenced for 50pb single-read and performed on an Illumina HiSeq2500 V4 using 1x50 sequencing to read depth of > 25 million reads per sample at CNAG-CRG facility at Barcelona (Spain).

treatment_protocol: Brains of P7 Gfap::GFP mice were selected by their green fluorescence and were combined in each experiment. Four brains were pooled for each sample. The brains were extracted in ice-cold KREBS solution and cut in the vibratome in 300ul slices and cells were dissociated as in a previous publication (Gezelius et al., 2016).

value: FVB

value: Astrocytes

value: Postnatal day 7


title: P0_TOM_MGV1


title: VPMb


title: VPMa


title: VPMc


title: MGVd


title: MGVa


title: MGVb


title: MGVc


title: DLGe


title: DLGd


title: DLGb


title: DLGa


title: DLGc


title: CXd

source_name: Cortex

value: Cortex


title: CXc


title: CXb


title: CXa


title: 9_Sito_1h

city: Rehovot

first: Mike

last: Fainzilber

address: 234 Herzl Street

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description: beta-sitosterol injected mouse  - tissue harvested 1hr after injection

data_processing:
Fastq files for each sample were generated by the usage of Illumina CASAVA-1.8.2 software (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome GRCm38 using, TopHat (v2.0.10).
Counting reads on reference genome GRCm38, Ensembl realese 82, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts, normalized_counts

extract_protocol:
Total RNA was extracted from hippocampi dissected from either wild type animals treated with vehicle or beta-sitosterol injection 1hr and 6hrs prior to dissection using the RNAqueous-Micro Kit (Ambion) according to manufacturer’s instructions. Replicates of high RNA integrity (RIN≥7) were processed for RNA-Seq at the Crown Institute for Genomics (G-INCPM, Weizmann Institute of Science).
TruSeq mRNA

treatment_protocol: beta-sitosterol (SIGMA-ALDRICH, Cat#S1270) was administered intraperitoneally at 100mg/kg

value: wild-type

value: 100mg/kg beta-sitosterol

tag: timepoint

value: hippocampus


title: 8_Sito_1h


title: 6_Sito_1h


title: 7_Sito_1h


title: 4_Veh_1h

description: vehicle-treated mouse  - tissue harvested 1hr after injection

value: vehicle


title: 5_Veh_1h


title: 20_Sito_6h

description: beta-sitosterol injected mouse  - tissue harvested 6hrs after injection


title: 3_Veh_1h


title: 18_Sito_6h


title: 19_Sito_6h


title: 14_Veh_6h

description: vehicle-treated mouse  - tissue harvested 6hrs after injection


title: v6h21

description: vehicle-treated mouse - tissue harvested 6hrs after injection

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome GRCm38 using STAR (2.4.2a).
Counting reads on reference genome GRCm38, Ensembl realese 92, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq Normalization)

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from hippocampi dissected from either wild type animals treated with vehicle or stigmasterol injection 1hr and 6hrs prior to dissection using the RNAqueous-Micro Kit (Ambion) according to manufacturer’s instructions. Replicates of high RNA integrity (RIN≥7) were processed for RNA-Seq at the Crown Institute for Genomics (G-INCPM, Weizmann Institute of Science).
TruSeq mRNA

treatment_protocol: beta-sitosterol (SIGMA-ALDRICH, Cat#S2424) was administered intraperitoneally at 100mg/kg

value: Hippocampus

tag: agent

tag: time point


title: 17_Sito_6h


title: 13_Veh_6h


title: 11_Veh_6h


title: 12_Veh_6h


title: v6h14


title: 2_Veh_1h


title: v6h12


title: St6h23

description: Stigmasterol-treated mouse - tissue harvested 6hrs after injection

value: Stigmasterol


title: v1h4

description: vehicle-treated mouse - tissue harvested 1hr after injection


title: v1h5


title: St6h22


title: St6h13


title: St1h8

description: Stigmasterol-treated mouse - tissue harvested 1hr after injection


title: St1h11


title: St1h1


title: ChIP_Prim_Gata1

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: Genome-wide library of Immunoprecipitated fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, mm9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions.
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs (bedtools bedpe | cut -f 1,2,6) - for visualisation.
Pileup of fragments (bedtools genomecov -counts).
Generating bigwig tracks.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage conversion of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30).

source_name: Definitive erythroid

growth_protocol: Primary primitive erythroblasts were derived from yolk sacs at embryonic day 10.5 (E10.5). A total of ~1x106 erythroblasts were obtained from each single embryo.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed on 3-5x10^6 cells per replicate using the ChIP Assay Kit (Cat. No. 17-295, Millipore). All stages beyond the fixation stage used kit solutions as per the manufacturer’s instructions. A single 10 minute 1% formaldehyde fixation was used for all antibodies. The cross-linking reaction was quenched by addition of glycine (Sigma-Aldrich) to a final concentration of 130mM), then washed once in PBS and snap frozen. Samples were stored at -80C prior to further processing. Cells were lysed in SDS lysis buffer with Complete Proteinase Inhibitor Cocktail (PIC, Roche). Samples were then fragmented using the Covaris S220 Focused ultra-sonicator with the following settings (Duty Cycle: 2%, Intensity: 3.0, Cycles/burst: 200, Power mode: Freq. Sweeping, Duration: 120s, Temp: 6C, Batches: 4). Sonicated chromatin samples were diluted 1:10 in ChIP dilution buffer containing PIC to 2mL. Before addition of the antibody, 100 μL was taken from each 2mL sample to be used as a 5% input. The chromatin was pre-cleared with Protein A agarose for 30 min before immunoprecipitation overnight at 4C rotating (the volumes added are also shown). Protein A agarose beads were added the next morning for 60 min at 4C, after which the beads were sequentially washed in Low Salt Buffer (1x), High Salt Buffer (1x), LiCl Buffer (1x) and TE Buffer (2x) with the final TE buffer wash at room temperature. Bound chromatin fragments were eluted from beads in elution buffer (1% SDS, 0.1M NaHCO3), de-crosslinked by incubating samples at 65C for 5 hours, then proteinase K treated for one hour at 55C. DNA was precipitated using phenol/chloroform extraction and ethanol precipitation with GlycoBlue (15mg/mL) (Thermo Scientific) to visualise the pellet prior to dissolving in 55 μL of H2O.
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: Erythrocytes from mouse yolk sac

tag: chip antibody

value: ab11852 (Abcam)


title: ChIP_Def_FetLiver_Gata1

growth_protocol: Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cell suspension was expanded for 5–7 d in Stempro (Invitrogen) supplemented with Epo (1 U/ml), SCF (50 ng/ml) and dexamethasone (1 μM). After expansion of the cultures, mature red blood cells were removed by negative selection for Ter119 using anti-Ter119 magnetic beads (Miltenyi Biotec), to obtain a population of erythroid precursors, which was then purified by CD44 positive cell sorting before being placed into expansion media to recover for 6 hours.

value: Cultured fetal liver cells


title: ChIP_Prim_Input_rep5

source_name: Primitive Erythroid

growth_protocol: Primary primitive erythroblasts were derived from yolk sacs at embryonic day 10.5 (E10.5). A total of ~1x10^6 erythroblasts were obtained from each single embryo.


title: ChIP_Prim_Input_rep6


title: ChIP_Prim_Input_rep7


title: ChIP_Prim_Input_rep2


title: ChIP_Prim_Input_rep3


title: ChIP_Prim_Input_rep4


title: ChIP_Prim_H3K4me3_rep3

value: ab8580 (Abcam)


title: ChIP_Prim_H3K4me3_rep4


title: v1h9


title: ChIP_Prim_Input_rep1


title: ChIP_Prim_H3K4me1_rep5

value: 07-436 (Merck Millipore)


title: ChIP_Prim_H3K4me3_rep1


title: ChIP_Prim_H3K4me1_rep7


title: ChIP_Prim_H3K27ac_rep2

value: ab4729 (abcam)


title: ChIP_Prim_H3K27ac_rep3


title: ChIP_Prim_H3K27ac_rep1


title: ChIP_Prim_H3K27ac_rep4


title: ChIP_Prim_CTCF_rep7

value: 07-729 (Merck Millipore)


title: ChIP_Prim_CTCF_rep6


title: ChIP_Def_ter119_Spleen_H2A1119Ub

growth_protocol: Spleen derived erythroid cells were obtained from spleens of C57BL/6-cross-CBA/J F1 hybrid mice treated with phenylhydrazine (40 mg g-1 body weight per dose, with three doses given 12 h apart; mice were killed on day 5). Spleens, consisting of >80 % CD71+ ter119+ erythroid cells due to hemolytic anemia, were dissociated in Phosphate buffered solution (PBS) and strained through a 30 µM filter (Miltenyi Biotec) to remove clumps. For ter119+ selection, 3×10^8 cells were resuspended in 3 ml of FACS buffer (PBS with 10% FBS) and stained with 0.9 µg anti-ter119-PE (130-102-338; Miltenyi Biotec). Stained cells were conjugated to anti-PE microbeads (130-048-801; Miltenyi Biotec) and passed through 3 LS Columns (Miltenyi Biotec).

value: Erythrocytes from spleen


title: Neuron - Brg1 WT, KCl treated - rep2

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

data_processing:
Adapter sequences were recognized and removed by in-house scripts.
bowtie2 was used to map trimmed reads to GRCm38 reference genome with option "--fast-local".
MACS2 was used to call narrow peaks with options "--nomodel --shift -100 --extsize 200 "
Reads of nucleosome-free DNA fragments were identified based on fragment length less than 100 bp in genome.
Nucleosome free regions were detected by MACS2 using reads of nucleosome-free fragments. Two replicates were merged.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig, narrow-peak format is BED6+4, with each column being chromosome, start, end, name, score, strand, signalValue, pValue, qValue, peak.

source_name: Neuron

growth_protocol: Primary cortical neurons were cultured from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).

extract_protocol:
Neurons (50,000 cells/sample, n=2 in each condition) were lysed with lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). The transposition reaction was performed using Tn5 transposase from the Nextra kit (Illumina, FC-121-1030) at 37 ºC for 30 min. Transposed DNA samples were purified using a Qiagen MinElute Kit (catalog no. 28004) followed by PCR amplification.
Sequencing libraries were generated using Ad1_noMX with barcoded primers and were amplified (7-9 cycles) before DNA purification and concentration. All samples were sequenced using an Illumina sequencer with 75-bp paired end reads and 60 million reads were obtained for each library.

treatment_protocol: For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.

value: Brg1 WT

value: Primary cultured cortical neurons

value: 50 mM KCl treated 1h


title: Neuron - Brg1 WT, no KCl treatment - rep1

value: No KCl treatment


title: Neuron - Brg1 WT, KCl treated - rep1


title: Neuron - Brg1 WT, no KCl treatment - rep2


title: ChIP_Prim_CTCF_rep5


title: ChIP_Prim_H3K4me3_rep2


title: Neuron - Brg1 cKO, KCl treated - rep1

value: Brg1-cko (BAF53bCre Brg1F/F)


title: Neuron - Brg1 cKO, KCl treated - rep2


title: ChIP_Prim_H3K4me1_rep6


title: Neuron - Brg1 cKO, no KCl treatment - rep2


title: NK.27-11+.Sp Rep2

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

country: France

institute: Hospices Civils de Lyon

data_processing:
Alignment and QC by the ENCODE pipeline (BigDataScript version 0.3.4, https://github.com/kundajelab/atac_dnase_pipelines).
Peak calling with MACS2 version 2.1.2 and the following parameters:  --gsize "hs" --bdg --qvalue 0.00001 --shift 75 --extsize 150 --nomodel --keep-dup all --call-summits –nolambda
Peak processing as described in Corces et al, Science 2018 (500 bp wide, overlap resolution, at least in 2 samples).
Reads per peak counted on sorted “tagAlign” files using bedtools coverage version 2.27.1.
Count normalization using edgeR version 3.24.3 (TMM).
Peak annotation using custom R scripts and Biomart exports from Ensembl (2020-11-19).
Genome_build: mm10
Supplementary_files_format_and_content: Two maps are provided :  - « NK_T_count-L_count-NKT » peaks were collected from NK and T cells and used only for counting in other samples (mPTCLs and NKT cells).  - « NK_T_L_count-NKT » peaks were collected from mPTCLs, NK and T cells and used only for counting in other samples.    Three files are provided with each map :  - « counts.txt » are raw counts in peaks.  - « CPM.txt » are log2 Counts Per Millions after normalization, as provided by EdgeR.  - « peaks.txt » provides annotation for each peak.

source_name: NK cells

extract_protocol:
10.000 cells were Facs-sorted and tagmented as previously described (Corces et al. Science 2018).
ATAC-seq libraries were constructed by ligating Nextera sequencing primers (Buenrostro et al. Nature 2015) using PCR amplification.

value: WT

tag: phenotype

value: sorted on CD27- CD11b+ spleen NK cells


title: 19_diABZI_12h_4

city: Philadelphia

first: Sara

last: Cherry

state: PA

address: 472A Stemmler Hall

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

data_processing:
Raw fastq files were trimmed to remove adapters and low quality reads with bbduk v38.79 (https://sourceforge.net/projects/bbmap/) using the parameters “ref=/bbmap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=r trimq=10”.
Transcripts were counted using salmon v1.2.1 in pseudoalignment mode with the parameters “-l A --validateMappings --rangeFactorizationBins 4 --seqBias”. Reads from diABZI-treated cells were aligned to the Homo sapiens GRCh38 (hg38) transcriptome. Reads from SARS-CoV-2 infected cells were mapped to a chimeric transcriptome comprised of the Homo sapiens GRCh38 (hg38) transcriptome and the SARS-CoV-2 transcriptome. Reads from mouse lung were mapped to the GRCm38.p6 mouse transcriptome.
Transcripts were collapsed to the gene level and differential abundance calculations were performed with DESeq2
Genome_build: hg38 (human) and m38.p6 (mouse)
Supplementary_files_format_and_content: CSV comparison files are the differential abundance calculations for each condition from DESeq2
Supplementary_files_format_and_content: quant.sf files contain transcript-level counts from Salmon

source_name: mouse lung

growth_protocol:
Calu3 cells: Calu-3 cells (ATCC HTB-55) were cultured in Minimum Essential Medium (MEM) supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) non-essential amino acids, 0.1% (v/v) penicillin/streptomycin, 4 mM L-glutamine at 37°C and 5% CO2
Mice: Animal studies were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. Animals were housed in groups and fed standard chow diets. Eight- to nine-week-old mice of both sexes were used.

extract_protocol:
Calu3 cells: Total RNA was isolated using TRIzol Reagent (Invitrogen) and purified using RNA Clean & Concentrator Kits (Zymo Research).
Mice: Lung tissues were snap frozen in liquid nitrogen and homogenized with a bead beating grinder and lysis system. 900ul of TRIzol Reagent was added to 100ul of homogenized tissue.
RNAseq Libraries for next-generation sequencing were prepared using the Illumina TruSeq stranded mRNA kit with Illumina TruSeq unique dual indices. Quality and quantity control of RNA and libraries were performed using an Agilent 4200 TapeStation and Qubit 4, respectively. Libraries were diluted to a final concentration of 4 nM and sequenced on an Illumina NextSeq 500 instrument to produce 75–base pair single end reads.

treatment_protocol:
Calu3 cells: Cells (7x105 cells/well) were seeded into 6-well plates. The next day, if indicated, cells were pretreated with compounds for 1 h at 37°C. Cells were inoculated with SARS-CoV-2 (MOI 0.5) for the indicated time.
Mice: Animals were treated via an intranasal route with 10 µg diABZI or vehicle control.

value: intranasal diABZI

tag: time


title: 13_PBS_12h_3

value: intranasal PBS


title: 15_PBS_12h_5


title: 20_diABZI_12h_5


title: 18_diABZI_12h_3


title: 17_diABZI_12h_2


title: 12_PBS_12h_2


title: 14_PBS_12h_4


title: 11_PBS_12h_1


title: 09_diABZI_6h_4

description: Compare_condition_diABZI.06_vs_mock.06.csv


title: 05_PBS_6h_5


title: 03_PBS_6h_3


title: 04_PBS_6h_4


title: 16_diABZI_12h_1


title: 01_PBS_6h_1


title: 08_diABZI_6h_3


title: 06_diABZI_6h_1


title: Neuron - Brg1 cKO, no KCl treatment - rep1


title: NK.27-11+.Sp Rep3


title: 07_diABZI_6h_2


title: Sample 19_female_H3K4me1_2nd

city: Wakayama

first: Gen

last: Yamada

address: 811–1 Kimiidera

department: Institute of Advanced Medicine

institute: Wakayama Medical University

data_processing:
Read quality was checked for each sample using FASTQC version 0.11.5.
Reads were mapped to the reference mouse genome UCSC version mm10 using option ‘-k 2’ in Bowtie2 version 2.3.2.
Duplicate reads were excluded with SAMtools version 1.5.
Peak detection was done using the MACS algorithm version 2.1.1.20160309 with option '--to-large --nomodel'.
Genome_build: mm10
Supplementary_files_format_and_content: The BED files were genrated utiizing MACS algorithm.

growth_protocol: Pregnant ICR mice were housed in breeding cages followed with approved Wakayama Medical University guidelines. Noon on the day when the vaginal plug was detected was designed as E0.5.

extract_protocol:
eExG were crosslinked with 20mM EGS (Thermo Fisher Scientific Inc.)  and 1% formaldehyde. Cross-linked chromatin was digested by MNase (Takara) and sonicated.
Immunoprecipitated DNA library for Ion Torrent was prepared in accordance with NEB Next Fast DNA Library Prep Set for Ion Torrent (NEW ENGLAND BioLabs. Inc). Immunoprecipitated DNA library for NextSeq was prepared in accordance with KAPA LTP Library preparation Kit (KAPA), SeqCap Adaptor Kit A (Roche), and Agencourt AMPure XP Beads (Beckman Coulter). High-thoughput sequencing was performed by using Ion Proton system (Thermo Fisher Scientific) and NextSeq 500 Desktop Sequencer (Illumina).

value: CD1 (ICR)

tag: Sex

value: female

tag: embryonic day

tag: tissue/cell type

value: murine  embryonic external genitalia (eExG)

value: Anti-Histone H3 (mono methyl K4)   (Abcam:8895)


title: Sample 20_female_Sp1_1st

value: Anti-Sp1  (Bethyl  Lab. INC:A303-944A)


title: Sample 17_female_input_2nd


title: Sample 16_male_Sp1_1st

value: male


title: 02_PBS_6h_2

tag: treatment


title: Sample 15_male_H3K4me1_2nd


title: Sample 18_female_H3K27Ac_2nd

value: Anti-Histone H3 (acetyl K27)   (Abcam:4729)


title: Sample 14_male_H3K27Ac_2nd


title: 10_diABZI_6h_5


title: Sample 13_male_input_2nd


title: IL22 technical replicate 2

city: Chapel Hill

first: Misty

last: Good

state: NC

address: 101 Manning Drive 4th Floor CB 7596

institute: University of North Carolina at Chapel Hill

description: IL22 treated enteroids, mouse 1, well 2

data_processing:
from Kumar et al. (2016)-  doi: 10.1016/j.immuni.2016.02.007
Rawreads from Illumina NextSeq500’s in fastq format were trimmed to remove adaptor/primer sequences
Trimmed reads were then aligned using BWA (version 0.5.9, settings aln -o 1 -e 10 -i 5 -k 2 -t 8) against the mouse genome build 37.2 in geneSifter AnalysisEdition for Next Generation Sequencing (Geospiza, Seattle, WA).
Additional alignment and post-processing were done with Picard tools (version 1.58) including local realignment and score recalibration to generate a finale genomic aligned set of reads.
Reads mapping to the genome were characterized as exon, intron, or intergenic using the matched annotation for the genomic reference sequence.
The remaining unmapped reads from the genomic alignment were then aligned to a splice reference created using all possible combinations of known exons and then categorizing these as known or novel splice events.
This aligned data was then used to calculate gene expression by taking the total of exon and known splice reads for each annotated gene to generate a count value per gene.
For each gene there was also a normalized expression value generated in two ways: 1) Reads per Mapped Million (RPM), which was calculated by taking the count value and dividing it by the number of million mapped reads, 2) Reads per Mapped Million per Kilobase (RPKM), which was calculated by taking the RPM vale and dividing it by the kilobase length of the longest transcript for each gene.
The RPM values were subsequently used for comparing gene expression across samples to remove the bias ofdifferent numbers of reads mapped per sample.
RPKM values were subsequently used for comparing relative expression of genes to one another to remove the bias of different numbers of mapped reads and different transcript lengths.
The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: mouse genome build 37.2
Supplementary_files_format_and_content: Supplemental table 2.xls: A spreadsheet summarizing RNA-seq analysis and differential gene expression in intestinal enteroids from adult mice and treated with PBS or 2 ng/ml of Il22 for 24 hours.

source_name: enteroids

growth_protocol: All animal experiments were performed in an American Association for the Accreditation of Laboratory Animal Care-accredited and specific pathogen-free animal facility at the Washington University School of Medicine in St. Louis. C57BL/6 mice were bred, maintained and housed in accordance with the procedures outlined in the Guide for the Care and Use of Laboratory Animals under an animal study proposal approved by the Institutional Animal Care and Use Committee (IACUC) (protocol #20190190) of the Washington University School of Medicine in St. Louis.

extract_protocol:
Total RNA was extracted using Trizol with Ambion's protocol.
mRNA was purified with oligo-dT beads, and used for cDNA synthesis with random primers after a fragmentation step with magnesium followed by heat-catalyzed hydrolysis. The cDNA 3’ ends were adenylated, followed by adaptor ligation and a 15-cycle PCR to enrich DNA fragments. cDNA libraries were generated using a v2 Guide Quantification of cDNA libraries was performed by using Kapa Biosystems primer premix kit with Illumina-compatible DNA primers. The cDNA libraries were pooled at a final concentration 1.8 pM. Single-read sequencing was performed on Illumina Genome Analyzer IIx and NextSeq 500.

treatment_protocol: Murine enteroids were generated from isolated crypts from the small intestines of adult (8 weeks) or neonatal mice (7 days) as previously described40. The crypts were resuspended in Matrigel and cultured for 24 hours in 50% L-WRN conditioned medium supplemented with 10 μM Y-27632 and SB 202190. The following day, the enteroids were differentiated in Advanced DMEM/F12 medium (Gibco) supplemented with 2 mM GlutaMax (Invitrogen), 10 mM HEPES]. For differentiation, the enteroids were cultured in differentiation media consisting of basal culture medium with (1X) N2 supplement (Invitrogen), (1X) B27 supplement (Invitrogen), and 1 mM N-acetylcysteine (Sigma Aldrich), 50 ng/mL murine recombinant EGF (Invitrogen), 10 ng/mL murine recombinant Noggin (PeproTech), 10 ng/mL human recombinant R-spondin 1 (Miltenyi Biotec). After 4 days in the differentiation medium, the enteroids were treated with 2 ng/ml of recombinant mouse IL-22 (Biolegend) for 24 hours before being further processed.

tag: tissue

value: enteroids

tag: background

value: 6 weeks

tag: nec or control mice

value: control

value: 2 ng/ml of recombinant mouse IL-22 for 24 hours


title: Control 1 technical replicate 1

description: Control enteroids, mouse 1, well 1

value: untreated


title: Control 2 techncal replicate 1

description: Control enteroids, mouse 2, well 1


title: Control 2 technical replicate 2

description: Control enteroids, mouse 2, well 2


title: ESCs, WT.0h.RNA-seq

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode  (mm10 vM13) transcriptome using Bowtie2  (v2.2.5) and RSEM  (v1.3.0)
Gene expression level was calculated using EDASeq  (v2.4.1) GC-normalized method
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value file containing GC-normalized RNA-seq data

source_name: mouse embryonic stem cells (mESCs)

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: Treated with 2µg/ml doxycycline

tag: cell type

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

value: no doxycycline

tag: passage


title: IL22 technical replicate 1

description: IL22 treated enteroids, mouse 1, well 1


title: ESCs, Ss18-KO.8h.RNA-seq

tag: strain

tag: genotype

value: treated with doxycycline for 8h


title: ESCs, Ss18-ChIP-seq.8h

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions


title: ESCs, Ss18-KO.0h.RNA-seq

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium  (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)


title: ESCs, Ss18-ChIP-seq.0h


title: ESCs, Ss18-KO.24h.RNA-seq

value: treated with doxycycline for 24h


title: ESCs, Jun-ChIP-seq.8h

value: Abcam, ab31419


title: ESCs, H3K27ac-ChIP-seq.12h

value: treated with doxycycline for 12h

value: H3K27ac (Abcam, ab4729)


title: ESCs, H3K27ac-ChIP-seq.8h


title: ESCs, Dox.8h.ATAC

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ATAC-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

value: Dox


title: ESCs, Dox.12h.ATAC


title: ESCs, H3K27ac-ChIP-seq.0h


title: ESCs, H3K27ac-ChIP-seq.4h

value: treated with doxycycline for 4h


title: Control 1 technical replicate 2

description: Control enteroids, mouse 1, well 2

tag: age


title: RNA-seq_A375_control_rep4

city: Boston

first: Jingyi

last: Wu

address: 360 Longwood Ave

department: Department of Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Base-calling was performed using bcl2fastq2-v2.20.0
reads were aligned using salmon  (version 0.14.1) with parameters --gcBias --seqBias --validateMappings. Summary to gene level quantification was performed using Tximport (version 1.14.2)
genome build: Genome Reference Consortium Human Build 38 release 92
processed data files format and content: gene-by-sample raw count matrix

source_name: A375 - in vitro

growth_protocol: All cell lines were tested for mycoplasma and cultured in RPMI (VWR) or DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Approximately one million cells per sample were resuspended in RLT lysis buffer with ß-mercaptoethanol (1:100 dilution) and total RNA was isolated using an RNeasy Kit.
Poly(A)-enriched sequencing libraries were constructed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to A375 cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). No additional treatments were administered.

tag: cell line

tag: genotype/variation

value: Control


title: RNA-seq_A375_control_rep3


title: ESCs, WT.24h.RNA-seq


title: ESCs, Dox.4h.ATAC

tag: agent


title: RNA-seq_A375_control_rep2


title: RNA-seq_A375_control_rep1


title: RNA-seq_A375_KO_rep4

value: Setdb1 KO


title: ESCs, Dox.0h.ATAC


title: ESCs, WT.8h.RNA-seq


title: RNA-seq_A375_KO_rep1


title: X5_RS_S9

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Post-sequencing, read quality was assessed using FastQC v.0.11.4 and trimmed using Trim Galore v0.4.1. Reads were mapped to the GRCh38 genome using STAR v2.5.2. The number of reads that map to genes was calculated using HTSeq v0.6.0.
Normalization and differential gene expression analysis was performed using the R package edgeR, version 3.16.5 (R version 3.3.3). Genes with FDR-adjusted p-value<0.05 were identified as differentially expressed. Hierarchical clustering and heatmap visualization of genes showing differential expression between SIPS (Dox 1+21d) and control samples was performed using the online tool Morpheus (https://software.broadinstitute.org/morpheus) (Broad Institute).
Genome_build: GRCh38

source_name: vascular smooth muscle cells

extract_protocol:
mRNA was isolated using Nucleospin RNA columns (Macherey-Nagel) and concentrations determined by Nanodrop
RNA libraries were prepared using the TruSeq mRNA library preparation kit (Illumina, UK) and sequenced on a NextSeq sequencer (Illumina, UK) using a 75 cycle high output kit

value: vascular smooth muscle cells


title: RNA-seq_A375_KO_rep2


title: RNA-seq_A375_KO_rep3


title: X5_Dox1d_S3


title: X4_Dox21d_S15


title: X4_Dox1d_S14


title: X5_Ctr_S1


title: 3

city: Guangzhou

first: Yun

last: Ling

address: 107 Yanjiang West Road

institute: Sun Yat-sen University

data_processing:
Basecalls performed using RTA version 2
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch.
To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Genome_build: mm10
Supplementary_files_format_and_content: TagCount values for each Sample

source_name: SK-BR-3 cells

growth_protocol: The SK-BR-3 cell line (ATCC, USA) was cultured in Dulbecco’s modified Eagle’s medium (DMEM) high glucose supplemented with 10% fetal bovine serum, 100 U/ml of penicillin, and 100 μg/ml of streptomycin in 5% CO2 at 37˚C. When the cells reached 80-90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum.

extract_protocol:
Total RNA was extracted from cells using magnetic beads (Life Technologies, NY, USA), in accordance with the manufacturer’s protocol.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SK-BR-3 were transfected with circCDYL probe and NC probe

value: transfect with NC probe

value: breast cancer cells


title: X4_Ctr_S13


title: X3_Dox21d_S11


title: X3_RS_S12


title: X2_Dox21d_S5


title: X3_Ctr_S7


title: X2_RS_S6


title: X3_Dox1d_S10


title: X2_Dox1d_S4


title: X2_Ctr_S2


title: calu3_sars-cov2_3_24h

source_name: Calu3 cells

value: Calu3 - lung epithelial cells

value: mock-infection


title: calu3_sars-cov2_3_48h


title: MDA_MB_231_DMSO_2

first: Maria

last: Barrero

address: Crta. Majadahonda-Pozuelo KM 2.2

data_processing:
RNA-seq processing:
RNA-seq analysis was performed with the nextpresso pipeline v1.9, using the following tools:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19

source_name: MDA-MB-231 cells

extract_protocol:
Cells were trypsinized and total RNA was extracted using the RNeasy kit (Qiagen).
From 1 µg of total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit. Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced for 50 bases in a single-read format (Illumina HiSeq 2000).

value: DMSO


title: 4

value: transfect with circCDYL probe


title: calu3_sars-cov2_2_24h


title: calu3_sars-cov2_1_24h


title: calu3_noninfected_3_48h


title: calu3_noninfected_3_24h


title: calu3_sars-cov2_2_48h


title: calu3_sars-cov2_1_48h


title: X4_RS_S16


title: Calu3_drug_6h_set2

value: diABZI


title: calu3_noninfected_1_48h


title: X5_Dox21d_S8


title: calu3_noninfected_2_24h


title: calu3_noninfected_1_24h


title: Calu3_drug_12h_set1


title: Calu3_DMSO_6h_set1


title: Calu3_drug_12h_set2


title: Calu3_DMSO_12h_set2


title: Calu3_DMSO_12h_set1


title: Calu3_drug_6h_set1


title: HepG2_live178

city: Hong Kong

first: Xinlei

last: Wang

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

institute: HKUST

data_processing:
Index and adapter were trimmed in data downloaded form Basespace
Quality control was done using Fastqc
Alignment and quantification were done by mapping raw reads to GRCh38 using kallisto 0.46.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression/Transcript expression matrix(TPM)

source_name: HepG2 live178

growth_protocol: Both HepG2 and HCT-116 cell lines were culured with DMEM medium, supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum

extract_protocol: cDNA library was constructed using Smart-seq2 protocl, sequencing library was prepared using Illuminar Nextera DNA Library Prep Kit(Illumina, cat#FC-131-1096), we followed library contruction protocal provided by C1 Fluidigm(Fluidigm)

treatment_protocol: 80% methanol was used for cell fixation, fixed cells were stored in -80℃ for one week before further processing


title: HepG2_live177

source_name: HepG2 live177


title: HepG2_live173

source_name: HepG2 live173


title: HepG2_live176

source_name: HepG2 live176


title: HepG2_live171

source_name: HepG2 live171


title: HepG2_live175

source_name: HepG2 live175


title: HepG2_live174

source_name: HepG2 live174


title: calu3_noninfected_2_48h


title: HepG2_live170

source_name: HepG2 live170


title: HepG2_live172

source_name: HepG2 live172


title: HepG2_live162

source_name: HepG2 live162


title: HepG2_live168

source_name: HepG2 live168


title: HepG2_live165

source_name: HepG2 live165


title: HepG2_live163

source_name: HepG2 live163


title: HepG2_live166

source_name: HepG2 live166


title: HepG2_live169

source_name: HepG2 live169


title: HepG2_live167

source_name: HepG2 live167


title: HepG2_live161

source_name: HepG2 live161


title: HepG2_live160

source_name: HepG2 live160


title: Calu3_DMSO_6h_set2

source_name: Calu3 cells


title: HepG2_live158

source_name: HepG2 live158


title: HepG2_live159

source_name: HepG2 live159


title: HepG2_live157

source_name: HepG2 live157


title: HepG2_live154

source_name: HepG2 live154


title: HepG2_live153

source_name: HepG2 live153


title: HepG2_live156

source_name: HepG2 live156


title: HepG2_live151

source_name: HepG2 live151


title: HepG2_live155

source_name: HepG2 live155


title: HepG2_live150

source_name: HepG2 live150


title: HepG2_live145

source_name: HepG2 live145


title: HepG2_live146

source_name: HepG2 live146


title: HepG2_live147

source_name: HepG2 live147


title: HepG2_live148

source_name: HepG2 live148


title: HepG2_live164

source_name: HepG2 live164


title: HepG2_live149

source_name: HepG2 live149


title: HepG2_live141

source_name: HepG2 live141


title: HepG2_live142

source_name: HepG2 live142


title: HepG2_live144

source_name: HepG2 live144


title: HepG2_live139

source_name: HepG2 live139


title: HepG2_live138

source_name: HepG2 live138


title: HepG2_live135

source_name: HepG2 live135


title: HepG2_live133

source_name: HepG2 live133


title: HepG2_live136

source_name: HepG2 live136


title: HepG2_live131

source_name: HepG2 live131


title: HepG2_live137

source_name: HepG2 live137


title: HepG2_live134

source_name: HepG2 live134


title: HepG2_live140

source_name: HepG2 live140


title: HepG2_live152

source_name: HepG2 live152


title: HepG2_live125

source_name: HepG2 live125


title: HepG2_live127

source_name: HepG2 live127


title: HepG2_live143

source_name: HepG2 live143


title: HepG2_live132

source_name: HepG2 live132


title: HepG2_live129

source_name: HepG2 live129


title: HepG2_live126

source_name: HepG2 live126


title: HepG2_live123

source_name: HepG2 live123


title: HepG2_live122

source_name: HepG2 live122


title: HepG2_live118

source_name: HepG2 live118


title: HepG2_live120

source_name: HepG2 live120


title: HepG2_live117

source_name: HepG2 live117