title: smartseq_TD_3

data_processing:
The reads were mapped to the mm10 using STAR.
The summarizeOverlaps function from the GenomicAlignments package was used to define gene expression level by counting the alignments to exons
Assembly: mm10
Supplementary files format and content: normalized count by DESeq2

source_name: Sorted tumor cell from T cell depletion treatment

growth_protocol: Braf/Pten mTmG mice were treated with 4-hydroxytamoxifen (4-HT) on the skin surface to induce tumor formation.

extract_protocol:
500 viable GFP+ cancer cells from Braf/Pten-mTmG mice were isolated by FACS cell sorters directly into lysis buffer
Performed by low-input Smart-seq2 mRNA sequencing protocol.

treatment_protocol: Tumor bearing Braf/PTEN mice, two weeks after tumor induction, were treated with anti-CD4 and anti-CD8 antibodies.

value: Sorted tumor cell


title: TCR-seq_C1

status: Public on Nov 15 2022

type: SRA

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

library_source: transcriptomic

data_processing:
TCR repertoire analysis and clonotype identification was done by MiXCR
The diversity estimation was quantified by “immunarch” package in R
Assembly: Mouse TCR library
Library strategy: TCR_seq

molecule: total RNA

organism: Mus musculus

source_name: Sorted T cells from Braf/Pten induciable melanoma tumor

growth_protocol: Braf/Pten mice were treated with 4-hydroxytamoxifen (4-HT) on the skin surface to induce tumor formation.

extract_protocol:
TILs were lysis by Lysis/Binding Buffer for mRNA purification.
Murine TCR beta-chain specific primer was used for amplification

treatment_protocol: Tumor bearing Braf/PTEN mice, two weeks after tumor induction, were treated with a gradually decreased dosage of anti-CD4 and anti-CD8 antibodies.

tag: strain

tag: cell type

value: Sorted CD45+ CD3+ CD8+ CD44+ tumor-infiltrating T cells

tag: tumor type

value: Braf/Pten inducible melanoma tumor

tag: treatment

value: control


title: smartseq_TD_2

value: T cell depletion


title: smartseq_TD_1


title: LAX7R BCL6 ChIPseq

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

country: USA

institute: UCSF

library_source: genomic

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Assembly: human hg18 build
Supplementary files format and content: bigwig and bigbed formats

molecule: genomic DNA

organism: Homo sapiens

source_name: LAX7R ALL cell

growth_protocol: The human SEM and RCH-ACV ALL cell lines purchased from DSMZ (Braunschweig, Germany) and maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, CA) with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin. Primary human ALL samples ICN12 ICN13 and LAX7R were cultured on OP9 stroma in Minimum Essential Medium (MEMα, Life Technologies) with GlutaMAX containing 20% FBS, 100 IU ml−1 penicillin, 100 μg ml−1 streptomycin and 1mM sodium pyruvate at 37°C in a humidified incubator with 5% CO2. (reference: Geng et al. Cancer Cell  . 2015 Mar 9;27(3):409-25. doi: 10.1016/j.ccell.2015.02.003; Hurtz et al. Genes Dev . 2019 Sep 1;33(17-18):1265-1279. doi: 10.1101/gad.327593.119.).

extract_protocol:
ChIP protocol: ALL cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.
Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

value: relapsed B-cell acute lymphomablastic leukemia with KRAS-G12V mutation

tag: chip antibody

tag: chip antibody host, amount, catalog number and provider

value: Rabbit, 2ug, 4242, Cell Signaling


title: ICN12 Input

source_name: ICN12 ALL cell

value: E2A-PBX1 B-cell acute lymphomablastic leukemia

value: Rabbit,  2ug, 2729, Cell Signaling


title: ICN12 BCL6 ChIPseq


title: smartseq_NC_2

source_name: Sorted tumor cell from control treatment


title: smartseq_NC_3


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® Derm replicate 1

status: Public on Nov 16 2022

type: RNA

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Individual samples were hybridized on Agilent SurePrint G3 Human GE v2 8x60K Microarrays (G4851B; design ID 039494)

scan_protocol: Microarrays were scanned immediately after washing on an Agilent Technologies G2505C DNA Microarray Scanner. Raw data on pixel intensities were extracted from the scanned images using Agilent Feature Extraction Software (version 10.7.3.1; Agilent Technologies, Amstelveen, Netherlands) with default parameters (Protocol: GE1_107_Sep09; Grid 039494_D_F_20120628)

data_processing: All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot, the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transfor-mation, and quantile normalization. Further preprocessing included the omission of flagged probes and merging of replicate probes based on median.

source_name: Phenion® Full-Thickness Skin Model

label_protocol: 0.2 ug RNA samples were labelled with Cyanine 3 (Cy3) following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands)

growth_protocol: The human Phenion® Full-Thickness Skin Model (Henkel AG & Co, Düsseldorf , Germany) was handled and cultured under sterile conditions, applicable to standard cell culture conditions. Upon arrival the tissues were contained in a 24-well plate containing a semi-solid transport medium and a plastic insert to prevent damage during transport. After arrival, the tissues were immediately removed from their transport plate according to the manufacturer’s instruction. In short, culture dishes were prepared in a manner that allowed the culture of each tissue separately. The Air lift (ALI)-cell culture medium, culture dishes, culture supports and filter papers were all provided with the tissues by the manufacturer. A 24 or 48 hour recovery period at standard cell culture conditions (37°C in a humidified atmosphere containing 5% CO2) was implemented after transfer, after which all culture medium was removed and replaced by fresh ALI-culture medium (37°C). Every tissue used in these experiments was of identical age at this point and could be cultured for at least another 10 days.

extract_protocol: After exposure, the skin tissues were collected and cut into 4 quarters. Two opposite pieces were used for RNA isolation whereas the other two pieces were stored at -80°C. The skin pieces for RNA isolation were submerged in 1 mL pre-chilled (4°C) QIAzol (Qiagen, Venlo, The Netherlands). A T10 basic ULTRA-TURRAX® (IKA, Staufen, Germany) was used to homogenate the tissue in about 30 seconds after which the solution was kept on ice until further processing (no longer than 15 minutes). Total RNA was isolated from the homogenates using the miRNeasy isolation kit (Qiagen, Venlo, The Netherlands) as instructed by the manufacturer. After isolation, RNA concentrations were measured on a NanoDrop spectrophotometer and the integrity was determined with a Bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands). Only samples of good quality (clear 18S and 28S peaks and the RNA integrity number (RIN) >6) were used for hybridization. An average RIN >9 was measured. Extracted RNA was stored at -80°C until it was used as template for cDNA synthesis.

treatment_protocol: The 3D skin tissues were exposed to the fillers by injecting ~0.3 mL directly under the top lay-er in the epidermal layer using a cross-hatching technique. The cross-hatching pattern ensures an equal distribution of the fillers in the whole tissue model. The commercial fillers Perfectha® and Bio-Alcamid® were injected as provided. The RIVM preparations (#1 to #5) were diluted with PBS 1:1 in order to be able to inject them. Unexposed tissue was used as control. Exposures lasted for 24 hours at 37°C and were performed in triplicate. Each set of exposures was performed on a different date using a fresh batch of tissue models, all constructed from the same donor. Thus, for each exposure three biological replicates were made.

tag: cell model

value: Phenion® Full-Thickness Skin Model

tag: included in analysis?

value: yes

value: exposed to Perfectha® Derm


title: RCH-ACV BCL6 ChIPseq

source_name: RCH-ACV ALL cell


title: ICN13 Input

source_name: ICN13 ALL cell

value: MLL-AF4 B-cell acute lymphomablastic leukemia


title: TCR-seq_C4


title: smartseq_NC_1


title: SEM Input

source_name: SEM ALL cell


title: SEM BCL6 ChIPseq


title: RCH-ACV Input


title: Primary cancer cell line from WT mice, WT6 (RRBS)

data_processing:
Base calling was performed by Illumina Real Time Analysis (v2.7.7) software and the base calls 26 were converted to short reads using Illumina2bam (http://gq1.github.io/illumina2bam/) tool.
Trimmomatic (v0.32) (Bioinformatics 30.15 (2014): 2114-2120) was used for trimming the adapter sequences.
Trimmed short read sequences were aligned onto the mm10 mouse reference genome with BSMAP(v2.90)62 aligner in RRBS mode
Methylation levels at the CpG sites were detected by using an in-house software called biseqMethCalling (https://github.com/epigen/biseqMethCalling), which was developed to better support RRBS data analysis.
Assembly: mm10
Supplementary files format and content: bed (column names are Chr, Start, End, Methylated reads/Total reads, Methylation Score , and Strand)

source_name: Primary cancer cell line

growth_protocol: The primary tumors were chopped mechanicallyand digested with collagenase and dispase. The cell extract was disaggregated with trypsin and further cultured in DMEM with 10% getal bovine serum and !% penicillin-streptomycin.

extract_protocol: DNA were collected by Qiagen Blood & Cell Culture DNA Kits

tag: genotype

value: WT

tag: tissue

value: primary tumor


title: Primary cancer cell line from Rag1KO mice, KO3 (RRBS)


title: Primary cancer cell line from WT mice, WT2 (RRBS)


title: SKMEL5 1 uM binimetinib replicate 3

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.
RNAseq reads were aligned to the human transcriptome prepared with the hg38 primary assembly and the Ensembl version 95 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: hg38 with ensembl 95 annotation
Supplementary_files_format_and_content: text files with ensembl gene IDs and 6 columns of either integer count data or log2 tpm (with +1 offset prior to log transformation)

source_name: SKMEL5 cells

growth_protocol: SKMEL5 cells were obtained from ATCC and maintained in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco). Cells were maintained at 37C, 5% CO2 and tested for mycoplasma contamination prior to RNA isolation. Cells were maintained at 37C, 5% CO2 and tested for mycoplasma contamination prior to RNA isolation.

extract_protocol:
At the time of harvest, cells were washed with ice-cold 1X PBS over ice and lysed in TRIzol reagent (Thermo Fischer Scientific). Total RNA was isolated from each sample using Direct-zol RNA miniprep kit (Zymo Research) according to manufacturer’s instructions.
RNA were confirmed for quality using the Agilent Fragment Analyzer and 300ng of material was polyA selected using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) modified to include two rounds of polyA binding and 10 minute incubations. cDNA was generated using the NEB Ultra II directional kit (E7760) following manufacturers protocol using 12 cycles of PCR and an 0.9X SPRI clean. The resulting libraries were quality assessed using the Fragment Analyzer and quantified by qPCR prior to be sequenced on the Illumina HiSeq2000. The 50nt single-end reads with a depth of at least 10 million reads per sample were sequenced for all conditions.

treatment_protocol: SKMEL5 cells treated with 100 nM or 1 uM binimetinib (Selleckchem, MEK162) for 72h.

tag: cell line

value: SKMEL5 cells

value: 1 uM binimetinib


title: Term-Exos1

city: Nanjing

first: Xiangyun

last: Yan

address: 123rd Tian Fei Xiang, Mo Chou Road, Nanjing 210004

country: China

institute: Women’s Hospital of Nanjing Medical University,  Nanjing Maternity and Child Health Care Hospital

data_processing:
Illumina HiSeq 2000/MiSeq
For RNA seq technology, the sequencing error rate will increase with the length of sequenced reads, which is a feature of illumina high throughput sequencing platforms. Generally, the sequencing error rate of a single base position should be less than 1%, that is, corresponding to Q20 filtering.
After the completion of data quality control, first compare clean reads with the reference genome, and count the comparison rate of reads between each sample and the reference genome.
Then, based on the comparison results, judge the overall construction quality of RNA seq library.
Compare the assembly results with the existing gene annotation results, remove the known coding proteins and lncRNA genes, further filter the transcripts that are incorrectly or incompletely assembled to obtain candidate new lncRNAs, then predict their coding potential, remove the transcripts that may encode proteins, and the latest transcripts obtained are new potential lncRNAs.
Assembly: human NBCI genome build 36
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: exosomes from term human breast milk

extract_protocol:
Total RNA was extracted from human milk derived exosomes using Trizol Reagent (Invitrogen, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Fragments of 400-500 bp were recovered and purified,   and then enriched by PCR for 15 cycles. Each library was loaded into one lane of the Illumina   HiSeq 2500 for 2 × 150 bp pair-end sequencing. manufacturer's protocols.

value: human milk

tag: condition

value: term

tag: rna population

value: exosomal RNA

tag: sample collection

value: the breast milk samples obtained within 7 days after delivery


title: Term-Exos2


title: Pre-Exos3

source_name: exosomes from preterm human breast milk

value: preterm


title: Pre-Exos2


title: SKMEL5 1 uM binimetinib replicate 2


title: Primary cancer cell line from Rag1KO mice, KO7 (RRBS)


title: Primary cancer cell line from Rag1KO mice, KO1 (RRBS)


title: SKMEL5 1 uM binimetinib replicate 1


title: Pre-Exos1


title: SKMEL5 100 nM binimetinib replicate 2

value: 100 nM binimetinib


title: ICN13 BCL6 ChIPseq

value: Rabbit, 2ug, 4242, Cell Signaling


title: Primary cancer cell line from WT mice, WT4 (RRBS)


title: Term-Exos3


title: SKMEL5 100 nM binimetinib replicate 1


title: SKMEL5 100 nM binimetinib replicate 3


title: 22Rv1_shCON

city: Shanghai

first: junhong

last: li

state: Shanghai

address: 801 Heqing Road, Minhang District

department: Urology

institute: Shanghai Fifth People's Hospital , Fudan University

data_processing:
CASAVA used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 in the human genome using HISAT2
The gene transcript expression count was performed by Hiseq RNA-seq to generate a matrix of transcripts per kilobase of exon model per million mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: 22Rv1 expressing shRNA vector control

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruseqTM RNA sample prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: prostate cancer cells

tag: genotype/variation

value: shCON


title: WT cold stress rep.4

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

description:
htseqAllGenesCounts_ex2.txt
ex2_S4

data_processing:
bcl2fastq software used for basecalling.
Reads were aligned to Caenorhabditis elegans genome (WBcel235) using the STAR RNA-seq aligner software (version STAR_2.5.0a )
The STAR genome database was built with the ENSEMBL annotation file (release 81)
Raw read counts for 46748 Ensembl-annotated gene-level features were determined using HTSeq-count
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include raw counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: WT cold stress

growth_protocol: Worms were grown at 15 degrees from egg to day-1 stage, the conrol ones were harvested at this piont and the treatmented ones were transffered to 2 degrees incubator for 24 hours and then harvested.

extract_protocol:
Worms were harvested and washed three times in M9 buffer, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext RNA ultra II RNA library preparation kit (NEB) with 1 ug of total RNA for the construction of sequencing libraries.
Poly A selection

treatment_protocol: At day-1 of adulthood, worm were transferred from 15 defrees incubator to cold treatment in 2 degrees incubator for 24 hours before harvesting them.

tag: age

value: Day-1+24 hours  2 degrees

value: from egg till D1 (5 days) at 15 degrees, 24 hour 2 degrees thereafter

tag: stress

value: cold stress

value: WT (wild type)


title: WT cold stress rep.6

description:
htseqAllGenesCounts_ex2.txt
ex2_S16

tag: strain


title: ire-1(-/-) stress rep.3

description:
htseqAllGenesCounts_ex1.txt
ex1_S17

source_name: ire-1(-/-) stress


title: WT cold stress rep.5

description:
htseqAllGenesCounts_ex2.txt
ex2_S10


title: WT control rep.5

description:
htseqAllGenesCounts_ex2.txt
ex2_S7

source_name: WT control

value: from egg till D1 (5 days) at 15 degrees

value: control


title: WT control rep.6

description:
htseqAllGenesCounts_ex2.txt
ex2_S13


title: WT control rep.4

description:
htseqAllGenesCounts_ex2.txt
ex2_S1


title: WT cold stress rep.3

description:
htseqAllGenesCounts_ex1.txt
ex1_S16


title: ire-1(-/-) control rep.3

description:
htseqAllGenesCounts_ex1.txt
ex1_S14

source_name: ire-1(-/-) control


title: 22Rv1_shEIF3F

source_name: 22Rv1 expressing shRNA targeting EIF3F

tag: cell type


title: Tomato+; bone marrow; mesLN after transfer; naive

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

country: Germany

institute: FAU Erlangen

data_processing:
Immcantation 4.3.0
pResto; Quality control, Read assembly
Change-O, V(D)J reference alignment standardization, Clonal clustering, Germline reconstruction, Conversion and annotation
Supplementary files format and content: tab-delimited text files include filtered and annotated immune repertoires

source_name: mesenteric lymph node

extract_protocol:
RNA was isolated using the Rneasy Micro kit from Qiagen; RNA was collected in 14 µl Rnase-free water and 11.5 µl were used for cDNA generation
Library was prepared according to "Werner, A., et al., Determining immunoglobulin-specific B cell receptor repertoire of murine splenocytes by next-generation sequencing. STAR Protocols, 2022. 3(2): p. 101277" with addition of a primer specific for IgE

treatment_protocol:
Cells were labeled 31 days before transfer into wildtype recipient mice and we then compared cells isolated before transfer to cells after isolated after  transfer
Cells were pooled from 3-4 mice from either mesenteric lymph nodes or the bone marrow of either naïve or infected donor mice,  half of the cells were transferred into CD45.1 recipient mice infected 3 days prior while the other half was sorted for expression of the fluorescent protein
Cells were then isolated 7 days after transfer from either mesenteric lymph nodes or the bone marrow of the recipient mice and sorted for CD45.2+ fluorescent protein positive cells

value: mesenteric lymph node

value: Bcells; Plasma cells

value: Aid-Crert2 +/-; R26-LSL-tdTomato +/+

tag: origin before_transfer

value: bone marrow

tag: treatment donor

value: naïve

tag: fluorescent marker

value: positive

value: Nippostrongylus brasiliensis infection

tag: time

value: day 10


title: Tomato+; bone marrow; bone marrow after transfer; naive

source_name: bone marrow

tag: treatment


title: Tomato+; bone marrow; bone marrow after transfer; infected


title: C57BL/6; 5000 cells control


title: Tomato+; mesLN; mesLN after transfer; infected


title: C57BL/6 50000 cells control


title: Tomato+; bone marrow; mesLN after transfer; infected


title: Tomato+; mesLN; bone marrow after transfer; infected


title: WT control rep.3

description:
htseqAllGenesCounts_ex1.txt
ex1_S13


title: Tomato+; mesLN; bone marrow after transfer; naive


title: ire-1(-/-) stress rep.2

description:
htseqAllGenesCounts_ex1.txt
ex1_S11


title: ire-1(-/-) control rep.2

description:
htseqAllGenesCounts_ex1.txt
ex1_S8


title: WT control rep.2

description:
htseqAllGenesCounts_ex1.txt
ex1_S7


title: ire-1(-/-) stress rep.1

description:
htseqAllGenesCounts_ex1.txt
ex1_S5


title: WT cold stress rep.1

description:
htseqAllGenesCounts_ex1.txt
ex1_S4


title: WT control rep.1

description:
htseqAllGenesCounts_ex1.txt
ex1_S1


title: ire-1(-/-) control rep.1

description:
htseqAllGenesCounts_ex1.txt
ex1_S2


title: Tomato-; mesLN; bone marrow after transfer; infected

value: negative


title: Tomato+; mesLN; mesLN after transfer; naive


title: Tomato-; bone marrow; mesLN after transfer; infected


title: Tomato-; mesLN; bone marrow after transfer; naive


title: Tomato-; bone marrow; bone marrow after transfer; naive


title: WT cold stress rep.2

description:
htseqAllGenesCounts_ex1.txt
ex1_S10


title: Tomato-; mesLN; mesLN after transfer; naive


title: Tomato-; bone marrow; bone marrow after transfer; infected


title: Tomato-; mesLN; mesLN after transfer; infected


title: YZWJ29_P9

city: Kyoto

first: Masayoshi

last: Tsukahara

state: Kyoto

address: Shogoin kawahara-cho, sakyo-ku,

department: Research and Develpoment center

country: Japan

institute: CiRA foundation

description: SAMPLE 300

hyb_protocol: Gene expression hybridizatoin kits (Agilent) were used for hybridization.

scan_protocol: Slides were scanned on the SureScan microarray scanner system (Agilent).

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

source_name: HLA homozygous iPSC

label_protocol: Low input quick amp labeling kits (Agilent) were used for cRNA labeling.

growth_protocol: Human iPSCs were maintained on iMatrix-511 (Nippi) coated plate with StemFit (AK03N, Ajinomoto).

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

treatment_protocol: Differentiation into three germ layers were conducted by using STEMDiff Trilineage differentiation kit (STEMCELL Technologies).

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: YZWJ28_P9

description: SAMPLE 299


title: YZWJ24_P9

description: SAMPLE 298


title: Tomato-; bone marrow; before transfer; infected

tag: tissue

tag: genotype


title: YZWJ21_P10

description: SAMPLE 296


title: Tomato+; bone marrow; before transfer; naïve

value: naive

value: Day 42


title: Tomato-; bone marrow; before transfer; naive


title: YZWJ17_P10

description: SAMPLE 293


title: YZWJ20_P11

description: SAMPLE 295


title: Tomato+; bone marrow; before transfer; infected


title: YZWJ14_P10

description: SAMPLE 292


title: Tomato+; mesLN; before transfer; infected


title: Tomato-; mesLN; before transfer; naive


title: Tomato+; mesLN; before transfer; naïve


title: Tomato-; mesLN; before transfer; infected


title: YZWJ18_P10

description: SAMPLE 294


title: YZWJ13_P10

description: SAMPLE 291


title: CDC67_1mg_18hwoAD_2

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

description: digested cartilage tissue

data_processing:
The unstranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by featureCounts.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

source_name: Human articular cartilage

extract_protocol:
Culture protocol: Cartilage tissues were transferred into a hypoxia chamber (4% O2) immediately after being removed from OA patients and minced finely. Collagenase II at concentrations of 0.1%, , 1%, and 2% was applied for 4 or 18 hours to digest the minced tissue. Actinomycin D (ActD) was added to test its capacity in stabilizing the transcriptome. Cell yield, viability, cell size, and transcriptome were determined using counter chamber, flow cytometry, and RNA sequencing (RNA-seq). Collagenase II at 2% concentration released small chondrocytes from cartilage matrix during the first digestion hour and started to release large cells thereafter, reaching a complete release at 4 hours. During 4-hour digestions, collagenase II at 2% and 1% but not at lower concentrations yielded maximal release also of the large chondrocyte population. RNA-seq analysis, using RNA isoalted directly from the same donor as reference, revealed that a 4-hour digestion period with 1% or 2% collagenase II plus ActD optimally preserved the transcriptome. Thus, this study provides an isolation protocol for single chondrocytes from human articular cartilage optimized for transcriptome preservation and RNA-seq analysis.
RNA was isolated using RNeasy Plus Micro Kit (QIAGEN). RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions

tag: patient diagnosis

value: OA patient

value: Small chondrocytes

tag: cell condition

value: viable cells


title: CDC67_1mg_18hwoAD_1

description: digested cartilage tissue


title: YZWJ12_P9

description: SAMPLE 290


title: YZWJ11_P9

description: SAMPLE 289


title: YZWJ09_P10

description: SAMPLE 288


title: YZWJ01_P11

description: SAMPLE 285


title: YZWJ06_P9

description: SAMPLE 287


title: CDC67_1mg_18h_2

description: digested cartilage tissue


title: YZWJ02_P9

description: SAMPLE 286


title: QHJI14_No86_3_P14

description: SAMPLE 211

value: PBMC


title: QHJI14_No86_2_P14

description: SAMPLE 210


title: CDC66_20mg_4h_2

description: digested cartilage tissue


title: CDC66_10mg_4h_1

description: digested cartilage tissue


title: QHJI14_No86_1_P14

description: SAMPLE 209


title: CDC66_20mg_4h_1

description: digested cartilage tissue


title: CDC67exvivo_2

description: digested cartilage tissue


title: CDC67_20mg_4h_2

description: digested cartilage tissue


title: CDC66_10mg_4h_2

description: digested cartilage tissue


title: QHJI14_No85_3_P14

description: SAMPLE 208


title: QHJI14_No60_2_P14

description: SAMPLE 204


title: QHJI14_No85_2_P14

description: SAMPLE 207


title: QHJI14_No60_3_P14

description: SAMPLE 205


title: QHJI14_No85_1_P14

description: SAMPLE 206


title: CDC66exvivo_2

description: digested cartilage tissue


title: CDC67_10mg_4h_2

description: digested cartilage tissue


title: CDC67_20mg_4h_1

description: digested cartilage tissue


title: QHJI14_No60_1_P14

description: SAMPLE 203


title: QHJI14_No08_3_P14

description: SAMPLE 202


title: QHJI14_No08_2_P15

description: SAMPLE 201


title: CDC67_1mg_18h_1

description: digested cartilage tissue


title: CDC67_10mg_4h_1

description: digested cartilage tissue


title: CDC66_1mg_18hwoAD_2

description: digested cartilage tissue


title: CDC66_1mg_18h_2

description: digested cartilage tissue


title: CDC66_1mg_18hwoAD_1

description: digested cartilage tissue


title: CDC66exvivo_1

description: digested cartilage tissue


title: Cov19_donor6

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation EPIC Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: The idat files of the Illumina BeadChip datasets were quantile normalized before beta value estimation with the R package minfi.

label: Cy5 and Cy3

source_name: whole blood

extract_protocol: Genomic DNA of COVID-19 blood samples was isolated using the Maxwell 16LEV DNA Blood Kit (Promega, AS1290) in a Maxwell 16 instrument. 1200 ng DNA were bisulfite converted and analyzed with Illumina EPIC BeadChip microarrays

tag: age range

value: M

tag: ards

value: ARDS


title: QHJI14_No08_1_P14

description: SAMPLE 200


title: QHJI01_No78_3_P13

description: SAMPLE 199


title: QHJI01_No78_2_P13

description: SAMPLE 198


title: QHJI01_No68_3_P13

description: SAMPLE 196


title: Cov19_donor3

label_protocol: Standard Infinium HD Methylation Assay protocol

value: F


title: CDC65exvivo_2

description: digested cartilage tissue


title: CDC65_20mg_4h_2

description: digested cartilage tissue


title: QHJI01_No68_2_P13

description: SAMPLE 195


title: CDC67exvivo_1

description: digested cartilage tissue


title: Cov19_donor2


title: CDC65_20mg_4h_1

description: digested cartilage tissue


title: CDC65_1mg_18hwoAD_2

description: digested cartilage tissue


title: QHJI01_No68_1_P13

description: SAMPLE 194


title: CDC65exvivo_1

description: digested cartilage tissue


title: Tomato-; bone marrow; mesLN after transfer; naive

value: mesenteric lymph node

value: Bcells; Plasma cells

value: Aid-Crert2 +/-; R26-LSL-tdTomato +/+

value: bone marrow

value: naïve


title: QHJI01_No33_3_P13

description: SAMPLE 193

value: iPSC

value: Male


title: CDC65_1mg_18hwoAD_1

description: digested cartilage tissue


title: GM12878 genomic DNA

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Standard Illumina Protocol

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: GM12878 is cultrured in T25 tissue culture flask that has been filled with 20ml RPMI1640 medium supplemented with 15% FBS and Pen-Strep (1X).

extract_protocol: Cultured cells were harvested and embed into low melting point agrose.

value: cell line


title: CDC65_1mg_18h_2

description: digested cartilage tissue


title: Cov19_donor9


title: Cov19_donor4


title: CDC66_1mg_18h_1

description: digested cartilage tissue


title: QHJI01_No33_2_P13

description: SAMPLE 192

value: pCE episomal vector


title: QHJI01_No33_1_P13

description: SAMPLE 191


title: Cov19_donor7


title: Cov19_donor10

value: no ARDS


title: QHJI01_No10_3_P13

description: SAMPLE 190


title: Cov19_donor1


title: QHJI01_No10_2_P13

description: SAMPLE 189


title: QHJI01_No10_1_P13

description: SAMPLE 188


title: Cov19_donor8


title: CDC65_10mg_4h_2

description: digested cartilage tissue

value: OA patient


title: CDC63exvivo_2

description: digested cartilage tissue

value: Small chondrocytes


title: YZWJ23_P13

description: SAMPLE 297

value: Cord blood


title: QHJI01_No01_3_P13

description: SAMPLE 187

value: PBMC


title: QHJI01_No01_2_P13

description: SAMPLE 186


title: CDC63exvivo_1

description: digested cartilage tissue

value: viable cells


title: CDC63_20mg_4h_2

description: digested cartilage tissue


title: QHJI01_No01_1_P13

description: SAMPLE 185


title: QHJI15_P8

description: SAMPLE 184


title: CDC63_1mg_18hwoAD_2

description: digested cartilage tissue


title: QHJI14_P8

description: SAMPLE 183


title: CDC63_1mg_18hwoAD_1

description: digested cartilage tissue


title: CDC65_1mg_18h_1

description: digested cartilage tissue


title: QHJI13_P8

description: SAMPLE 182


title: QHJI12_P8

description: SAMPLE 181


title: QHJI10_P8

description: SAMPLE 180


title: CDC63_10mg_4h_2

description: digested cartilage tissue


title: QHJI09_P8

description: SAMPLE 179


title: CDC63_1mg_18h_1

description: digested cartilage tissue


title: CDC65_10mg_4h_1

description: digested cartilage tissue


title: P11

description: digested cartilage tissue

data_processing:
The unstranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by htseq.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

extract_protocol:
Culture protocol: Cartilage tissues were transferred into a hypoxia chamber (4% O2) immediately after being removed from OA patients and minced finely. Collagenase II at concentrations of 2%, or  0.1% was applied for 0.5, 1, 2, 4, and 18 hours to digest the minced tissue.  Cell yield, viability, cell size, and transcriptome were determined using counter chamber, flow cytometry, and RNA sequencing (RNA-seq). During 4-hour digestions, collagenase II at 2% yielded maximal release, similar as 0.1% collagenase II-18 hour digestion. also of the large chondrocyte population
RNA was isolated using RNeasy Mini Kit. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions


title: P5

description: digested cartilage tissue


title: CDC63_10mg_4h_1

description: digested cartilage tissue


title: QHJI07_P8

description: SAMPLE 177


title: QHJI06_P8

description: SAMPLE 176


title: QHJI08_P8

description: SAMPLE 178


title: P4

description: digested cartilage tissue


title: P2

description: digested cartilage tissue


title: CDC63_20mg_4h_1

description: digested cartilage tissue


title: P3

description: digested cartilage tissue


title: QHJI04_P8

description: SAMPLE 174


title: P1

description: digested cartilage tissue


title: QHJI03_P8

description: SAMPLE 173


title: CDC63_1mg_18h_2

description: digested cartilage tissue


title: QHJI02_P8

description: SAMPLE 172


title: QHJI01_P8

description: SAMPLE 171


title: Day 7 p.i., Liver, AIN93G-fed mice [S-047]

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

data_processing:
Raw sequence read quality was checked with FastQC (v0.11.7) and MultiQC (v1.5)
Sequencing adapters were trimmed using BBDuk (v 38.26), setting k=20 and ktrim=r
Trimmed reads were aligned as pairs to the mouse reference genome mm10 (GRCm38) using STAR (v 2.7.2b) with default settings. STAR also generates raw feature level counts
RSeQC (v 2.6.4) was used to confirm the strandedness of the library
Assembly: Gene annotations (v 98) and the mouse genome (GRCm38) were obtained from Ensembl
Supplementary files format and content: tab delimited raw counts (*ReadsPerGene.out.tab files) from STAR (v 2.7.2b)

source_name: Liver

extract_protocol:
RNA extraction was performed using Trisure (Bioline) according to the manufacturer’s instructions
RNA libraries were prepared with the Illumina TruSeq Stranded mRNA kit according to the manufacturer's instructions

value: Liver

value: Wild type

tag: infection status

value: Day 7 post infection


title: CD45, activation, bottom, Cas9

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Samples were demultiplexed based on different biological conditions (read 1) and barcodes specific for each Cas9 variant (read 2)
20 bp sgRNA sequences were extracted from read 1 based on the 5' anchor sequence
sgRNA sequences were  mapped to the reference sgRNA library with one mismatch allowed (bowtie -v 1 -m 1).
Assembly: hg38
Supplementary files format and content: Csv files were generated for each biological sample (mix of four Cas9 variants) by bowtie alignment to sgRNA reference sequences. Normalized counts of each sgRNA combined with each Cas9 variant are shown. The normalization was performed by adding a +1 pseudocount to each sgRNA+Cas9 variant pair, dividing each count by the sum of all counts in the sample, multiplying by 10^6 and deriving log2.
Library strategy: DNA-seq

growth_protocol: Lentivirus was produced by  transfection of HEK  293FT cells with the transfer plasmid containing a barcoded Cas9 effector and sgRNA library, packaging  plasmid psPAX2 (Addgene 12260) and envelope plasmid pMD2.G (Addgene 12259) using polyethylenimine linear MW 25000 (Polysciences 23966). After 72 h, we harvested  cell media containing lentiviral particles and filtered it through 0.45 μm filter  Steriflip-HV (Millipore SE1M003M00). Each sgRNA library and Cas9 effector combination was  transduced into K562 (CRISPRko) or A375 (CRISPRa) cells individually, to avoid barcode swapping, and thus Cas9 misidentification, during  lentiviral integration. To minimize the fraction of cells with multiple sgRNAs, the transduction was performed at a multiplicity of infection (MOI)  ~ 0.4 . 1,000× coverage of each  sgRNA library was maintained throughout the experiment. For selection of transduced cells, we  cultured the cells in presence of 1 μg ml-1 puromycin for at least 7 days after  transduction. Transduced cells were maintained as separate cell cultures for 14 days and pooled only prior to antibody staining and FACS.

extract_protocol:
gDNA was extracted using GeneJET DNA Purification Kit (Thermo Fisher Scientific).
gDNA was  used in the first PCR reaction, in multiple reactions not exceeding 10 μg gDNA per 100 uL PCR  reaction. After the first PCR to process gDNA, the samples were  subjected to a second PCR to add barcodes and sequencing adaptors. PCR products were run on a 2% agarose gel to extract the correct size band. PCR products from different samples were then pooled together in  equimolar ratios. Sequencing was performed on the NextSeq 500 instrument using the MidOutput Mode  v2 with 75 bp paired-end reads (Illumina).

treatment_protocol: >108 cells were taken for antibody staining (~10,000× library representation).  107 cells were set aside for the pre-sort control (~1,000× coverage). Cells were harvested, washed with PBS and stained for 5 minutes at room temperature with  LIVE/DEAD Fixable Violet Dead Stain Kit (ThermoFisher L34864). Subsequently, CD45-PE (clone 2D1, pre-conjugated, Biolegend) antibody staining was performed for 20 minutes on ice, followed by two PBS washes. Cell sorting was performed using a Sony SH800S cell sorter.

tag: cell line

tag: cas9 variants

tag: fc antibody

tag: sorted cells

value: sorted bottom 10% of CD45 expression


title: CD45, activation, bottom, Cas9NG


title: CD45, activation, bottom, xCas9

value: xCas9 3.7


title: Day 7 p.i., Liver, AIN93G-fed mice [S-046]


title: Day 7 p.i., Liver, AIN93G-fed mice [S-045]


title: CD45, activation, top, xCas9NG

value: sorted top 10% of CD45 expression


title: CD45, activation, top, Cas9NG


title: CD45, activation, top, xCas9


title: Day 7 p.i., Liver, Chow-fed mice [S-044]

value: Chow


title: CD45, activation, top, Cas9


title: QHJI05_P8

description: SAMPLE 175

tag: cell type

value: iPSC


title: Day 7 p.i., Liver, Chow-fed mice [S-043]


title: Day 7 p.i., Liver, Chow-fed mice [S-041]


title: CD45, activation, presort, xCas9NG

value: unsorted cells


title: CD45, activation, presort, Cas9NG


title: Day 7 p.i., Liver, Chow-fed mice [S-042]


title: CD45, activation, bottom, xCas9NG


title: Naïve, Liver, AIN93G-fed mice [S-040]

value: Naïve


title: CD45, activation, presort, Cas9


title: Naïve, Liver, AIN93G-fed mice [S-039]


title: Day 7 p.i., Liver, AIN93G-fed mice [S-048]


title: Naïve, Liver, AIN93G-fed mice [S-038]


title: CD45, nuclease, bottom, xCas9NG


title: CD45, nuclease, bottom, Cas9NG


title: CD45, nuclease, bottom, xCas9


title: Naïve, Liver, AIN93G-fed mice [S-037]


title: Naïve, Liver, Chow-fed mice  [S-036]


title: Naïve, Liver, Chow-fed mice  [S-033]


title: Naïve, Liver, Chow-fed mice  [S-034]


title: Naïve, Liver, Chow-fed mice  [S-035]


title: CD45, nuclease, bottom, Cas9


title: Day 7 p.i., Brown adipose tissue, AIN93G-fed mice [S-032]

source_name: Brown adipose tissue

value: Brown adipose tissue


title: CD45, nuclease, top, xCas9


title: CD45, nuclease, top, Cas9


title: CD45, nuclease, top, Cas9NG


title: CD45, nuclease, presort, xCas9NG


title: CD45, nuclease, presort, Cas9NG


title: Day 7 p.i., Brown adipose tissue, AIN93G-fed mice [S-031]


title: CD45, activation, presort, xCas9


title: CD45, nuclease, presort, xCas9


title: Day 7 p.i., Brown adipose tissue, AIN93G-fed mice [S-029]


title: Day 7 p.i., Brown adipose tissue, AIN93G-fed mice [S-030]


title: CD45, nuclease, presort, Cas9


title: Day 7 p.i., Brown adipose tissue, Chow-fed mice [S-026]


title: Day 7 p.i., Brown adipose tissue, Chow-fed mice [S-027]


title: Day 7 p.i., Brown adipose tissue, Chow-fed mice [S-025]


title: Day 7 p.i., Brown adipose tissue, Chow-fed mice [S-028]


title: Naïve, Brown adipose tissue, AIN93G-fed mice [S-022]


title: Naïve, Brown adipose tissue, AIN93G-fed mice [S-023]


title: Naïve, Brown adipose tissue, AIN93G-fed mice [S-024]


title: CD45, nuclease, top, xCas9NG


title: Naïve, Brown adipose tissue, AIN93G-fed mice [S-021]


title: Naïve, Brown adipose tissue, Chow-fed mice  [S-018]


title: Naïve, Brown adipose tissue, Chow-fed mice  [S-017]


title: Naïve, Brown adipose tissue, Chow-fed mice  [S-019]


title: Naïve, Brown adipose tissue, Chow-fed mice  [S-020]


title: QHJI01_No78_1_P13

description: SAMPLE 197

value: Male

value: pCE episomal vector


title: Day 7 p.i., Hypothalamus, AIN93G-fed mice [S-013]

source_name: Hypothalamus

value: Hypothalamus


title: Control3_T_1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
RNAseq reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i) (Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR
Read counts for all genes annotated in GENCODE (hg19) were calculated using the read summarization program featureCounts (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: FeatureCounts.txt contains counts across CDS regions taken from Gencode v29 annotations

source_name: Control 3

growth_protocol: Human iPSC-derived striatal neruons (Smith-Geater et al., 2020)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a KAPA Hyperprep total RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Lenti viral vectors expressing either Cas13d/NT or Cas13d/CAGEX were added to each culture at day 16 from the start of differentiation

value: Control 3

value: striatal neurons

value: Control

tag: time

value: Day 32


title: Control3_L_1

tag: treatment


title: Control3_L_4


title: Control3_T_4


title: Control3_T_2


title: Control3_T_3


title: Control3_L_3


title: Day 7 p.i., Hypothalamus, AIN93G-fed mice [S-016]

value: Wild type


title: Control3_L_2


title: Control2_L_4

source_name: Control 2

value: Control 2


title: Control2_T_1


title: Control2_T_2


title: Control2_T_4


title: Control2_T_3


title: Control2_L_3


title: Day 7 p.i., Hypothalamus, Chow-fed mice [S-012]

value: Day 7 post infection


title: Control2_L_2


title: Control2_L_1


title: Day 7 p.i., Hypothalamus, Chow-fed mice [S-010]


title: Day 7 p.i., Hypothalamus, Chow-fed mice [S-009]


title: Control1_T_3

source_name: Control 1

value: Control 1


title: Control1_T_2


title: Day 7 p.i., Hypothalamus, AIN93G-fed mice [S-014]


title: Control1_T_1


title: Naïve, Hypothalamus, AIN93G-fed mice [S-006]


title: Control1_L_4


title: Control1_L_2


title: Naïve, Hypothalamus, Chow-fed mice  [S-004]


title: Control1_L_3


title: HD77_L_4

value: HD


title: HD77_T_4


title: Naïve, Hypothalamus, Chow-fed mice  [S-003]

value: Chow


title: Naïve, Hypothalamus, AIN93G-fed mice [S-005]


title: Control1_T_4


title: HD77_T_3


title: Naïve, Hypothalamus, Chow-fed mice  [S-001]


title: Day 7 p.i., Hypothalamus, Chow-fed mice [S-011]


title: HD77_T_1


title: HD77_L_3


title: CD8 T cells, control, rep2

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

institute: Max Planck Institute for heart and lung research

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MM10

source_name: CD8 T cells

extract_protocol:
Rneasy mini kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse CD8+ T cells were treated with 5 mM itaconate or NaCl, as a control, for 48 hours.

tag: strain

value: NaCl


title: CD8 T cells, control, rep3


title: CD8 T cells, itaconate treated, rep1

value: 5 mM itaconate


title: HD77_T_2


title: HD77_L_2


title: CD8 T cells, control, rep1


title: Naïve, Hypothalamus, AIN93G-fed mice [S-007]

value: Naïve


title: Naïve, Hypothalamus, AIN93G-fed mice [S-008]


title: HD66_T_4


title: HD77_L_1


title: Control1_L_1


title: CD8 T cells, itaconate treated, rep2


title: CD8 T cells, itaconate treated, rep3


title: Rspo3 mutant enteroid smRNA-seq sample #2

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

description:
PR3_2
Batch 1. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement.
smRNA_RLOG-LIMMA_normalized_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNA-seq), or proseq2.0 (leChRO).
RNA- and leChRO-seq HCT116 data was normalized using DESeq2. Mutant enteroid RNA- and smRNA-seq data was rlog transformed followed by limma batch correction.
Genome_build: Mouse enteroids: mm9 (small RNAseq) or vM10 (RNAseq). HCT116: hg19 for both RNA- and leChRO-seq datasets.
Supplementary_files_format_and_content: Normalized counts

source_name: Small Intestine

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
Cells were lysed using the lysis buffer described in Chu, T. et al. Nature Genetics (2018). Chromatin was pelleted and supernatant was collected and stored in Trizol LS. RNA was isolated using manufacturer's protocol.

value: Small Intestine

tag: genotype/variation

value: Rspo3 mutant enteroid


title: Rspo3 mutant enteroid smRNA-seq sample #1

description:
PR3_1
Batch 1. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: HD66_T_3


title: Wild-type enteroid smRNA-seq sample #2

description:
M2
Batch 1. WT
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Wild-type enteroid


title: Wild-type enteroid smRNA-seq sample #1

description:
F2
Batch 1. WT
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Kras/Rspo3/Smad4 mutant enteroid smRNA-seq sample #3

description:
961_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
RNA was isolated using the the Norgen Total RNA Purification Kit according to the manufacturer's protocol.

value: Kras/Rspo3/Smad4 mutant enteroid


title: Kras/Rspo3/p53/Smad4 mutant enteroid smRNA-seq sample #4

description:
N4_2
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Kras/Rspo3/p53/Smad4 mutant enteroid


title: Kras/Rspo3/Smad4 mutant enteroid smRNA-seq sample #1

description:
47_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Kras/Rspo3/p53/Smad4 mutant enteroid smRNA-seq sample #3

description:
N4_1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: HD66_L_2

value: striatal neurons


title: HD109_T_4


title: HD109_T_3


title: Kras/Rspo3/p53/Smad4 mutant enteroid smRNA-seq sample #2

description:
N3
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: HD66_T_2


title: HD66_L_3


title: HD66_T_1


title: HD66_L_4


title: HD66_L_1


title: Kras/Rspo3/p53/Smad4 mutant enteroid smRNA-seq sample #1

description:
N1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- and Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Kras/Rspo3/p53 mutant enteroid smRNA-seq sample #2

description:
KRP_2
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- mutation induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Kras/Rspo3/p53 mutant enteroid


title: HD109_T_2

value: Day 32


title: Naïve, Hypothalamus, Chow-fed mice  [S-002]

value: Hypothalamus

value: Wild type


title: HD109_T_1


title: Kras/Rspo3/p53 mutant enteroid smRNA-seq sample #1

description:
KRP_1
Batch 1. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Trp53-/- mutation induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: HD109_L_4


title: Ctnnb1/Kras/p53 mutant enteroid smRNA-seq sample #1

description:
S33KP
Batch 1. Ctnnb1S33F mutation induced using CRISPR base editing. KrasG12D and Trp53-/- mutations induced using enteroids from LSL-Kras/p53fl/fl mouse model
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Ctnnb1/Kras/p53 mutant enteroid


title: HD109_L_3


title: Ctnnb1 mutant enteroid smRNA-seq sample #5

description:
S33_M2
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Ctnnb1 mutant enteroid


title: HD109_L_2

value: HD


title: Ctnnb1 mutant enteroid smRNA-seq sample #4

description:
S33_M1
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Kras/Rspo3/Smad4 mutant enteroid smRNA-seq sample #2

description:
72_KRS19
Batch 2. KrasG12D mutation induced using enteroids from KrasLSL-G12D conditional model. Ptprk-Rspo3 fusion induced via CRISPR/Cas9 chromosome rearrangement. Smad4KO mutations induced using CRISPR/Cas9.
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Ctnnb1 mutant enteroid smRNA-seq sample #3

description:
S33_F2
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Ctnnb1 mutant enteroid smRNA-seq sample #2

description:
S33_F1
Batch 2. Ctnnb1S33F mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Negative control_0_8

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human S1500+ v2.0
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

source_name: Spleen

growth_protocol: All experiments were performed with human lymphoblastoid TK6 (IVTG) cells (#13051501) purchased from Sigma-Aldrich (Oakville, ON). Cells were grown in RPMI1640 cell culture medium (ThermoFisher Scientific, Ottawa, ON) supplemented with 10% horse serum (ThermoFisher Scientific, Ottawa, ON), 2 mM L-Glutamine (ThermoFisher Scientific, Ottawa, ON), 1.8 mM sodium pyruvate (ThermoFisher Scientific, Ottawa, ON), and 100 U/mL of penicillin and streptomycin (ThermoFisher Scientific, Ottawa, ON). Cells were incubated at 37°C with 5% CO2 and maintained below 1x106/mL and >90% viability.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 (BioSpyder Technologies, Carlsbad, CA, USA) assay was completed following the manufacturer’s instructions in a 96-well plate format. Each 96-well plate included three assay controls in duplicate: a negative no-cell lysate (1X TempO-Seq® Enhanced Lysis buffer only), Human Reference Total RNA (Takara Bio, CA, USA), and Human Brain Reference Total RNA (Takara Bio, CA, USA). Briefly, for each treatment, 2 µL of cell lysate in 1X TempO-Seq® Enhanced Lysis buffer was hybridized to the Human S1500+ Surrogate detector oligo (DO) probe mix (V2.0), incubated at 70°C for 10 minutes, then ramped down to 45°C over 50 minutes (0.5°C/minute). A nuclease digestion followed to remove excess or incorrectly bound DOs at 37°C for 1 hour. The bound DO pairs were then ligated together at 37°C for 1 hour and 15 minutes at 80°C to generate templates for amplification. A 10 µL aliquot of amplification template was transferred to its respective well in the TempO-Seq® PCR Pre-Mix and Primers plate and amplified on the CFX96 thermocycler (Bio-Rad, Mississauga, ON, Canada) with the following program: 37°C for 10 min, 95°C for 1 min; 25 cycles of 95°C for 10 sec, 65°C for 30 sec, 68°C for 30 sec; 68°C for 2 min. For library building and purification, three 96-well plates (288 sample libraries) were pooled together (5 µL per sample) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Cleanup Kit (Clontech Laboratories Inc., Bethlehem, PA, USA) with the adjustments specified by the TempO-Seq® Assay User Guide. The pooled purified TempO-Seq® libraries were then diluted, quantified, and assessed for quality using the Agilent High Sensitivity D1000 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and the qPCR KAPA Library Quantification Kit (Universal qPCR Master Mix) for Illumina NextSeq 500. Samples were sequenced on a total of two NextSeq® 500/550 High Output (75-cycle) flow cells using an Illumina NextSeq® 500 Sequencing Platform (Illumina, San Diego, CA, USA). A separate pool was completed for a fourth plate and an additional 96 sample libraries were added to the sequencing data for subsequent analysis.
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 - Index Sets F, G, H were used to index libraries (in two pools)

treatment_protocol: The cell density was adjusted to 1.5 x 105/mL, aliquoted in 96-well plates (100 µL/well), and exposed to 1% v/v solubilized test chemicals in DMSO in a six-point concentration range on a half-log distribution scale in duplicate. Six DMSO solvent controls were included per plate. For test chemicals requiring metabolic activation, the media were supplemented with 0.5% S9 Mix, Aroclor-1254 Induced Mutazyme® (Moltox, Boone, NC, USA). Treated cells were incubated at 37°C with 5% CO2 for 4H. Cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, and resuspended in 1X TempO-Seq Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA). If treated with 0.5% rat liver S9 fraction, cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, resuspended in fresh media, and incubated at 37°C with 5% CO2 for a 3h recovery period. Following incubation, cells were collected, washed, and resuspended in 1X TempO-Seq® Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA) and frozen at -80℃.

value: Spleen

value: Lymphoblast

tag: chemical

value: (-) Lysis

tag: chemical long_name

value: Negative Control

tag: dose

value: Negative control_0

tag: batch

value: Plate 4_IndexG

tag: sequencing pool

tag: technical control

value: T

tag: reference rna

value: F

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TAGCTCTTC

tag: i5 index_id

value: GGTCTAGCT

tag: cas-rn


title: HD109_L_1

tag: cell line

tag: cell type

value: striatal neurons

tag: genotype

tag: time


title: DMSO_0_24

tag: tissue

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

tag: treatment

value: CGTAACTTA


title: DMANN_1768_+S9_2

value: DMANN

tag: chemical long_name

value: D-mannitol

tag: dose

tag: batch

value: GCACCTATT


title: Apc/Kras/p53 mutant enteroid smRNA-seq sample #1

description:
Min_PlusKP
Batch 1. ApcQ883* mutation induced using CRISPR base editing. KrasG12D and Trp53-/- mutations induced using enteroids from LSL-Kras/p53fl/fl mouse model
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Small Intestine

tag: genotype/variation

value: Apc/Kras/p53 mutant enteroid


title: Ctnnb1 mutant enteroid smRNA-seq sample #1

description:
F2S333
Batch 1. Ctnnb1S33F mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Ctnnb1 mutant enteroid


title: Apc mutant enteroid smRNA-seq sample  #1

description:
F2_MIN
Batch 1. ApcQ883* mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv

value: Apc mutant enteroid


title: Apc mutant enteroid smRNA-seq sample  #3

description:
Apc_Min
Batch 2. ApcQ883* mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv


title: Apc mutant enteroid smRNA-seq sample  #2

description:
M2_MIN
Batch 1. ApcQ883* mutation induced using CRISPR base editing
smRNA_RLOG-LIMMA_normalized_counts.csv


title: NSACB18_1768_+S9_2

value: Spleen

value: Lymphoblast

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

value: ATACGCAGC


title: DMANN_1768_+S9_1

value: Plate 4_IndexG

value: F

tag: well

tag: i7 index_id

tag: index

tag: i5 index_id

value: GCCGTTACA


title: NSACB18_1768_+S9_1

tag: cell line

tag: cell type

value: TAGCTCTTC

value: TCTAACCAT

tag: cas-rn


title: D4

city: Stanford

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Cellranger and Seurat were used to align and analyse the expression profiles.
Assembly: hg38

source_name: SGBS

growth_protocol: Cells grown at 37°C with 5% CO2, with media replaced every 2-3 days. Culture media was composed of DMEM/Nutrient Mix F-12, 33 uM biotin, 17 uM pantothenic acid, 10 % FBS and antibiotics (100 IU/ml penicillin and 100 ug/ml streptomycin).

extract_protocol:
Cells were trypsinized, filtered and stained with the live/dead stain SYTOX Green Ready Flow Reagent (Thermo Fisher) according to the manufacturer’s protocol. Cells were stored on ice throughout the procedure. Live (SYTOX-negative) mCherry-positive single cells were isolated using fluorescence-activated cell sorting (FACS). Live cells underwent microfluidic single-cell capture on the 10X Chromium Controller device during which single cells were encapsulated with individual Gel Beads-in-emulsion (GEMs) using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit (10X Genomics).
In-drop reverse transcription and cDNA amplification was conducted according to the manufacturer’s protocol to construct expression libraries (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit, 10X Genomics). Library size was checked using Agilent Bioanalyzer 2100.

treatment_protocol: Days 0-4 of differentiation: DMEM/F-12, 33 uM biotin, 17 uM pantothenic acid, 0.01 mg/ml human transferrin, 100 nM cortisol, 200 pM triiodothyronine, 20 nM human insulin, 25 nM dexamethasone, 250 uM IBMX, 2 uM rosiglitazone, antibiotics. Days 4-8 of differentiation: DMEM/F-12, 33 uM biotin, 17 uM pantothenic acid, 0.01 mg/ml human transferrin, 100 nM cortisol, 200 pM triiodothyronine, 20 nM human insulin and antibiotics.

value: SGBS

value: 4 days of adipogenic differentiation


title: Negative control_0_7

tag: tissue

tag: chemical

value: (-) Lysis

value: Negative Control

value: Negative control_0

value: T

value: GACTTCATT

value: GGTCTAGCT


title: NSACB18_2500_+S9_2

tag: chemical long_name

tag: treatment


title: DMANN_2500_+S9_1

value: DMANN

value: D-mannitol

tag: dose

tag: batch


title: NSACB18_2500_+S9_1

value: Spleen

value: Lymphoblast

tag: sequencing pool


title: D0

value: prior to differentiation


title: Brain_0_8

value: (+) Brain

value: Brain +ve control

value: Plate 4_IndexG

tag: technical control

value: F

value: TGCATGACA


title: Femur non-union 1-16-20

city: Indianapolis

first: Keith

last: Avin

state: IN

address: 950 W. Walnut Street

department: Nephrology

institute: Indiana University

description: 10x Genomics

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis of multiple samples.
Assembly: GRCh38
Supplementary files format and content: HDF5 file of filtered gene-barcode matrices

source_name: intramedullary canal

extract_protocol: Cells within the samples were isolated and analyzed using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers.

value: intramedullary canal

tag: age

tag: Sex

value: male

tag: collection date

value: Nonunion


title: Femur non-union 1-14-20

description: 10x Genomics


title: 2-6-20 Femur NonUnion Fresh

description: 10x Genomics

value: female


title: 5/24/19 femur non-union reaming

description: 10x Genomics


title: IMN_canal_020119

description: 10x Genomics


title: DMSO_0_22

value: DMSO

value: Dimethyl sulfoxide

tag: reference rna

tag: solvent control

value: T

tag: well

tag: i7 index_id

value: CGTAACTTA


title: DMANN_3536_+S9_2

tag: cell line

tag: cell type

value: DMANN

value: D-mannitol

tag: index

tag: i5 index_id

value: GCACCTATT


title: DMANN_3536_+S9_1

tag: tissue

value: Spleen

value: Lymphoblast

tag: chemical

tag: chemical long_name

value: GCCGTTACA

tag: cas-rn


title: NSACB18_3536_+S9_2

tag: dose

tag: treatment

tag: batch

value: Plate 4_IndexG

tag: sequencing pool

value: ATACGCAGC


title: DMSO_0_23

tag: technical control

value: F

value: GACTTCATT


title: D8

value: SGBS

value: 8 days of adipogenic differentiation


title: 1/31/19 femur nonunion

description: 10x Genomics

value: intramedullary canal

tag: age

tag: Sex

value: female

tag: collection date

value: Control-no treatment


title: 9/5/19 control femur reaming

description: 10x Genomics


title: NSACB18_3536_+S9_1

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: TGCATGACA

value: TCTAACCAT


title: DMANN_2500_+S9_2

tag: cell line

tag: cell type

value: DMANN

tag: index

tag: i5 index_id


title: Brain_0_7

tag: tissue

tag: chemical

value: (+) Brain

tag: chemical long_name

value: Brain +ve control

value: T

value: TAAGGTAGC

value: GGTCTAGCT

tag: cas-rn


title: DMANN_5000_+S9_2

value: Spleen

value: Lymphoblast

value: D-mannitol

tag: dose

tag: treatment

tag: batch

value: Plate 4_IndexG

tag: sequencing pool

value: GCACCTATT


title: DMSO_0_21

value: DMSO

value: Dimethyl sulfoxide

tag: technical control

value: F

value: CGTAACTTA


title: DMANN_5000_+S9_1

tag: reference rna

value: GCCGTTACA


title: NSACB18_5000_+S9_2

tag: solvent control

value: ATACGCAGC


title: MS Scr p53-wt control

city: Austin

first: Yu-Tai

last: Chang

state: Texas

address: 1601 Trinity St Bldg B

department: Livestrong Cancer Institutes

institute: UT Austin Dell Medical School

description:
PE150
fpkm_genename_MS_KOvsScr.txt
readcount_genename_MS_KOvsScr.txt

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the  clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the  reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses  sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity  than other RNA-seq aligners for both experimental and simulated data.
Quantification: FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: tab-delimited text files include READCOUNT values for each sample

growth_protocol: MM.1S cells were cultured in complete media consisting of high glucose RPMI media (Invitrogen) supplemented with 10% fetal bovine serum (Sigma-Aldrich), 1% penicillin-streptomycin (Invitrogen), and 1% L-glutamine (Invitrogen).

extract_protocol:
Total RNA was extracted from MM.1S Scr and three distinct p53-KO (A7, B6, B12) clones with the Quick-RNA Miniprep Plus Kit (Zymo Research).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. (Novogene RNAseq service)
RNAseq on an Illumina platform and paired-end reads were generated.

treatment_protocol: p53-KO and Scr control cells were generated using lentiviral vectors (LentiCRISPR_v2; Addgene) expressing CRISPR-Cas9 and TP53-targeted or non-targeted scrambled guide-RNAs. Single-cell p53-KO clones were expanded under 0.2ug/mL puromycin selection and validated by sequencing of a genomic PCR amplicon across the edited locus.

value: bone marrow

value: multiple myeloma cells

tag: genotype

value: WT

value: lentiviral transfection


title: MS A7 p53-KO single clone

value: p53 knockout


title: The transcriptome profile of SRC-3 silenced T-HESC, Replicate 2

city: HOUSTON

first: Vineet

middle: Kumar

last: Maurya

state: TX

address: ONE BAYLOR PLAZA

department: Molecular & Cell Biology

institute: BAYLOR COLLEGE OF MEDICINE

data_processing:
Raw reads of 50 nucleotides, paired-end filtered for the default quality score of the Partek Flow Genome Analysis Software (version 10.0.21.0801).
Reads were mapped to the human genome (UCSC hg38) using Tophat version 2.0.4 and assembled using HISAT2 (version 2.1.0).
Aligned and filtered reads were quantified to the National Center for Biotechnology Information RefSeq Transcripts 100 (2021-11-01) by the Quantify to annotation model (Partek E/M) function with default parameters.
Assembly: hg38
Supplementary files format and content: FPKM was calculated for each gene in each sample by using the Partek Flow Genome Analysis Software (version 10.0.21.0801).

source_name: Telomerase-immortalised endometrial stromal cell

growth_protocol: The immortalized human endometrial stromal cell (T-HESC) line was obtained from the American Type Culture Collection (ATCC (CRL4003)) and maintained in phenol-red free DMEM/F12 medium supplemented with 10% charcoal/dextran-treated FBS (sFBS: Sigma-Aldrich Inc., St. Louis, MO), 1% ITS-A (insulin, transferrin, selenite and sodium pyruvate), 500 ng/ml puromycin, 100 units/ml penicillin, and 0.1 mg/ml streptomycin (ThermoFisher Scientific Inc., Waltham, MA), medium was changed every other day.

extract_protocol:
T-HESCs were treated with NT siRNA or siRNA targeting SRC-3 for 48 hours and then total RNA was isolated using RNeasy total RNA isolation kit (Qiagen) for RNA-seq as per manufacturer instructions.
Total RNA was subject to the double stranded DNA synthesis using the Ovation RNA-seq System V2 (Tecan Genomics, 7102-32). DNA libraries were generated with the Nextera DNA Flex Library Prep Kit (Illumnia, 20018704) and the Nextera DNA CD indexes (Illumnia, 20018708).
Libraries were sequenced on the Illumnia NovaSeq 6000 system for a 50-nucleotide read length in the paired end format.

treatment_protocol: Cells were cultured in six-well plates in triplicate before transfection with sixty picomoles of the non-targeting (NT (scrambled control sequence)) siRNA (GE Healthcare Dharmacon Inc., Lafayette, CO (D-001810-10-05)) or siRNA targeting SRC-3 (Dharmacon Inc., (L-00 3759-00-0005)), using the Lipofectamine RNAiMAX transfection reagent (Invitrogen Inc., Carlsbad CA) for 48 hours.

value: SRC-3 siRNA


title: MS B12 p53-KO single clone


title: NSACB18_5000_+S9_1

value: Spleen

tag: well

tag: i7 index_id

value: TAAGGTAGC

value: TCTAACCAT


title: MS B6 p53-KO single clone

tag: cell line

tag: cell type


title: The transcriptome profile of T-HESC, Replicate 2

value: Telomerase-immortalised endometrial stromal cell

value: NT siRNA


title: Control femur ICT 12-3-19

description: 10x Genomics

value: intramedullary canal

tag: age

tag: Sex

value: male

tag: collection date

value: Control-no treatment


title: The transcriptome profile of T-HESC, Replicate 1


title: UHRR_0_8

tag: tissue

value: Lymphoblast

tag: chemical

value: (+) UHRR

tag: chemical long_name

value: Universal human +ve control

value: Plate 4_IndexG

value: T

value: F

tag: index

value: TCAGTACAT

tag: i5 index_id

value: GGTCTAGCT


title: DMSO_0_20

value: DMSO

value: Dimethyl sulfoxide

tag: dose

tag: treatment

tag: batch

tag: sequencing pool

value: CGTAACTTA

tag: cas-rn


title: 10/29/2019 Control Femur Canal

description: 10x Genomics

value: female


title: The transcriptome profile of SRC-3 silenced T-HESC, Replicate 1

value: Telomerase-immortalised endometrial stromal cell

value: SRC-3 siRNA


title: H9 cells, RNA-seq, rep 3

city: Cambridge

first: Julian

middle: E

last: Sale

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
RNA-seq reads were quality trimmed with trim_galore (v0.4.4), aligned with tophat (v2.1.1) and compared with cufflinks (v2.2.1).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include count values

growth_protocol: Human H9 embryonic stem cells were cultured at 37°C, 5% CO2 in Essential 8 Flex medium on Vitronectin-XF coated plates. Cells were passaged every 3-4 days based on cell density. Cells tested negative for mycoplasma contamination throughout the study.

extract_protocol:
RNA was isolated from all samples in parallel using the RNeasy Kit (Qiagen) following the manufacturer’s instructions and quantified before running on an Agilent RNA Pico 6000 chip using an Agilent 2100 Bioanalyzer. RNA with a RIN score above 7 was used to generate RNA libraries
Libraries were prepared using the NEBNext UltraII RNA library preparation kit and NEBNext rRNA depletion kit (New England Biolabs). cDNA libraries were generated from 750 ng of RNA, amplified for 8 PCR cycles, and barcoded with NEBNext Multiplex Oligos for Illumina (New England Biolabs).

value: hESC

tag: genotype

value: WT


title: DMANN_7071_+S9_2

value: Spleen

value: DMANN

value: D-mannitol

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: GCACCTATT


title: NSACB18_7071_+S9_2

tag: cell line

tag: cell type

value: Lymphoblast

value: Plate 4_IndexG

value: ATACGCAGC


title: DMANN_7071_+S9_1

tag: tissue

tag: chemical

value: F

value: TCAGTACAT

value: GCCGTTACA


title: H9 cells, RNA-seq, rep 1


title: H9 cells, Input CUT&RUN

data_processing:
CUT&RUN reads were aligned with bowtie2 (v2.2.6) using (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700) parameters. Alignments were then filtered with samtools for maximum quality alignments (-q 42), converted to bigwigs (--normalizeUsing BPM --smoothLength 350 --extendReads 150 --centerReads) at binSizes of 50 nt. Replicates were processed independently and merged accordingly after assessing reproducibility.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig

extract_protocol:
TOP2A and TOP2B CUT&RUNs were performed using the CUT&RUN Assay Kit (Cell Signaling) and following the manufacturer’s instructions starting with ~ 100,000 cells and performing the antibody incubation overnight at 4C.
CUT&RUN libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB) with minor modifications to avoid denaturation and loss of small DNA fragments.

tag: chip antibody


title: NSACB18_7071_+S9_1

tag: chemical long_name

tag: index

tag: i5 index_id

value: TCTAACCAT


title: H9 cells, TOP2B CUT&RUN, rep 9

value: Anti-Topoisomerase II beta (Abcam, ab72334)


title: DMANN_10000_+S9_2

tag: dose

tag: treatment

tag: batch

value: ATTCGCTCT


title: UHRR_0_7

value: (+) UHRR

value: Universal human +ve control

tag: sequencing pool

value: T

value: GGTCTAGCT

tag: cas-rn


title: DMSO_0_19

value: Spleen

value: DMSO

value: Dimethyl sulfoxide

tag: technical control

tag: reference rna

value: CGTAACTTA


title: H9 cells, TOP2B CUT&RUN, rep 7

value: hESC


title: DMANN_10000_+S9_1

value: Lymphoblast

value: DMANN

value: D-mannitol

value: Plate 4_IndexG

tag: solvent control

tag: well


title: H9 cells, TOP2B CUT&RUN, rep 8

tag: cell line


title: H9 cells, TOP2B CUT&RUN, rep 6

tag: cell type


title: NSACB18_10000_+S9_2

tag: tissue

value: F

tag: i7 index_id

value: ATACGCAGC


title: H9 cells, TOP2B CUT&RUN, rep 5

tag: chip antibody

value: Anti-Topoisomerase II beta (Abcam, ab72334)


title: NSACB18_10000_+S9_1

tag: chemical

tag: chemical long_name

value: ATTCGCTCT

value: TCTAACCAT


title: H9 cells, TOP2B CUT&RUN, rep 4


title: H9 cells, TOP2B CUT&RUN, rep 1


title: H9 cells, TOP2A CUT&RUN, rep 9

value: Anti-Topoisomerase II alpha (Abcam, ab52934)


title: H9 cells, TOP2A CUT&RUN, rep 7


title: H9 cells, TOP2A CUT&RUN, rep 8


title: H9 cells, RNA-seq, rep 2

tag: genotype

value: WT


title: NSACB13_221_+S9_1

tag: dose

tag: index

value: ACTCATGTA

tag: i5 index_id

value: GATTGTGTT


title: NSACB13_221_+S9_2

value: Spleen

tag: treatment

tag: batch

tag: sequencing pool

value: ATACCGGCA


title: NSACB12_17.7_+S9_2

tag: technical control

tag: reference rna

value: GCACCTATT

tag: cas-rn


title: NSACB14_460_+S9_1

tag: cell line

tag: solvent control

tag: well

value: CGTAACTTA


title: H9 cells, TOP2A CUT&RUN, rep 6

tag: cell type

value: hESC


title: NSACB12_17.7_+S9_1

tag: tissue

value: Lymphoblast

tag: i7 index_id

value: GCCGTTACA


title: H9 cells, TOP2A CUT&RUN, rep 5

tag: chip antibody


title: H9 cells, TOP2A CUT&RUN, rep 4


title: NSACB1_16.9_+S9_1

tag: chemical

tag: chemical long_name

value: Methanone

value: Plate 4_IndexG


title: NSACB14_650_+S9_2

tag: dose

value: F

tag: index

value: GTTTATACT

value: GGTCTAGCT


title: NSACB14_650_+S9_1

tag: treatment

tag: i5 index_id


title: H9 cells, TOP2A CUT&RUN, rep 3


title: H9 cells, TOP2A CUT&RUN, rep 2


title: H9 cells, TOP2A CUT&RUN, rep 1


title: NSACB14_460_+S9_2

tag: batch

tag: sequencing pool


title: H9 cells, TOP2B CUT&RUN, rep 3

value: Anti-Topoisomerase II beta (Abcam, ab72334)


title: H9 cells, ATAC-seq, rep 3

data_processing:
ATAC-seq reads were aligned with bowtie2 (v2.2.6) using --local mode. Alignments were then filtered with samtools for maximum quality alignments (-q 42), converted to bigwigs (--normalizeUsing BPM --smoothLength 350 --extendReads 150 --centerReads) at binSizes of 50 nt. Replicates were processed independently and merged accordingly after assessing reproducibility.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were harvested using Accutase to obtain a single cell suspension and counted, followed by a wash using cold DPBS. Cells (50,000) were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extracts. Nuclei were immediately used in the transposase reaction (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water) for 30 min at 37 °C, followed by DNA purification.
Library fragments were amplified using the KAPA HiFi HotStart ReadyMix and 1.25 M of custom Nextera PCR primers. Libraries were purified using dual purification (0.5–0.7×) with SPRI AMPure XP beads and its quality assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit.

tag: genotype


title: NSACB12_25_+S9_2

tag: technical control

tag: reference rna

tag: cas-rn


title: H9 cells, ATAC-seq, rep 2

tag: cell line


title: NSACB13_313_+S9_1

tag: cell type

tag: solvent control

tag: well


title: NSACB12_25_+S9_1

tag: tissue

tag: i7 index_id


title: H9 cells, ATAC-seq, rep 1


title: H9 cells, TOP2B CUT&RUN, rep 2

tag: chip antibody


title: NSACB14_919_+S9_2

tag: chemical

tag: chemical long_name

tag: dose

value: GAACTGTAT


title: NSACB1_23.9_+S9_1

tag: treatment

tag: index

tag: i5 index_id

value: TCTAACCAT


title: NSACB14_919_+S9_1

tag: batch

tag: sequencing pool


title: NSACB1_16.9_+S9_2

tag: technical control

tag: reference rna

value: ACTCATGTA

value: ATACGCAGC


title: NSACB13_442_+S9_2

value: Spleen

tag: cell line

tag: cas-rn


title: NSACB13_442_+S9_1

tag: cell type

tag: solvent control

value: GATTGTGTT


title: NSACB12_35.4_+S9_2

tag: tissue

tag: well

value: GCACCTATT


title: NSACB13_313_+S9_2

tag: i7 index_id

value: ATACCGGCA


title: NSACB12_35.4_+S9_1

tag: chemical


title: T47D Normoxia rep1

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to Genome Reference Consortium GRCh37 (hg19) using HISAT2 (2.05) (http://daehwankimlab.github.io/hisat2/) and non-uniquely mapped fragments were excluded using Picard tools (2.0.1) (http://broadinstitute.github.io/picard/)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text files from htseq

source_name: Breast cancer cell line

growth_protocol: Culture medium was supplemented with 10%FBS, L-glutamine and penicillin-streptomycin. Culture medium used was DMEM (for T47D), F12K (for A549 and PC-3) and McCoy's 5a (for HCT-116). Cells were plated on 15cm plates and harvested at approximately 60-80% confluency.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with an on-column Dnase-treatment (Qiagen). Poly-A mRNA was purified using NEBNext Poly-A mRNA Magnetic Isolation Module.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology).

tag: ambient o2 concentration

tag: duration of hypoxia

tag: culture medium

value: DMEM


title: T47D Normoxia rep2


title: T47D Normoxia rep3


title: T47D Hypoxia rep2

value: 16 hours


title: T47D Hypoxia rep1


title: PC3 Normoxia rep3

source_name: Prostate cancer cell line


title: PC3 Normoxia rep2


title: T47D Hypoxia rep3


title: NSACB1_33.8_+S9_2

value: Lymphoblast

tag: chemical long_name

tag: dose

tag: treatment

tag: index


title: NSACB1_33.8_+S9_1

value: Methanone

tag: batch

tag: sequencing pool

tag: technical control

tag: i5 index_id


title: PC3 Hypoxia rep3

tag: cell line


title: PC3 Normoxia rep1


title: NSACB1_23.9_+S9_2

tag: cell type

value: Plate 4_IndexG

tag: reference rna

tag: solvent control

tag: cas-rn


title: PC3 Hypoxia rep2


title: NSACB14_1300_+S9_2

tag: tissue

tag: chemical

value: F

tag: well

tag: i7 index_id

value: GGGTTGTTA


title: NSACB14_1300_+S9_1

tag: chemical long_name

value: CGTAACTTA


title: HCT-116 Normoxia rep3

source_name: Colorectal cancer cell line

tag: ambient o2 concentration

tag: duration of hypoxia

tag: culture medium

value: McCoy's 5a


title: PC3 Hypoxia rep1


title: NSACB13_625_+S9_2

tag: dose

tag: treatment

tag: batch

tag: index


title: NSACB12_50_+S9_2

tag: cell line

tag: sequencing pool

tag: technical control

tag: i5 index_id


title: HCT-116 Normoxia rep2


title: HCT-116 Normoxia rep1


title: NSACB13_625_+S9_1

tag: cell type

tag: reference rna

tag: solvent control

tag: cas-rn


title: NSACB12_50_+S9_1

tag: tissue

tag: chemical

tag: well

tag: i7 index_id

value: GCCGTTACA


title: NSACB1_47.7_+S9_2

tag: chemical long_name


title: HCT-116 Hypoxia rep2

tag: ambient o2 concentration

tag: duration of hypoxia

tag: culture medium


title: HCT-116 Hypoxia rep1


title: NSACB14_1834_+S9_2

tag: dose

tag: treatment

tag: batch

tag: index

value: AAGACTCTT

value: GGTCTAGCT


title: NSACB1_47.7_+S9_1

tag: cell line

tag: sequencing pool

tag: technical control

tag: i5 index_id

value: TCTAACCAT


title: NSACB14_1834_+S9_1

value: Spleen

tag: cell type

tag: reference rna

tag: solvent control

tag: cas-rn


title: A549 Normoxia rep2

source_name: Lung cancer cell line


title: NSACB13_884_+S9_2

tag: tissue

tag: chemical

tag: well

tag: i7 index_id


title: A549 Hypoxia rep3

tag: ambient o2 concentration

tag: duration of hypoxia

tag: culture medium


title: A549 Normoxia rep3


title: HCT-116 Hypoxia rep3


title: NSACB12_70.8_+S9_2

tag: chemical long_name

tag: dose

tag: treatment

tag: batch


title: NSACB13_884_+S9_1

tag: cell line

tag: sequencing pool

tag: technical control

tag: index

value: GATTGTGTT


title: NSACB12_70.8_+S9_1

tag: cell type

tag: reference rna

tag: solvent control

tag: i5 index_id


title: A549 Normoxia rep1


title: NSACB1_67.5_+S9_1

tag: tissue

tag: chemical

tag: well

tag: cas-rn


title: A549 Hypoxia rep1

tag: ambient o2 concentration

tag: duration of hypoxia

tag: culture medium


title: NSACB1_67.5_+S9_2

tag: chemical long_name

tag: dose

tag: treatment

tag: i7 index_id

value: ATACGCAGC


title: NSACB14_2600_+S9_2

tag: cell line

tag: batch

tag: sequencing pool

tag: technical control

value: TCCTCAGCC


title: NSACB14_2600_+S9_1

tag: cell type

tag: reference rna

tag: solvent control

tag: index


title: NSACB13_1250_+S9_2

tag: tissue

tag: chemical

tag: well

tag: i5 index_id

value: ATACCGGCA


title: NSACB13_1250_+S9_1

tag: cas-rn


title: NSACB12_100.1_+S9_2

tag: chemical long_name

value: GCACCTATT


title: NSACB12_100.1_+S9_1

value: Lymphoblast

tag: dose


title: hAxioloid 96h_MG_RA

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

data_processing:
The 10X Genomics Cell Ranger pipeline (version 6.0.1) was used to perform sample demultiplexing, alignment to the hg38 human reference genome, barcode/UMI processing, and gene counting for each cell.
Putative doublet clusters were removed using Scrublet (version 0.2.3).
Assembly: hg38
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: hAxioloid

growth_protocol: Human iPS cells were seeded on iMatrix-511 silk coated dishes at a density of 1.3×10^4 cells/well into 6 well plates 5 days prior to Axioloid induction and used at ~ 60% confluency. All subsequent induction steps were performed in AK02N medium without component C (AK02N-C). Initially, hiPSCs were pulsed with a strong mesoderm and primitive streak fate inducing combination of bFGF (20 ng ml−1) and WNT agonist CHIR99021 (5 μM) for 24 h. 24 h after the initial pulse, cells were dissociated with Accutase and cultured for 24 h in 96 well U-bottom low attachment plates at 500 cells/well in 50 μl of AK02N-C based aggregation medium supplemented with CHIR99021 (5 μM), basic FGF (20 ng ml−1), TGFb inhibitor SB431542 (10 μM) and ROCK inhibitor Y27632 (10 μM). 24 h after aggregation, 150 μl of AK02N-C medium was added into each well and exchanged again after 24 h with 150 μl of fresh AK02N-C medium.

extract_protocol:
Axioloids were collected into wells of a 96-well plate and washed three times by transferring to another well filled with 0.1% BSA in HBSS(-). Axioloids of the desired stage and number were then transferred to another well filled with 100 μl of enzyme P solution of the Neural Tissue Dissociation Kit (P) and incubated at 37 ℃ for 10 minutes. After adding 100 μl of 0.1% BSA in HBSS(-) Axioloids were dissociated  by pipetting with an uncut P200 tip 20 times. The dissociated cells were filtered through Flowmi Cell Strainers with 40 μm porosity into a BSA-coated 2 ml tube. Cells were washed twice in 1% BSA in HBSS(-) with centrifugation steps at 400 x g for 6 minutes at room temperature. Cells were then resuspended in 1% BSA in HBSS(-) using a BSA-coated uncut-P200 tip and the concentration of the cell suspension was determined with hemocytometer. The cell suspension was subjected to library preparation using Chromium Next GEM Single Cell 3ʹ Kit v3.1, aiming for a target cell recovery of 5000-10000.
RNA library preparation was preformed following the instructions provided by the manufacturer 10X Genomics (CG000315 Rev B)
scRNAseq

treatment_protocol: 48 h after aggregation Axioloids were transferred one-by-one into BSA-treated 96 well flat-bottom low attachment plates and embedded into 80 μl of AK02N-C medium containing 10% growth factor-reduced Matrigel and cultured further at 37°C and 5% CO2 for 24 to 48 h. Depending on the experimental setup retinoic acid signaling molecules, i.e. retinoic acid (RA) (100 nM), retinol (ROL) (10 µM) or all trans-retinal (RAL) (1 µM) were added to the MG containing medium throughout the embedding phase.

value: iPSC-derived mesodermal cell aggregates

tag: time point

tag: embedding

value: Matrigel

tag: treatment

value: retinoic acid


title: hAxioloid 96h_MG_RAL

value: retinal


title: hAxioloid 120h_MG


title: hAxioloid 120h_MG_RA


title: hAxioloid 120h


title: NSACB1_95.5_+S9_2

tag: cell line

value: Methanone

tag: batch

value: Plate 4_IndexG

value: F

tag: i7 index_id


title: hAxioloid 96h_MG_exp2


title: NSACB1_95.5_+S9_1

tag: cell type

tag: sequencing pool

tag: technical control


title: hAxioloid 96h_exp2


title: A549 Hypoxia rep2

tag: ambient o2 concentration

tag: duration of hypoxia

value: 16 hours

tag: culture medium


title: Negative control_0_6

tag: tissue

tag: chemical

value: (-) Lysis

value: Negative Control

value: Negative control_0

value: Plate 3_IndexH

value: T

tag: reference rna

tag: solvent control

tag: well

tag: index

value: GATAGCGGA

value: GGTCTAGCT


title: hAxioloid 96h_exp1

tag: time point

tag: embedding


title: hAxioloid 48h

tag: treatment


title: Negative control_0_5

value: Spleen

tag: cell line

tag: chemical long_name

tag: dose

tag: batch

value: AGCCGATTA

tag: i5 index_id

tag: cas-rn


title: Brain_0_6

tag: cell type

value: Lymphoblast

value: (+) Brain

value: Brain +ve control

tag: sequencing pool

tag: technical control

tag: i7 index_id

value: ACCTGAGGC


title: hAxioloid 120h_MG_RAL

tag: tissue

value: iPSC-derived mesodermal cell aggregates

value: Matrigel

value: retinal


title: hAxioloid 96h_MG_exp1


title: DMSO_0_16

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

value: F

tag: reference rna

tag: solvent control

value: CGTAACTTA


title: iHEECs/Luc/Luc EGR1 siRNA rep 2

data_processing:
Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the  human genome Consortium Human Build hg38  with STAR version 2.5.1b.The number of reads aligned to known genes was determined by the Python-based software package HTSeq.To reduce possible PCR bias, read duplicates were removed with Picard Tools.
The Bioconductor package EdgeR was applied to the gene expression data to detect differentially expressed genes between the two groups
The false discovery rate (FDR) of differentially expressed genes was estimated using the Benjamini and Hochberg method. Gene expression comparisons with an FDR ≤ 0.05 and an absolute fold change (IFCI) ≥ 1.5 were considered to be significantly differentially expressed between the two groups.
Assembly: Genome Reference Consortium Human Build hg38
Supplementary files format and content: logCPM

source_name: iHEEC/Luc

extract_protocol:
iHEECs/Luc were treated with NT siRNA or siRNA targeting EGR1 for 48 hours and then total RNA was isolated using RNeasy total RNA isolation kit (Qiagen) for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iHEECs/Luc were treated withNT siRNA or siRNA targeting EGR1 for 48 hours

value: endometriotic epithelial cells

value: iHEEC/Luc

value: EGR1 siRNA


title: iHEECs/Luc/Luc EGR1 siRNA rep 1


title: hAxioloid 72h

tag: time point


title: Brain_0_5

value: Plate 3_IndexH

value: T

tag: well

tag: index

value: TAGCGACAA

value: GGTCTAGCT


title: iHEECs/Luc/Luc EGR1 siRNA rep 3

tag: cell line

tag: treatment


title: iHEECs/Luc/Luc NT siRNA rep 3

value: NT siRNA


title: iHEECs/Luc/Luc NT siRNA rep 2


title: iHEECs/Luc/Luc NT siRNA rep 1


title: DMSO_0_14

value: Spleen

value: Lymphoblast

tag: chemical long_name

tag: dose

value: GCTATCGAT


title: DMSO_0_13

tag: batch

value: ATTGGTTGC

tag: i5 index_id


title: PBMCs from preeclampsia patient 5

city: Beijing

first: Juntao

address: No. 1, Shuaifu Garden, Dongcheng District

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences

description: Pregnant woman at a gestational range of 28 to 32 weeks

data_processing:
Raw reads of fastq files were derived from the raw BCL files using Illumina’s bcl2fastq converter.
Low-quality raw reads were removed in the presence of following quality assessment parameters: (i) the reads containing N of more than 3; (ii) more than 20% bases with quality value of ≤ 5; and (iii) the reads contained adapter sequence.
Alignment of reads to the GRCh38 genome was performed with STAR (14) included in CellRanger pipeline (version 3.1.0).
Genome_build:  GRCh38 for human data
Supplementary_files_format_and_content: The barcode, gene, expression matrix file of each sample

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from whole blood samples from each group using SepMate isolation tubes (StemCell Technologies, Cambridge, MA, USA).
Single-cell libraries were established using 10× Chromium single-cell 5’ library construction kit (10× Genomics, San Francisco, CA, USA) according to the manufacturer’s instructions.
The libraries were sequenced on the NovaSeq 6000 platform to generate 150 bp paired-end reads to an average depth of 30 million reads per cell.

tag: Sex

value: Female

tag: age

value: 34 years old

tag: blood pressure

tag: cell type

value: PBMCs

tag: disease state

value: preeclampsia


title: PBMCs from preeclampsia patient 6

description: Woman at 6 to 35 weeks postpartum


title: DMSO_0_18

tag: tissue

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

tag: sequencing pool

tag: technical control

value: F

tag: i7 index_id

value: GATAGCGGA

value: CGTAACTTA

tag: cas-rn


title: PBMCs from preeclampsia patient 3

value: 32 years old


title: EPEG_0.028_-S9_2

tag: cell line

value: EPEG

value: Etoposide

value: Plate 3_IndexH

tag: reference rna

tag: solvent control

tag: well

tag: index

value: TGATTAAGC

value: GCACCTATT


title: EPEG_0.039_-S9_2

value: Spleen

value: Lymphoblast

tag: chemical long_name

tag: dose

tag: treatment

tag: batch

value: TCAGCTAAT

tag: i5 index_id


title: DMSO_0_17

tag: cell type

value: T

value: AGCCGATTA


title: EPEG_0.028_-S9_1

tag: tissue

value: GCCGTTACA


title: PBMCs from preeclampsia patient 2

description: Woman at 6 to 35 weeks postpartum

tag: Sex

value: Female

tag: age

tag: blood pressure

value: PBMCs

tag: disease state

value: preeclampsia


title: PBMCs from health control 2

description: Woman at 6 to 35 weeks postpartum

value: 36 years old

value: healthy control


title: EPEG_0.055_-S9_2

tag: chemical

tag: sequencing pool

tag: technical control

value: F

tag: i7 index_id

value: TGCTTATTC

tag: cas-rn


title: EPEG_0.055_-S9_1

tag: cell line

value: EPEG

value: Etoposide

tag: reference rna

tag: solvent control

tag: well

tag: index


title: PBMCs from health control 3

value: 33 years old


title: PBMCs from preeclampsia patient 1

value: 32 years old


title: EPEG_0.039_-S9_1

value: Spleen

tag: chemical long_name

tag: dose

tag: treatment

tag: batch

value: Plate 3_IndexH

tag: i5 index_id


title: EPEG_0.078_-S9_2

tag: tissue

tag: cell type

value: Lymphoblast

value: ATTCGAATC

value: GCACCTATT


title: EPEG_0.078_-S9_1

tag: chemical

value: GCCGTTACA


title: DMSO_0_15

value: DMSO

value: Dimethyl sulfoxide

tag: sequencing pool

value: T

value: TAGCGACAA

value: CGTAACTTA


title: PBMCs from health control 1

tag: Sex

value: Female

tag: age

value: 36 years old

tag: blood pressure

value: PBMCs

tag: disease state

value: healthy control


title: PBMCs from health control 4

description: Woman at 6 to 35 weeks postpartum

value: 33 years old


title: UHRR_0_6

tag: cell line

value: (+) UHRR

value: Universal human +ve control

tag: technical control

tag: reference rna

value: F

tag: i7 index_id

value: GCTATCGAT

value: GGTCTAGCT

tag: cas-rn


title: EPEG_0.11_-S9_2

value: Spleen

value: Lymphoblast

value: EPEG

tag: chemical long_name

value: Etoposide

tag: dose

value: Plate 3_IndexH

tag: solvent control

tag: well

tag: index

value: ATCGCGACT

value: GCACCTATT


title: UHRR_0_5

tag: tissue

tag: cell type

tag: treatment

tag: batch

value: T

value: ATTGGTTGC

tag: i5 index_id