title: day0_ES

city: Boston

first: James

middle: Alexander

last: Briggs

state: Massachusetts

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

description:
Sample 1
Timepoint label = 1 in processed data files (both protocols)
direct_programming.filtered_normalized_counts.csv.gz
direct_programming.raw_umifm_counts.csv.gz
standard_protocol.filtered_normalized_counts.csv.gz
standard_protocol.raw_umifm_counts.csv.gz

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). The filtered_normalized_counts files have normalized counts for transcriptomes passing all filtering steps. In both cases, columns = cells (with the exception of the first column), rows = genes (with the exception of the first two rows). Column 1 gives the label for each row. Row 1 contains the timepoint label (1 = day 0; 2 = day 5/6; 3 = day 11/12). In raw_umifm_counts files, row 2 contains flag for cell pass filtering (0=fail, 1=pass). In filtered_normalized_counts files, row 2 contains an integer cluster label. Cluster labels follow Briggs, JA and Li, VC et al. For direct_programming, clusterIDs -1:11 = outlier, ESC, NP, EMN, LMN, FN, NN, Gl1, Gl2, Mus, Meso, Endo, respectively. For the standard_protocol, clusterIDs -1:11 = outlier, ESC, NP, PNP, PVNP, MNP, EMN, LMN, Oligo, Astro, Mus, Stro. Rows 3+ contain counts for each gene (gene symbol is in column 1). The SPRING_combined_trajectories file contains a subset of cells from each protocol merged together under the same format except row 1 = Cluster ID, and rows 2+ contain counts for each gene. Data has been total count normalized. The included cells are described in the manuscript and represent the major motor neuron differentiation pathway of both protocols. Cluster 1 = ES; clusters 2-4 = direct_programming (NP, EMN, LMN); clusters 5-10 = standard_protocol (NP, PNP, PVNP, MNP, EMN, LMN).

source_name: Embryonic stem cell (ESC)

growth_protocol: ESCs were cultured in standard media (DMEM with LIF + 15% fetal bovine serum) on 0.2% gelatin-coated dishes.

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (2017), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: I. CELL CULTURE: Twenty-four hours before starting differentiation, ESCs were trypsinized and seeded onto plates pre-coated with a mix of poly-d-lysine (100 ug/ml) and laminin (50 ug/ml) instead of gelatin for adherence. ESCs were counted by a Beckman Coulter Counter and seeded at a density of approximately 200,000 cells per well of a 6-well dish. At day 0 (ESCs), the media was switched from standard ES media to N2B27 media (Invitrogen). Doxycycline was also added at 3 ug/ml starting to induce expression of the NIL transcription factors. Media was changed daily. For the standard programming protocol, the steps described in Wu et al. were followed strictly. II. MOUSE WORK: The B6.Cg-Tg(Hlxb9-GFP)1Tmj/J mice (JAX# 005029) were bred with C57BL/6J (JAX# 000664) for embryonic motor neurons dissection. All animal protocols were approved the Institutional Animal Care and Use Committee at Boston Children’s Hospital. On gestational day 13 (E13), the female mice were anesthetized and all embryos were collected by caesarian section. Only GFP embryos were used for further dissection. The spinal cords were isolated and their meninges were removed. Each isolated spinal cord was dissociated by trypsin and mechanical trituration. After filtering the cells with 100 μm strainers, the cells were spun down and re-suspended in PBS, and subjected to flow cytometry. Cells were run through a 100 μm nozzle at low pressure (20 p.s.i.) on a BD FACSaria II machine (Becton Dickinson, USA). A neural density filter (2.0 setting) was used to allow visualization of large cells.

value: Embryonic stem cell (ESC)

tag: timepoint/stage

value: Day 0 (undifferentiated)

tag: # cells (pass filter)

tag: strain

tag: differentiation protocol

value: starting population


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNZZRAAPEI-47

status: Public on Oct 17 2017

type: SRA

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

library_source: transcriptomic

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw gene counts for all the detected genes in the Tcells and Monocytes

molecule: total RNA

organism: Homo sapiens

source_name: Monocytes

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: cell type

value: Monocytes

tag: stimulation

value: unstim

tag: subjectid

tag: timepoint

tag: bin

tag: group

value: case

tag: age

tag: gender

value: female

tag: previousdiagnosisoftb

value: No

tag: tst

tag: qft

value: positive


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNYERAAPEI-14

value: control


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNAAARAAPEI-53

value: mTb


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNYLRAAPEI-30


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNZHRAAPEI-122


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNAAFRAAPEI-87


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNWWRAAPEI-129


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNXXRAAPEI-94


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNYKRAAPEI-22

value: IC


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNZARAAPEI-88


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNZWRAAPEI-44

value: negative


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNZERAAPEI-95


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNXORAAPEI-53


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNXFRAAPEI-30


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNZORAAPEI-18


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNZDRAAPEI-94


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZBRAAPEI-89


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNAAIRAAPEI-90

value: male


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNZGRAAPEI-115


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNYBRAAPEI-122


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNYFRAAPEI-15


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNYCRAAPEI-129


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNYPRAAPEI-43


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNYORAAPEI-39

value: Yes


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNRJRAAPEI-89


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNTWRAAPEI-53


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNMORAAPEI-11


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNPARAAPEI-44


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNTMRAAPEI-22


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNRORBAPEI-36


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNIORAAPEI-93

source_name: T cells

value: Tcells


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNPCRAAPEI-46


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNLGRAAPEI-14


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNSPRAAPEI-13


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNRKRAAPEI-39


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNPMRAAPEI-90


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNVPRAAPEI-122


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNHWRAAPEI-35


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNJJRAAPEI-45


title: 140409_I266_FCC4E1TACXX_L1_RHUMuweNAAERAAPEI-84


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNIHRAAPEI-71


title: 140404_I263_FCC3R2CACXX_L8_RHUMuweNPSRAAPEI-129


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNRHRAAPEI-87


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNURRAAPEI-19


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNSNRAAPEI-11


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNWIRAAPEI-53


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNLNRAAPEI-30


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNUDRAAPEI-89


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNHRRAAPEI-26


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNTZRAAPEI-75

value: Not a PP case


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNLSRAAPEI-44


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNUURAAPEI-33


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNTXRAAPEI-56


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNTFRAAPEI-13


title: 140404_I263_FCC3R2CACXX_L7_RHUMuweNWVRAAPEI-122


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNWMRAAPEI-84


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNLFRAAPEI-13


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNWWRAAPEI-129


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNPURAAPEI-14


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNGQRABPEI-35


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNRHRAAPEI-30


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNRCRAAPEI-53


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNTORAAPEI-33


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNPRRAAPEI-122


title: 140404_I263_FCC3R2CACXX_L1_RHUMuweNLWRAAPEI-53


title: 140211_I260_FCC3R7HACXX_L4_RHUMuweNKXRAAPEI-87


title: 140404_I263_FCC3R2CACXX_L1_RHUMuweNGURAAPEI-43


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNLDRAAPEI-11


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNLLRAAPEI-19


title: 140211_I260_FCC3R7HACXX_L4_RHUMuweNLARAAPEI-90


title: 140211_I260_FCC3R7HACXX_L4_RHUMuweNKYRAAPEI-88


title: 140211_I260_FCC3R7HACXX_L3_RHUMuweNKVRAAPEI-75


title: 140211_I260_FCC3R7HACXX_L3_RHUMuweNKURAAPEI-74


title: 140211_I260_FCC3R7HACXX_L3_RHUMuweNKWRAAPEI-84


title: 140404_I263_FCC3R2CACXX_L6_RHUMuweNORRAAPEI-36


title: 140211_I260_FCC3R7HACXX_L3_RHUMuweNKTRAAPEI-56


title: 140211_I260_FCC3R7HACXX_L2_RHUMuweNKPRAAPEI-45


title: 140211_I260_FCC3R7HACXX_L2_RHUMuweNKSRAAPEI-53


title: 140211_I260_FCC3R7HACXX_L2_RHUMuweNKQRAAPEI-46


title: 140211_I260_FCC3R7HACXX_L1_RHUMuweNKMRAAPEI-39


title: 140211_I260_FCC3R7HACXX_L1_RHUMuweNKLRAAPEI-36


title: 140220_I238_FCC3RA3ACXX_L3_RHUMuweNOKRAAPEI-16


title: 140220_I238_FCC3RA3ACXX_L3_RHUMuweNOLRAAPEI-17


title: 140211_I260_FCC3R7HACXX_L4_RHUMuweNKZRAAPEI-89


title: 140220_I238_FCC3RA3ACXX_L4_RHUMuweNONRAAPEI-19


title: 140404_I263_FCC3R2CACXX_L1_RHUMuweNOXRAAPEI-36


title: 140404_I263_FCC3R2CACXX_L1_RHUMuweNUBRAAPEI-87


title: 140220_I238_FCC3RA3ACXX_L4_RHUMuweNOMRAAPEI-18


title: 140220_I238_FCC3RA3ACXX_L6_RHUMuweNOSRAAPEI-39


title: 140220_I238_FCC3RA3ACXX_L6_RHUMuweNOQRAAPEI-33


title: 140220_I238_FCC3RA3ACXX_L3_RHUMuweNOIRAAPEI-14


title: 140220_I238_FCC3RA3ACXX_L6_RHUMuweNORRAAPEI-36


title: 140220_I238_FCC3RA3ACXX_L7_RHUMuweNOWRAAPEI-46


title: 140220_I238_FCC3RA3ACXX_L7_RHUMuweNOVRAAPEI-45


title: 140220_I238_FCC3RA3ACXX_L8_RHUMuweNOARAAPEI-74


title: 140220_I238_FCC3RA3ACXX_L7_RHUMuweNOXRAAPEI-47


title: 140220_I238_FCC3RA3ACXX_L8_RHUMuweNOZRAAPEI-56


title: 140220_I238_FCC3RA3ACXX_L4_RHUMuweNOORAAPEI-22


title: 140220_I238_FCC3RA3ACXX_L8_RHUMuweNOBRAAPEI-75


title: 140211_I260_FCC3R7HACXX_L1_RHUMuweNKORAAPEI-44


title: 140220_I238_FCC3RA3ACXX_L2_RHUMuweNOHRAAPEI-13


title: 140211_I260_FCC3R7HACXX_L2_RHUMuweNKRRAAPEI-47


title: 140220_I238_FCC3RA3ACXX_L2_RHUMuweNOGRAAPEI-12


title: 140220_I238_FCC3RA3ACXX_L1_RHUMuweNODRAAPEI-8


title: 140220_I238_FCC3RA3ACXX_L2_RHUMuweNOFRAAPEI-11


title: 140220_I238_FCC3RA3ACXX_L2_RHUMuweNOERAAPEI-9


title: 140220_I238_FCC3RA3ACXX_L4_RHUMuweNOPRAAPEI-30


title: 140225_I247_FCC3RAAACXX_L1_RHUMuweNOCRAAPEI-84


title: 140220_I238_FCC3RA3ACXX_L6_RHUMuweNOTRAAPEI-43


title: 140220_I238_FCC3RA3ACXX_L3_RHUMuweNOJRAAPEI-15


title: 140225_I247_FCC3RAAACXX_L1_RHUMuweNOFRAAPEI-89


title: 140225_I247_FCC3RAAACXX_L2_RHUMuweNOGRAAPEI-90


title: 140225_I247_FCC3RAAACXX_L2_RHUMuweNOIRAAPEI-95


title: 140225_I247_FCC3RAAACXX_L2_RHUMuweNOHRAAPEI-94


title: 140225_I247_FCC3RAAACXX_L2_RHUMuweNOJRAAPEI-8


title: 140225_I247_FCC3RAAACXX_L3_RHUMuweNOLRAAPEI-11


title: 140220_I238_FCC3RA3ACXX_L8_RHUMuweNOYRAAPEI-53


title: 140225_I247_FCC3RAAACXX_L3_RHUMuweNOMRAAPEI-12


title: 140225_I247_FCC3RAAACXX_L3_RHUMuweNONRAAPEI-13


title: 140225_I247_FCC3RAAACXX_L4_RHUMuweNORRAAPEI-17


title: 140220_I238_FCC3RA3ACXX_L7_RHUMuweNOURAAPEI-44


title: 140225_I247_FCC3RAAACXX_L4_RHUMuweNOORAAPEI-14


title: 140225_I247_FCC3RAAACXX_L6_RHUMuweNOVRAAPEI-30


title: 140225_I247_FCC3RAAACXX_L6_RHUMuweNOTRAAPEI-19


title: 140225_I247_FCC3RAAACXX_L4_RHUMuweNOPRAAPEI-15


title: 140225_I247_FCC3RAAACXX_L6_RHUMuweNOURAAPEI-22


title: 140225_I247_FCC3RAAACXX_L6_RHUMuweNOSRAAPEI-18


title: 140225_I247_FCC3RAAACXX_L4_RHUMuweNOQRAAPEI-16


title: 140225_I247_FCC3RAAACXX_L7_RHUMuweNOZRAAPEI-43


title: 140225_I247_FCC3RAAACXX_L7_RHUMuweNOWRAAPEI-33


title: 140225_I247_FCC3RAAACXX_L8_RHUMuweNPCRAAPEI-46


title: 140225_I247_FCC3RAAACXX_L8_RHUMuweNPBRAAPEI-45


title: 140225_I247_FCC3RAAACXX_L8_RHUMuweNPDRAAPEI-47


title: 140225_I247_FCC3RAAACXX_L8_RHUMuweNPARAAPEI-44


title: 140225_I247_FCC3RAAACXX_L3_RHUMuweNOKRAAPEI-9

value: indeterminate


title: 140225_I247_FCC3RAAACXX_L1_RHUMuweNODRAAPEI-87


title: 140304_I232_FCC3RC2ACXX_L2_RHUMuweNTQRAAPEI-39


title: 140304_I232_FCC3RC2ACXX_L2_RHUMuweNTPRAAPEI-36


title: 140304_I232_FCC3RC2ACXX_L1_RHUMuweNTMRAAPEI-22


title: 140304_I232_FCC3RC2ACXX_L2_RHUMuweNTORAAPEI-33


title: 140304_I232_FCC3RC2ACXX_L1_RHUMuweNTJRAAPEI-17


title: 140225_I247_FCC3RAAACXX_L7_RHUMuweNOYRAAPEI-39


title: 140304_I232_FCC3RC2ACXX_L7_RHUMuweNUDRAAPEI-89


title: 140304_I232_FCC3RC2ACXX_L8_RHUMuweNUKRAAPEI-12


title: 140225_I247_FCC3RAAACXX_L7_RHUMuweNOXRAAPEI-36


title: 140304_I232_FCC3RC2ACXX_L1_RHUMuweNTLRAAPEI-19


title: 140304_I232_FCC3RC2ACXX_L8_RHUMuweNUIRAAPEI-9


title: 140304_I232_FCC3RC2ACXX_L1_RHUMuweNTKRAAPEI-18


title: 140304_I232_FCC3RC2ACXX_L8_RHUMuweNUJRAAPEI-11


title: 140304_I232_FCC3RC2ACXX_L8_RHUMuweNUHRAAPEI-8


title: 140304_I232_FCC3RC2ACXX_L7_RHUMuweNUGRAAPEI-95


title: 140304_I232_FCC3RC2ACXX_L7_RHUMuweNUFRAAPEI-94


title: 140304_I232_FCC3RC2ACXX_L6_RHUMuweNUARAAPEI-84


title: 140304_I232_FCC3RC2ACXX_L4_RHUMuweNTWRAAPEI-53


title: 140304_I232_FCC3RC2ACXX_L6_RHUMuweNUCRAAPEI-88


title: 140225_I247_FCC3RAAACXX_L1_RHUMuweNOERAAPEI-88


title: 140304_I232_FCC3RC2ACXX_L4_RHUMuweNTYRAAPEI-74


title: 140304_I232_FCC3RC2ACXX_L6_RHUMuweNUBRAAPEI-87


title: 140304_I232_FCC3RC2ACXX_L7_RHUMuweNUERAAPEI-90


title: 140304_I232_FCC3RC2ACXX_L4_RHUMuweNTXRAAPEI-56


title: 140304_I232_FCC3RC2ACXX_L4_RHUMuweNTVRAAPEI-47


title: 140304_I232_FCC3RC2ACXX_L3_RHUMuweNTURAAPEI-46


title: 140304_I232_FCC3RC2ACXX_L3_RHUMuweNTTRAAPEI-45


title: 140304_I232_FCC3RC2ACXX_L3_RHUMuweNTSRAAPEI-44


title: 140304_I246_FCC3RCEACXX_L1_RHUMuweNUORAAPEI-16


title: 140304_I246_FCC3RCEACXX_L2_RHUMuweNUSRAAPEI-22


title: 140304_I246_FCC3RCEACXX_L2_RHUMuweNUQRAAPEI-18


title: 140304_I246_FCC3RCEACXX_L3_RHUMuweNUWRAAPEI-39


title: 140304_I246_FCC3RCEACXX_L4_RHUMuweNVARAAPEI-46


title: 140304_I246_FCC3RCEACXX_L3_RHUMuweNUTRAAPEI-30


title: 140304_I246_FCC3RCEACXX_L4_RHUMuweNUZRAAPEI-45


title: 140304_I246_FCC3RCEACXX_L6_RHUMuweNVBRAAPEI-47


title: 140304_I246_FCC3RCEACXX_L3_RHUMuweNUVRAAPEI-36


title: 140304_I246_FCC3RCEACXX_L6_RHUMuweNVCRAAPEI-53


title: 140304_I246_FCC3RCEACXX_L4_RHUMuweNUYRAAPEI-44


title: 140304_I246_FCC3RCEACXX_L6_RHUMuweNVERAAPEI-74


title: 140304_I232_FCC3RC2ACXX_L6_RHUMuweNTZRAAPEI-75


title: 140304_I246_FCC3RCEACXX_L8_RHUMuweNVKRAAPEI-90


title: 140304_I246_FCC3RCEACXX_L8_RHUMuweNVMRAAPEI-95


title: 140304_I246_FCC3RCEACXX_L7_RHUMuweNVHRAAPEI-87


title: 140304_I246_FCC3RCEACXX_L8_RHUMuweNVLRAAPEI-94


title: 140304_I246_FCC3RCEACXX_L7_RHUMuweNVGRAAPEI-84


title: 140304_I246_FCC3RCEACXX_L2_RHUMuweNURRAAPEI-19


title: 140304_I246_FCC3RCEACXX_L1_RHUMuweNULRAAPEI-13


title: 140304_I232_FCC3RC2ACXX_L3_RHUMuweNTRRAAPEI-43


title: 140304_I246_FCC3RCEACXX_L1_RHUMuweNUMRAAPEI-14


title: 140304_I232_FCC3RC2ACXX_L2_RHUMuweNTNRAAPEI-30


title: 140304_I246_FCC3RCEACXX_L3_RHUMuweNUURAAPEI-33


title: 140304_I246_FCC3RCEACXX_L6_RHUMuweNVDRAAPEI-56


title: 140304_I246_FCC3RCEACXX_L1_RHUMuweNUNRAAPEI-15


title: 140304_I246_FCC3RCEACXX_L2_RHUMuweNUPRAAPEI-17


title: 140303_I260_FCC3REDACXX_L7_RHUMuweNTDRAAPEI-11


title: 140303_I260_FCC3REDACXX_L7_RHUMuweNTERAAPEI-12


title: 140304_I246_FCC3RCEACXX_L8_RHUMuweNVJRAAPEI-89


title: 140303_I260_FCC3REDACXX_L8_RHUMuweNTFRAAPEI-13


title: 140303_I260_FCC3REDACXX_L8_RHUMuweNTHRAAPEI-15


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title: 279_09_0721_DAY_0_T_Ag85_279_L8.LB20


title: 280_09_0628_DAY_0_T_Ag85_280_L7.LB16


title: 27_07-1115_DAY_0_T-Ag85_27_L2.LB4


title: 277_03_0714_DAY_0_T_Ag85_277_L6.LB8


title: 264_03_0711_DAY_0_T_Ag85_264_L5.LB5


title: 262_09_0578_DAY_0_T_Ag85_262_L3.LB19


title: 260_09_0789_DAY_0_T_Ag85_260_L3.LB15


title: 261_09_0532_DAY_0_T_Ag85_261_L3.LB16


title: 259_09_0625_DAY_0_T_Ag85_259_L4.LB22


title: 245_09_0624_DAY_0_T_Ag85_245_L2.LB12


title: 244_07-1104_DAY_0_T-Ag85_244_L1.LB21


title: 25_04-0238_DAY_0_T-Ag85_25_L2.LB3


title: 299_07-0135_DAY_0_T-Ag85_299_L7.LB6


title: 243_07-0200_DAY_0_T-Ag85_243_L5.LB23


title: 241_07-0355_DAY_0_T-Ag85_241_L5.LB22


title: 227_04-0030_Day_0_T-Ag85_227_L4.LB14


title: 226_07-0180_DAY_0_T-Ag85_226_L4.LB13


title: 225_07-0208_DAY_0_T-Ag85_225_L4.LB12


title: 224_07-0386_DAY_0_T-Ag85_224_L3.LB11


title: 209_09_0462_DAY_0_T_Ag85_209_L5.LB6


title: 208_09_0587_DAY_0_T_Ag85_208_L2.LB9


title: 210_09_0377_DAY_0_T_Ag85_210_L1.LB3


title: 206_01_0673_DAY_0_T_Ag85_206_L8.LB22


title: 191_07_0630_DAY_0_T_Ag85_191_L3.LB18


title: 205_07-0424_DAY_0_T-Ag85_205_L6.LB7


title: 263_03_0227_DAY_0_T_Ag85_263_L6.LB11


title: 192_07-0236_DAY_0_T-Ag85_192_L5.LB3


title: 223_09_0520_DAY_0_T_Ag85_223_L1.LB6


title: 174_04-1073_Day_0_T-Ag85_174_L8.LB21


title: 228_07-0197_DAY_0_T-Ag85_228_L5.LB16


title: 188_07_0425_DAY_0_T_Ag85_188_L3.LB15


title: 190_07-0290_DAY_0_T-Ag85_190_L5.LB2


title: 187_07-0440_DAY_0_T-Ag85_187_L5.LB1


title: 173_07_0414_DAY_0_T_Ag85_173_L3.LB13


title: 246_09_0712_DAY_0_T_Ag85_246_L4.LB27


title: 171_07_0218_DAY_0_T_Ag85_171_L7.LB19


title: 172_07_0177_DAY_0_T_Ag85_172_L4.LB21


title: 170_07_0257_DAY_0_T_Ag85_170_L2.LB10


title: D3+2 ChAct+Bmp4

city: Cambridge

first: Sumin

last: Jang

address: 52 Oxford Street, Rm 402

institute: Harvard University

description: Sample 14

data_processing:
Raw reads were first demultiplixed by CelSeq index, allowing for one sequence mismatch (CelSeq indexes were designed with a minimum Hamming distance of 3, allowing for error correction of one mismatch). The transcript reads for each cell were aligned to the RefSeq mouse transcriptome (downloaded in March 2013 from NCBI, corresponding to the GRCm38 genome release) using Tophat with default parameters (Trapnell et al. 2009). Unaligned reads were then aligned to the GRCm38 genome using Bowtie (Langmead et al. 2009), followed by alignment to the ERCC spike-in controls. At this point, any remaining unaligned reads were then mapped to the genome again using GSNAP (Wu and Nacu, 2010) allowing for soft clipping.
After alignment, all reads mapping to exons of the same gene were collapsed by their Unique Molecular Identifier (on the metadata read) and were used to generate the over cell-by-gene expression matrix. Because CelSeq is strongly 3' biased and the full 3' UTR may not be fully represented in the RefSeq transcriptome, if a read mapped within 1kb of the 3' end of a gene and was in the same orientation as the gene, we assessed it as a transcript-mapping read for that gene. Non-exon read mapping percentages were calculated, but these were not used in quantifying gene expression.
Finally, 20,000 UMI (Unique Molecular Identifier)'s were randomly selected for each cell sample.
Genome_build: GRCCm38
Supplementary_files_format_and_content: Each row corresponds to a gene (labeled in first column), each column is a cell, whose identity is explained in supplementary file "Figure 2 - Source data 1.xlsx". Each column's name and its relation to the 14 samples and raw data files are explained in "Supplemental File 2.xlsx"

organism: Mus musculus

source_name: mESC

extract_protocol: none provided by the submitter

tag: growth conditions

value: 3 days in ChAct, followed by 2 days in ChAct + 25ng/mL Bmp4

tag: passage number


title: 169_07_0391_DAY_0_T_Ag85_169_L5.LB3


title: 156_07-1158_DAY_0_T-Ag85_156_L2.LB20


title: 153_07_0229_DAY_0_T_Ag85_153_L6.LB11


title: D3+1 ChAct+Bmp4

description: Sample 13

value: 3 days in ChAct, followed by 1 day in ChAct + 25ng/mL Bmp4


title: D3+2 ChAct+LDN

description: Sample 12

value: 3 days in ChAct, followed by 2 days in ChAct + 1uM LDN193189


title: 154_07_0293_DAY_0_T_Ag85_154_L4.LB27


title: 155_04_0859_DAY_0_T_Ag85_155_L8.LB23

value: case


title: 207_09_0507_DAY_0_T_Ag85_207_L8.LB27


title: 152_04_0152_DAY_0_T_Ag85_152_L2.LB7

value: female


title: D3 ChAct

description: Sample 10

value: 3 days in ChAct


title: D2 ChAct

description: Sample 9

value: 2 days in ChAct


title: D1 ChAct

description: Sample 8

value: 1 day in 3uM CHIR99021 + 10ng/mL Activin A ("ChAct")


title: 137_09_0278_DAY_0_T_Ag85_137_L5.LB1

value: No

value: positive


title: D2+2 PD03+Bmp4

description: Sample 7

value: 2 days in 0.4uM PD03, followed by 2 days in 0.4uM PD03 + 25ng/mL Bmp4


title: TEM P10 rep2

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the hg38 genome assembly using Hisat2(version:2.0.4).
Gene abundance measurements were generationed and normalized using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Donor_2 TEM P10

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

value: HepLPCs

tag: culture condition

value: in the transition and expansion medium (Passage 10)

tag: ethnicity

value: Asian


title: 136_09_0398_DAY_0_T_Ag85_136_L3.LB19

value: Tcells

value: control

value: male


title: 138_09_0406_DAY_0_T_Ag85_138_L5.LB2


title: TEM P5 rep2

source_name: Donor_2 TEM P5

value: in the transition and expansion medium (Passage 5)


title: D2+1 PD03+Bmp4

description: Sample 6

tag: strain

value: 2 days in 0.4uM PD03, followed by 1 day in 0.4uM PD03 + 25ng/mL Bmp4


title: TEM Day10 rep2

source_name: Donor_2 TEM Day10

value: in the transition and expansion medium (Passage 1, 10 days)


title: D2+2 PD03+LDN

description: Sample 5

value: 2 days in 0.4uM PD03, followed by 2 days in 0.4uM PD03 + 1uM LDN193189


title: TEM Day4 rep2

source_name: Donor_2 TEM Day4

value: in the transition and expansion medium (Passage 1, 4 days)


title: 134_01_0757_DAY_0_T_Ag85_134_L2.LB10

value: case

value: female


title: 135_09_0397_DAY_0_T_Ag85_135_L3.LB15


title: D2+1 PD03+LDN

description: Sample 4

value: 2 days in 0.4uM PD03, followed by 1 day in 0.4uM PD03 + 1uM LDN193189


title: 133_09_0818_DAY_0_T_Ag85_133_L2.LB7

value: No


title: D3+1 ChAct+LDN

description: Sample 11

value: 3 days in ChAct, followed by 1 day in ChAct + 1uM LDN193189


title: TEM P5 rep1

source_name: Donor_1 TEM P5


title: 12_09_0226_DAY_0_T_Ag85_12_L7.LB14


title: D1 PD03

description: Sample 2


title: TEM P10 rep1

source_name: Donor_1 TEM P10


title: 120_03_0697_DAY_0_T_Ag85_120_L1.LB4


title: Bmal1 CKO 3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

library_source: genomic

data_processing:
TrimGalore
Bowtie2
MACS2 peak caller
Genome_build: mm10

molecule: genomic DNA

source_name: retina

growth_protocol: Pups weaned at P20

extract_protocol:
Retinal chromatin DNA was extracted using a rabbit anti-BMAL1 antibody
Rubicon Genomics ThruPlex® DNA kit

treatment_protocol: No external treatment

tag: tissue

value: retina

tag: genotype/variation

value: Bmal1 CKO


title: TEM Day10 rep1

source_name: Donor_1 TEM Day10

tag: cell type

value: HepLPCs


title: 151_09_0796_DAY_0_T_Ag85_151_L4.LB25

tag: stimulation

tag: subjectid


title: Lif2i

description: Sample 1

value: Lif2i (pluripotency-maintenance)


title: 116_07_0369_DAY_0_T_Ag85_116_L1.LB5

value: Tcells

tag: timepoint

tag: bin


title: 119_03_0545_DAY_0_T_Ag85_119_L1.LB1

tag: group

tag: age

value: positive


title: 115_07_0361_DAY_0_T_Ag85_115_L1.LB3

value: control

tag: gender

value: male

tag: previousdiagnosisoftb


title: Control 3

value: wild type


title: 11_01_0940_DAY_0_T_Ag85_11_L6.LB8

tag: tst

tag: qft


title: HepLPCs-Hep rep1

source_name: Donor_1 HepLPCs-Hep

value: HepLPCs-Hep

value: in the differentiation medium (Passage 5, 8 days)

value: Asian


title: Control 2


title: 102_04_0843_DAY_0_T_Ag85_102_L1.LB1


title: HepLPCs-Hep rep2

source_name: Donor_3 HepLPCs-Hep


title: TEM Day4 rep1

source_name: Donor_1 TEM Day4

value: in the transition and expansion medium (Passage 1, 4 days)


title: Sample 13 -44763

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

description: Double thymidine arrest + 1-hour release in S phase.

data_processing:
Basecalling performed with RTA 1.18.64.0
Alignment to hg19 using bowtie 0.12.5 with S  -p 6   --trim5 0 --trim3 0   -v 2 --best --strata --tryhard   -m 1 --chunkmbs 256
Filtered out reads mapping to chrMT
Peak calling using BayesPeak 1.18.2 with bin.size=1000
Correlation analysis with IntervalStats 24-Apr-2012 using hg19 as domain set
Peak shuffling with bedtools v2.19.1 bedtools shuffle -chrom -noOverlapping -i $1 -g GRCh37.fa.fai
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed, peaks

source_name: input

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 0.2 mM glutamine, penicillin, and streptomycin.

extract_protocol:
Samples were formaldehyde-crosslinked, lysed, sonicated, precipitated, and reverse crosslinked.
Illumina sample libraries were prepared according to NEB protocol E6040

treatment_protocol: Cells were arrested in G1/S by double thymidine arrest and released for 1 hour in S phase. Transfection with siRNA was done at the first thymidine arrest for a total of 48 hours.

tag: cell line

value: HeLa

tag: antibody


title: 10_01_0524_DAY_0_T_Ag85_10_L5.LB3

value: case

value: female


title: Sample 12 -53376

description: Double thymidine arrest + 1-hour release in S phase; 48 hour depletion with ESCO1 siRNA .

source_name: SMC3(ac) (ESCO2-deltaPBMA; ESCO1 siRNA)

value: Anti-SMC3(ac) (K. Shirahige; Nishiyama et al., 2010)


title: Control 1

value: retina


title: D2 PD03

description: Sample 3

tag: growth conditions

value: 2 days in 0.4uM PD03

tag: passage number


title: 100_04_0779_DAY_0_T_Ag85_100_L8.LB23

value: No


title: Sample 11 -53374

source_name: SMC3 (ESCO2-deltaPBMA; ESCO1 siRNA)

value: Anti-SMC3 (A845; JM Peters lab; Sumara et al., 2002)